pymol-users Mailing List for PyMOL Molecular Graphics System

Hello,
Does anyone know how to visualize the surface potentials of two molecules
simoutaneously using the APBS Tools2.1 plugin? Thanks.
-Yarrow
-- 
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

Greetings,
Due to increased spam attempts, I've temporarily stopped the creation
of new accounts. Once we get a handle on a better spam system, I'll
open up registration again.
If you want an account, please let me know.
I'll update the list once the new protection is installed.
Cheers,
-- Jason
-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi,
Just calling tkMessagebox like that causes a Tcl error which confuses
PyMOL, causing the crash. Try this code instead:
# begin Python block
python
import tkMessageBox
tkMessageBox.showinfo("title", "msg")
# end python block of code
python end
This wraps the code as one block and sends it to the Python interpreter.
Cheers,
-- Jason
On Mon, Jan 24, 2011 at 5:11 PM, rv...@li... <rv...@li...> wrote:
> Hi to all,
> I need to open a message box dialog inside a pyMOL plug-in.
>
> When I try the code:
>
> import tkMessageBox
> tkMessageBox.showinfo(‘title’, ‘msg’)
>
> pyMOL crashes (the window doesn’t appear and pyMOL blocks).
>
> I am just entering pyMOL and python. I never used Tkinter before.
>
> Could anyone help me?
> Thanks
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi David (and list),
Your PyMOL sessions are fine, it's the save syntax you're using.
Please use the following syntax when saving via the command line:
save fileName.pdb, aPyMOLSelection
It's important that the filename come first, and be immediately
followed by a comma. Please check "help save" for more information.
If you're saving a multi-state system (your PSE has two states) then
you can add the state flag as
save fileName.pdb, aPyMOLSelection, state=0
to save all states or
save fileName.pdb, aPyMOLSelection, state=2
to save state 2.
Cheers,
-- Jason
On Thu, Jan 27, 2011 at 7:59 PM, Jason Vertrees
<jas...@sc...> wrote:
> Hi David,
>
> Can you please send me the PSE? If not, do you have multiple states?
> Are you using the save command or the GUI?
>
> Cheers,
>
> -- Jason
>
> On Thu, Jan 27, 2011 at 1:50 PM, David A. Horita <dh...@wf...> wrote:
>> Hi,
>> I've apparently managed to create a pse of a protein that loads fine but
>> won't save the pdb coordinates (I get a file with END in it, and nothing
>> else).
>> Any ideas how to get the coordinates out?
>>
>> pymol 1.1b3 linux, windows (same pse has same result under both OS's)
>>
>> Thanks,
>> Dave
>>
>> -----------------------------
>> David A. Horita, Ph.D.
>> Department of Biochemistry
>> Wake Forest University School of Medicine
>> Winston-Salem, NC 27157-1016
>> Tel: 336 713-4194
>> Fax: 336 716-7671
>> email: dh...@wf...
>> web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm
>>
>> ------------------------------------------------------------------------------
>> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
>> Finally, a world-class log management solution at an even better price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi,
That was my first instinct as well and I tried that. However, the problem is that rotating the molecules gets very tricky since the molecules are now no longer in the same plane. So, if I translate one of them either towards or away from me and then rotate, that molecule will rotate away from the camera since the scene is centered around the other molecule.
Sean
 		 	 		 

Sean,
Just a thought, but the translate command looks like as if it should be possible to selectively modify the viewmatrix on a per object basis:
 "translate" translates the atomic coordinates of atoms in a
 selection. Alternatively, is modifies the matrix associated with
 a particular object or object-state.
May be if you create two objects of interest, split states by object and then play around with the translate command you could achieve that effect.
> -----Original Message-----
> From: Jason Vertrees [mailto:jas...@sc...]
> Sent: Thursday, January 27, 2011 11:03 PM
> To: Sean Law
> Cc: pym...@li...
> Subject: Re: [PyMOL] Independent Zooming in Grid Mode
> 
> Hi Sean,
> 
> PyMOL is currently not capable of providing and "inset"-like image or
> grid-mode with independent motions. Programming this at the Python
> level wouldn't be very easy.
> 
> Cheers,
> 
> -- Jason
> 
> On Wed, Jan 26, 2011 at 9:39 AM, Sean Law <mag...@ho...> wrote:
> > Hi PyMOLers,
> >
> > I was wondering if anybody had a solution for independent when using
> > grid_mode=on. I want to be able to show, side-by-side, the same
> structure
> > where one structure is "zoomed in" on a specific part on the
> biomolecule and
> > the other object is "zoomed out" (viewing the entire molecule). And
> as I
> > turn one of the two structures, the other one turns accordingly. I
> think
> > this would be useful when trying to keep track of the orientation of
> the
> > biomolecule or for docking.
> >
> > Any suggestions would be greatly appreciated.
> >
> > Sean
> >
> >> From: pym...@li...
> >> Subject: PyMOL-users Digest, Vol 56, Issue 9
> >> To: pym...@li...
> >> Date: 2011年1月24日 22:11:17 +0000
> >>
> >> Send PyMOL-users mailing list submissions to
> >> pym...@li...
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> or, via email, send a message with subject or body 'help' to
> >> pym...@li...
> >>
> >> You can reach the person managing the list at
> >> pym...@li...
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of PyMOL-users digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >> 1. Re: Faster way to find polymer chains? (Tsjerk Wassenaar)
> >> 2. Re: Faster way to find polymer chains? (Thomas Holder)
> >> 3. unable to open the file (wang_qi)
> >> 4. Re: unable to open the file (Christoph Gohlke)
> >> 5. Re: Faster way to find polymer chains? (Seth Harris)
> >> 6. dialogs in pyMOL (rv...@li...)
> >>
> >>
> >> --------------------------------------------------------------------
> --
> >>
> >> Message: 1
> >> Date: 2011年1月23日 10:48:20 +0100
> >> From: Tsjerk Wassenaar <ts...@gm...>
> >> Subject: Re: [PyMOL] Faster way to find polymer chains?
> >> To: Seth Harris <se...@gm...>
> >> Cc: pym...@li...
> >> Message-ID:
> >> <AAN...@ma...>
> >> Content-Type: text/plain; charset=ISO-8859-1
> >>
> >> Oops... That should've been:
> >>
> >> polychains = set([i.chain for i in cmd.get_model('polymer').atom])
> >>
> >> Sorry for that. :p
> >>
> >> Tsjerk
> >>
> >> On Sun, Jan 23, 2011 at 10:32 AM, Tsjerk Wassenaar
> <ts...@gm...>
> >> wrote:
> >> > Hi Seth,
> >> >
> >> > So you just want to have all unique chain identifiers for the
> >> > 'polymer' selection? Does the following give what you want?:
> >> >
> >> > polychains = set([i.chain for i in cmd.get_model('polymer')])
> >> >
> >> > Hope it helps,
> >> >
> >> > Tsjerk
> >> >
> >> > On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris <se...@gm...>
> wrote:
> >> >> Hi All,
> >> >> I am script-plowing through PDB files and extracting unique chain
> >> >> identifiers only for "polymers" using PyMOL's polymer selection.
> Right
> >> >> now
> >> >> my code is a kind of brute force thing like this:
> >> >> <code>
> >> >> ??cmd.create ("justpolys","polymer")
> >> >> ??polymer_chains=[]
> >> >> ??for a in cmd.index("justpolys"):
> >> >> ?? ?q_sel = "%s`%d"%a
> >> >> ?? ?#print q_sel+":",
> >> >> ?? ?cmd.iterate(q_sel, "stored.qry_info =
> (chain,resn,resi,name)")
> >> >> ?? ?#cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
> >> >> ?? ?#print
> >> >>
> >> >>
> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_inf
> o[3]
> >> >> ?? ?# Track any unique chains by adding to polymer_chains list if
> not
> >> >> already there
> >> >> ?? ?# first reformat to get rid of flanking ' marks
> >> >> ?? ?thischain=`stored.qry_info[0]`
> >> >> ?? ?thischain=thischain.replace("'","")
> >> >> ?? ?if thischain not in polymer_chains:
> >> >> ?? ? ?polymer_chains.append(thischain)
> >> >> </code>
> >> >> This works, but is quite slow as it iterates over every atom in
> every
> >> >> pdb
> >> >> just to get out the chain so it is quite redundant.
> >> >> Is there any way to iterate in a 'chain by chain' fashion? This
> q_sel
> >> >> stuff
> >> >> is recycled from something Warren suggested for a different
> purpose
> >> >> years
> >> >> ago, and I only have a loose idea of how that is interacting with
> the
> >> >> cmd.index part. Maybe there's a way to get just the chain from
> the
> >> >> get-go
> >> >> instead of all the individual atoms? Any reminders on that one or
> >> >> better
> >> >> method suggestions?
> >> >> Thanks,
> >> >> Seth
> >> >>
> >> >>
> >> >> -----------------------------------------------------------------
> -------------
> >> >> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD
> value)!
> >> >> Finally, a world-class log management solution at an even better
> >> >> price-free!
> >> >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> >> >> February 28th, so secure your free ArcSight Logger TODAY!
> >> >> http://p.sf.net/sfu/arcsight-sfd2d
> >> >> _______________________________________________
> >> >> PyMOL-users mailing list (PyM...@li...)
> >> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-
> users
> >> >> Archives: http://www.mail-archive.com/pymol-
> us...@li...
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Tsjerk A. Wassenaar, Ph.D.
> >> >
> >> > post-doctoral researcher
> >> > Molecular Dynamics Group
> >> > * Groningen Institute for Biomolecular Research and Biotechnology
> >> > * Zernike Institute for Advanced Materials
> >> > University of Groningen
> >> > The Netherlands
> >> >
> >>
> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> post-doctoral researcher
> >> Molecular Dynamics Group
> >> * Groningen Institute for Biomolecular Research and Biotechnology
> >> * Zernike Institute for Advanced Materials
> >> University of Groningen
> >> The Netherlands
> >>
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: 2011年1月23日 14:58:17 +0100
> >> From: Thomas Holder <sp...@us...>
> >> Subject: Re: [PyMOL] Faster way to find polymer chains?
> >> To: Seth Harris <se...@gm...>
> >> Cc: pym...@li...
> >> Message-ID: <4D3...@us...>
> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >>
> >> Hi Seth,
> >>
> >> I think this one-liner will do the job for you:
> >>
> >> print cmd.get_chains('polymer')
> >>
> >> Cheers,
> >> Thomas
> >>
> >> Seth Harris wrote, On 01/23/11 10:04:
> >> > Hi All,
> >> >
> >> > I am script-plowing through PDB files and extracting unique chain
> >> > identifiers only for "polymers" using PyMOL's polymer selection.
> Right
> >> > now my code is a kind of brute force thing like this:
> >> > <code>
> >> >
> >> > cmd.create ("justpolys","polymer")
> >> >
> >> > polymer_chains=[]
> >> >
> >> > for a in cmd.index("justpolys"):
> >> > q_sel = "%s`%d"%a
> >> > #print q_sel+":",
> >> > cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
> >> > #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
> >> > #print
> >> >
> >> >
> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_inf
> o[3]
> >> > # Track any unique chains by adding to polymer_chains list if not
> >> > already there
> >> > # first reformat to get rid of flanking ' marks
> >> > thischain=`stored.qry_info[0]`
> >> > thischain=thischain.replace("'","")
> >> > if thischain not in polymer_chains:
> >> > polymer_chains.append(thischain)
> >> > </code>
> >> >
> >> > This works, but is quite slow as it iterates over every atom in
> every
> >> > pdb just to get out the chain so it is quite redundant.
> >> >
> >> > Is there any way to iterate in a 'chain by chain' fashion? This
> q_sel
> >> > stuff is recycled from something Warren suggested for a different
> >> > purpose years ago, and I only have a loose idea of how that is
> >> > interacting with the cmd.index part. Maybe there's a way to get
> just the
> >> > chain from the get-go instead of all the individual atoms? Any
> reminders
> >> > on that one or better method suggestions?
> >> >
> >> > Thanks,
> >> > Seth
> >>
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 3
> >> Date: 2011年1月23日 23:02:17 +0800
> >> From: "wang_qi" <wan...@gm...>
> >> Subject: [PyMOL] unable to open the file
> >> To: "pymol-users" <pym...@li...>
> >> Message-ID: <201...@gm...>
> >> Content-Type: text/plain; charset="us-ascii"
> >>
> >> Hello, everyone,
> >>
> >> I have downloaded the pymol of version 1.3. and installed it on
> windows XP
> >> successfully. But when selecting "file-open" to load my file, it
> doesn't
> >> work and displays that the file is unable to be opend. Dose anyone
> meet this
> >> problem? Ana how how can i solve it?
> >>
> >> Thanks.
> >>
> >> Qi Wang
> >>
> >> 2011年01月23日
> >>
> >>
> >>
> >> wang_qi
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >>
> >> ------------------------------
> >>
> >> Message: 4
> >> Date: 2011年1月23日 08:27:33 -0800
> >> From: Christoph Gohlke <cg...@uc...>
> >> Subject: Re: [PyMOL] unable to open the file
> >> To: pym...@li...
> >> Message-ID: <4D3...@uc...>
> >> Content-Type: text/plain; charset="iso-8859-1"
> >>
> >> You can try the attached patch. It fixes three issues:
> >>
> >> * is_string() returns False in case of unicode filenames
> >> * Python/Tk bug http://bugs.python.org/issue5712
> >> * filenames containing whitespace
> >>
> >> Christoph
> >>
> >> On 1/23/2011 7:02 AM, wang_qi wrote:
> >> > Hello, everyone,
> >> > I have downloaded the pymol of version 1.3. and installed it on
> windows
> >> > XP successfully. But when selecting "file-open" to load my file,
> it
> >> > doesn't work and displays that the file is unable to be opend.
> Dose
> >> > anyone meet this problem? Ana how how can i solve it?
> >> > Thanks.
> >> > Qi Wang
> >> > 2011年01月23日
> >> > wang_qi
> >> >
> >> >
> >>
> >>
> >> -------------- next part --------------
> >> An embedded and charset-unspecified text was scrubbed...
> >> Name: pymol-fileopen.diff
> >>
> >> ------------------------------
> >>
> >> Message: 5
> >> Date: 2011年1月23日 12:14:17 -0800
> >> From: Seth Harris <se...@gm...>
> >> Subject: Re: [PyMOL] Faster way to find polymer chains?
> >> To: Thomas Holder <sp...@us...>
> >> Cc: pym...@li...
> >> Message-ID:
> >> <AAN...@ma...>
> >> Content-Type: text/plain; charset="iso-8859-1"
> >>
> >> Thanks Thomas and Tsjerk for pointing me back to the path...from my
> >> quicksand and brambles where I knew I was off! Brilliant. Seems to
> be an
> >> unfortunate habit I have in scripting where it's like "Why use a
> simple,
> >> elegant one-liner when a mess of impenetrable hack-arounds would
> do?" I
> >> had
> >> forgotten about those get_<goodstuff> commands.
> >>
> >> Much appreciated!
> >> -Seth
> >>
> >>
> >>
> >> On Sun, Jan 23, 2011 at 5:58 AM, Thomas Holder <
> >> sp...@us...> wrote:
> >>
> >> > Hi Seth,
> >> >
> >> > I think this one-liner will do the job for you:
> >> >
> >> > print cmd.get_chains('polymer')
> >> >
> >> > Cheers,
> >> > Thomas
> >> >
> >> > Seth Harris wrote, On 01/23/11 10:04:
> >> >
> >> > Hi All,
> >> >>
> >> >> I am script-plowing through PDB files and extracting unique chain
> >> >> identifiers only for "polymers" using PyMOL's polymer selection.
> Right
> >> >> now
> >> >> my code is a kind of brute force thing like this:
> >> >> <code>
> >> >>
> >> >> cmd.create ("justpolys","polymer")
> >> >>
> >> >> polymer_chains=[]
> >> >>
> >> >> for a in cmd.index("justpolys"):
> >> >> q_sel = "%s`%d"%a
> >> >> #print q_sel+":",
> >> >> cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
> >> >> #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
> >> >> #print
> >> >>
> >> >>
> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_inf
> o[3]
> >> >> # Track any unique chains by adding to polymer_chains list if not
> >> >> already there
> >> >> # first reformat to get rid of flanking ' marks
> >> >> thischain=`stored.qry_info[0]`
> >> >> thischain=thischain.replace("'","")
> >> >> if thischain not in polymer_chains:
> >> >> polymer_chains.append(thischain)
> >> >> </code>
> >> >>
> >> >> This works, but is quite slow as it iterates over every atom in
> every
> >> >> pdb
> >> >> just to get out the chain so it is quite redundant.
> >> >> Is there any way to iterate in a 'chain by chain' fashion? This
> q_sel
> >> >> stuff is recycled from something Warren suggested for a different
> >> >> purpose
> >> >> years ago, and I only have a loose idea of how that is
> interacting with
> >> >> the
> >> >> cmd.index part. Maybe there's a way to get just the chain from
> the
> >> >> get-go
> >> >> instead of all the individual atoms? Any reminders on that one or
> >> >> better
> >> >> method suggestions?
> >> >>
> >> >> Thanks,
> >> >> Seth
> >> >>
> >> >
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >>
> >> ------------------------------
> >>
> >> Message: 6
> >> Date: 2011年1月24日 23:11:09 +0100 (CET)
> >> From: "rv...@li..." <rv...@li...>
> >> Subject: [PyMOL] dialogs in pyMOL
> >> To: pym...@li...
> >> Message-ID:
> >> <10798172.456681295907069292.JavaMail.defaultUser@defaultHost>
> >> Content-Type: text/plain;charset="UTF-8"
> >>
> >> Hi to all,
> >> I need to open a message box dialog inside a pyMOL plug-in.
> >>
> >> When I try the code:
> >>
> >> import tkMessageBox
> >> tkMessageBox.showinfo(?title?, ?msg?)
> >>
> >> pyMOL crashes (the window doesn?t appear and pyMOL blocks).
> >>
> >> I am just entering pyMOL and python. I never used Tkinter before.
> >>
> >> Could anyone help me?
> >> Thanks
> >>
> >>
> >>
> >> ------------------------------
> >>
> >>
> >> --------------------------------------------------------------------
> ----------
> >> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> >> Finally, a world-class log management solution at an even better
> >> price-free!
> >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> >> February 28th, so secure your free ArcSight Logger TODAY!
> >> http://p.sf.net/sfu/arcsight-sfd2d
> >>
> >> ------------------------------
> >>
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyM...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>
> >>
> >> End of PyMOL-users Digest, Vol 56, Issue 9
> >> ******************************************
> >
> > ---------------------------------------------------------------------
> ---------
> > Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> > Finally, a world-class log management solution at an even better
> price-free!
> > Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> > February 28th, so secure your free ArcSight Logger TODAY!
> > http://p.sf.net/sfu/arcsight-sfd2d
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-
> us...@li...
> >
> 
> 
> 
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
> 
> -----------------------------------------------------------------------
> -------
> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> Finally, a world-class log management solution at an even better price-
> free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi Sean,
PyMOL is currently not capable of providing and "inset"-like image or
grid-mode with independent motions. Programming this at the Python
level wouldn't be very easy.
Cheers,
-- Jason
On Wed, Jan 26, 2011 at 9:39 AM, Sean Law <mag...@ho...> wrote:
> Hi PyMOLers,
>
> I was wondering if anybody had a solution for independent when using
> grid_mode=on. I want to be able to show, side-by-side, the same structure
> where one structure is "zoomed in" on a specific part on the biomolecule and
> the other object is "zoomed out" (viewing the entire molecule). And as I
> turn one of the two structures, the other one turns accordingly. I think
> this would be useful when trying to keep track of the orientation of the
> biomolecule or for docking.
>
> Any suggestions would be greatly appreciated.
>
> Sean
>
>> From: pym...@li...
>> Subject: PyMOL-users Digest, Vol 56, Issue 9
>> To: pym...@li...
>> Date: 2011年1月24日 22:11:17 +0000
>>
>> Send PyMOL-users mailing list submissions to
>> pym...@li...
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>> or, via email, send a message with subject or body 'help' to
>> pym...@li...
>>
>> You can reach the person managing the list at
>> pym...@li...
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of PyMOL-users digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Re: Faster way to find polymer chains? (Tsjerk Wassenaar)
>> 2. Re: Faster way to find polymer chains? (Thomas Holder)
>> 3. unable to open the file (wang_qi)
>> 4. Re: unable to open the file (Christoph Gohlke)
>> 5. Re: Faster way to find polymer chains? (Seth Harris)
>> 6. dialogs in pyMOL (rv...@li...)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: 2011年1月23日 10:48:20 +0100
>> From: Tsjerk Wassenaar <ts...@gm...>
>> Subject: Re: [PyMOL] Faster way to find polymer chains?
>> To: Seth Harris <se...@gm...>
>> Cc: pym...@li...
>> Message-ID:
>> <AAN...@ma...>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Oops... That should've been:
>>
>> polychains = set([i.chain for i in cmd.get_model('polymer').atom])
>>
>> Sorry for that. :p
>>
>> Tsjerk
>>
>> On Sun, Jan 23, 2011 at 10:32 AM, Tsjerk Wassenaar <ts...@gm...>
>> wrote:
>> > Hi Seth,
>> >
>> > So you just want to have all unique chain identifiers for the
>> > 'polymer' selection? Does the following give what you want?:
>> >
>> > polychains = set([i.chain for i in cmd.get_model('polymer')])
>> >
>> > Hope it helps,
>> >
>> > Tsjerk
>> >
>> > On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris <se...@gm...> wrote:
>> >> Hi All,
>> >> I am script-plowing through PDB files and extracting unique chain
>> >> identifiers only for "polymers" using PyMOL's polymer selection. Right
>> >> now
>> >> my code is a kind of brute force thing like this:
>> >> <code>
>> >> ??cmd.create ("justpolys","polymer")
>> >> ??polymer_chains=[]
>> >> ??for a in cmd.index("justpolys"):
>> >> ?? ?q_sel = "%s`%d"%a
>> >> ?? ?#print q_sel+":",
>> >> ?? ?cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
>> >> ?? ?#cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
>> >> ?? ?#print
>> >>
>> >> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
>> >> ?? ?# Track any unique chains by adding to polymer_chains list if not
>> >> already there
>> >> ?? ?# first reformat to get rid of flanking ' marks
>> >> ?? ?thischain=`stored.qry_info[0]`
>> >> ?? ?thischain=thischain.replace("'","")
>> >> ?? ?if thischain not in polymer_chains:
>> >> ?? ? ?polymer_chains.append(thischain)
>> >> </code>
>> >> This works, but is quite slow as it iterates over every atom in every
>> >> pdb
>> >> just to get out the chain so it is quite redundant.
>> >> Is there any way to iterate in a 'chain by chain' fashion? This q_sel
>> >> stuff
>> >> is recycled from something Warren suggested for a different purpose
>> >> years
>> >> ago, and I only have a loose idea of how that is interacting with the
>> >> cmd.index part. Maybe there's a way to get just the chain from the
>> >> get-go
>> >> instead of all the individual atoms? Any reminders on that one or
>> >> better
>> >> method suggestions?
>> >> Thanks,
>> >> Seth
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
>> >> Finally, a world-class log management solution at an even better
>> >> price-free!
>> >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> >> February 28th, so secure your free ArcSight Logger TODAY!
>> >> http://p.sf.net/sfu/arcsight-sfd2d
>> >> _______________________________________________
>> >> PyMOL-users mailing list (PyM...@li...)
>> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >> Archives: http://www.mail-archive.com/pym...@li...
>> >>
>> >
>> >
>> >
>> > --
>> > Tsjerk A. Wassenaar, Ph.D.
>> >
>> > post-doctoral researcher
>> > Molecular Dynamics Group
>> > * Groningen Institute for Biomolecular Research and Biotechnology
>> > * Zernike Institute for Advanced Materials
>> > University of Groningen
>> > The Netherlands
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: 2011年1月23日 14:58:17 +0100
>> From: Thomas Holder <sp...@us...>
>> Subject: Re: [PyMOL] Faster way to find polymer chains?
>> To: Seth Harris <se...@gm...>
>> Cc: pym...@li...
>> Message-ID: <4D3...@us...>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi Seth,
>>
>> I think this one-liner will do the job for you:
>>
>> print cmd.get_chains('polymer')
>>
>> Cheers,
>> Thomas
>>
>> Seth Harris wrote, On 01/23/11 10:04:
>> > Hi All,
>> >
>> > I am script-plowing through PDB files and extracting unique chain
>> > identifiers only for "polymers" using PyMOL's polymer selection. Right
>> > now my code is a kind of brute force thing like this:
>> > <code>
>> >
>> > cmd.create ("justpolys","polymer")
>> >
>> > polymer_chains=[]
>> >
>> > for a in cmd.index("justpolys"):
>> > q_sel = "%s`%d"%a
>> > #print q_sel+":",
>> > cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
>> > #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
>> > #print
>> >
>> > stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
>> > # Track any unique chains by adding to polymer_chains list if not
>> > already there
>> > # first reformat to get rid of flanking ' marks
>> > thischain=`stored.qry_info[0]`
>> > thischain=thischain.replace("'","")
>> > if thischain not in polymer_chains:
>> > polymer_chains.append(thischain)
>> > </code>
>> >
>> > This works, but is quite slow as it iterates over every atom in every
>> > pdb just to get out the chain so it is quite redundant.
>> >
>> > Is there any way to iterate in a 'chain by chain' fashion? This q_sel
>> > stuff is recycled from something Warren suggested for a different
>> > purpose years ago, and I only have a loose idea of how that is
>> > interacting with the cmd.index part. Maybe there's a way to get just the
>> > chain from the get-go instead of all the individual atoms? Any reminders
>> > on that one or better method suggestions?
>> >
>> > Thanks,
>> > Seth
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: 2011年1月23日 23:02:17 +0800
>> From: "wang_qi" <wan...@gm...>
>> Subject: [PyMOL] unable to open the file
>> To: "pymol-users" <pym...@li...>
>> Message-ID: <201...@gm...>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hello, everyone,
>>
>> I have downloaded the pymol of version 1.3. and installed it on windows XP
>> successfully. But when selecting "file-open" to load my file, it doesn't
>> work and displays that the file is unable to be opend. Dose anyone meet this
>> problem? Ana how how can i solve it?
>>
>> Thanks.
>>
>> Qi Wang
>>
>> 2011年01月23日
>>
>>
>>
>> wang_qi
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 4
>> Date: 2011年1月23日 08:27:33 -0800
>> From: Christoph Gohlke <cg...@uc...>
>> Subject: Re: [PyMOL] unable to open the file
>> To: pym...@li...
>> Message-ID: <4D3...@uc...>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> You can try the attached patch. It fixes three issues:
>>
>> * is_string() returns False in case of unicode filenames
>> * Python/Tk bug http://bugs.python.org/issue5712
>> * filenames containing whitespace
>>
>> Christoph
>>
>> On 1/23/2011 7:02 AM, wang_qi wrote:
>> > Hello, everyone,
>> > I have downloaded the pymol of version 1.3. and installed it on windows
>> > XP successfully. But when selecting "file-open" to load my file, it
>> > doesn't work and displays that the file is unable to be opend. Dose
>> > anyone meet this problem? Ana how how can i solve it?
>> > Thanks.
>> > Qi Wang
>> > 2011年01月23日
>> > wang_qi
>> >
>> >
>>
>>
>> -------------- next part --------------
>> An embedded and charset-unspecified text was scrubbed...
>> Name: pymol-fileopen.diff
>>
>> ------------------------------
>>
>> Message: 5
>> Date: 2011年1月23日 12:14:17 -0800
>> From: Seth Harris <se...@gm...>
>> Subject: Re: [PyMOL] Faster way to find polymer chains?
>> To: Thomas Holder <sp...@us...>
>> Cc: pym...@li...
>> Message-ID:
>> <AAN...@ma...>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Thanks Thomas and Tsjerk for pointing me back to the path...from my
>> quicksand and brambles where I knew I was off! Brilliant. Seems to be an
>> unfortunate habit I have in scripting where it's like "Why use a simple,
>> elegant one-liner when a mess of impenetrable hack-arounds would do?" I
>> had
>> forgotten about those get_<goodstuff> commands.
>>
>> Much appreciated!
>> -Seth
>>
>>
>>
>> On Sun, Jan 23, 2011 at 5:58 AM, Thomas Holder <
>> sp...@us...> wrote:
>>
>> > Hi Seth,
>> >
>> > I think this one-liner will do the job for you:
>> >
>> > print cmd.get_chains('polymer')
>> >
>> > Cheers,
>> > Thomas
>> >
>> > Seth Harris wrote, On 01/23/11 10:04:
>> >
>> > Hi All,
>> >>
>> >> I am script-plowing through PDB files and extracting unique chain
>> >> identifiers only for "polymers" using PyMOL's polymer selection. Right
>> >> now
>> >> my code is a kind of brute force thing like this:
>> >> <code>
>> >>
>> >> cmd.create ("justpolys","polymer")
>> >>
>> >> polymer_chains=[]
>> >>
>> >> for a in cmd.index("justpolys"):
>> >> q_sel = "%s`%d"%a
>> >> #print q_sel+":",
>> >> cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
>> >> #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
>> >> #print
>> >>
>> >> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
>> >> # Track any unique chains by adding to polymer_chains list if not
>> >> already there
>> >> # first reformat to get rid of flanking ' marks
>> >> thischain=`stored.qry_info[0]`
>> >> thischain=thischain.replace("'","")
>> >> if thischain not in polymer_chains:
>> >> polymer_chains.append(thischain)
>> >> </code>
>> >>
>> >> This works, but is quite slow as it iterates over every atom in every
>> >> pdb
>> >> just to get out the chain so it is quite redundant.
>> >> Is there any way to iterate in a 'chain by chain' fashion? This q_sel
>> >> stuff is recycled from something Warren suggested for a different
>> >> purpose
>> >> years ago, and I only have a loose idea of how that is interacting with
>> >> the
>> >> cmd.index part. Maybe there's a way to get just the chain from the
>> >> get-go
>> >> instead of all the individual atoms? Any reminders on that one or
>> >> better
>> >> method suggestions?
>> >>
>> >> Thanks,
>> >> Seth
>> >>
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 6
>> Date: 2011年1月24日 23:11:09 +0100 (CET)
>> From: "rv...@li..." <rv...@li...>
>> Subject: [PyMOL] dialogs in pyMOL
>> To: pym...@li...
>> Message-ID:
>> <10798172.456681295907069292.JavaMail.defaultUser@defaultHost>
>> Content-Type: text/plain;charset="UTF-8"
>>
>> Hi to all,
>> I need to open a message box dialog inside a pyMOL plug-in.
>>
>> When I try the code:
>>
>> import tkMessageBox
>> tkMessageBox.showinfo(?title?, ?msg?)
>>
>> pyMOL crashes (the window doesn?t appear and pyMOL blocks).
>>
>> I am just entering pyMOL and python. I never used Tkinter before.
>>
>> Could anyone help me?
>> Thanks
>>
>>
>>
>> ------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
>> Finally, a world-class log management solution at an even better
>> price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>>
>> ------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>> End of PyMOL-users Digest, Vol 56, Issue 9
>> ******************************************
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi David,
Can you please send me the PSE? If not, do you have multiple states?
Are you using the save command or the GUI?
Cheers,
-- Jason
On Thu, Jan 27, 2011 at 1:50 PM, David A. Horita <dh...@wf...> wrote:
> Hi,
> I've apparently managed to create a pse of a protein that loads fine but
> won't save the pdb coordinates (I get a file with END in it, and nothing
> else).
> Any ideas how to get the coordinates out?
>
> pymol 1.1b3 linux, windows (same pse has same result under both OS's)
>
> Thanks,
> Dave
>
> -----------------------------
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine
> Winston-Salem, NC 27157-1016
> Tel: 336 713-4194
> Fax: 336 716-7671
> email: dh...@wf...
> web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi all,
I'm traveling now, so I'm a little slow on responding. But, as
Michael has said, someone (or group) has been targeting the PyMOLWiki
with massive amounts of spam. I rolled back a change today (restoring
the main page content). If you see nonsense on the PyMOLWiki, please
feel free to clear it and msg me or Michael (or any other admin) and
we can delete the user and his/her changes.
The PyMOLWiki gets 4000+ views a day and has been visited over 5
million times. If we had 2 users and 30 hits, we'd make a bad target
for spam as no one would see it.
Cheers,
-- Jason
On Thu, Jan 27, 2011 at 2:26 PM, Michael Lerner <mgl...@gm...> wrote:
> There's been a flood of spam to the wiki recently. Most of it has been
> obvious spammy pages, but someone also deleted the main page. Cute.
>
> On Thu, Jan 27, 2011 at 12:54 PM, Schubert, Carsten [PRDUS]
> <CSC...@it...> wrote:
>>
>> I am just getting a blank page when I try to access the Pymol Wiki. Do
>> other people see the same problem?
>>
>> Carsten
>>
>>
>> ------------------------------------------------------------------------------
>> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
>> Finally, a world-class log management solution at an even better
>> price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120

There's been a flood of spam to the wiki recently. Most of it has been
obvious spammy pages, but someone also deleted the main page. Cute.
On Thu, Jan 27, 2011 at 12:54 PM, Schubert, Carsten [PRDUS] <
CSC...@it...> wrote:
> I am just getting a blank page when I try to access the Pymol Wiki. Do
> other people see the same problem?
>
> Carsten
>
>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> Finally, a world-class log management solution at an even better
> price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

Hi,
I've apparently managed to create a pse of a protein that loads fine but won't save the pdb coordinates (I get a file with END in it, and nothing else).
Any ideas how to get the coordinates out?
pymol 1.1b3 linux, windows (same pse has same result under both OS's)
Thanks,
Dave
-----------------------------
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016
Tel: 336 713-4194
Fax: 336 716-7671
email: dh...@wf...<mailto:dh...@wf...>
web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm<http://www1.wfubmc.edu/biochem/faculty/Horita.htm/>

OK, works here again as well. Main Page was somehow screwy or I had a
dirty cache in my browser
 
From: Nat Echols [mailto:nat...@gm...] 
Sent: Thursday, January 27, 2011 1:09 PM
To: pym...@li...
Subject: Re: [PyMOL] Wiki down?
 
On Thu, Jan 27, 2011 at 9:54 AM, Schubert, Carsten [PRDUS]
<CSC...@it...> wrote:
I am just getting a blank page when I try to access the Pymol Wiki. Do
other people see the same problem?
Working fine for me (using Safari on a Mac). 
 
-Nat

On Thu, Jan 27, 2011 at 9:54 AM, Schubert, Carsten [PRDUS] <
CSC...@it...> wrote:
> I am just getting a blank page when I try to access the Pymol Wiki. Do
> other people see the same problem?
>
Working fine for me (using Safari on a Mac).
-Nat

I am just getting a blank page when I try to access the Pymol Wiki. Do
other people see the same problem?
Carsten

On 2011年1月26日 10:13:25 -0500 Bradley Hintze
<bra...@ag...> wrote:
> Hi all,
> 
> I have a question regarding the changing of sphere size in a PyMOL API. When
> I use the command as presented on the PyMOLwiki, namely:
> 
> cmd.set ("sphere_scale", size=1, selection='', state=0, updates=1, log=0,
> quiet=1)
> 
> I get an error saying
> 
> set() got an unexpected keyword argument 'size'
> 
> I get the error wether 'size' is a string or an integer. What am I missing?
"size" is the wrong option, You want "value". Typing "help set" at the
PyMOL command prompt shows the following:
 cmd.set(string name, string value, string selection, int state,
 int updates, int quiet)
So you need to change your command to:
cmd.set ("sphere_scale", value=1, selection='', state=0, updates=1, log=0,
quiet=1)
Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497
<rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc

Hi Bradley,
The first argument is the setting, which is a string, and the second is the
value for that setting, which is also a string, to be interpreted according
to the setting. Actually, for sphere_scale it's also not size, but a
multiplication factor to the size.
Hope it helps,
Tsjerk
On Jan 26, 2011 4:42 PM, "Bradley Hintze" <bra...@ag...>
wrote:
Hi all,
I have a question regarding the changing of sphere size in a PyMOL API. When
I use the command as presented on the PyMOLwiki, namely:
cmd.set ("sphere_scale", size=1, selection='', state=0, updates=1, log=0,
quiet=1)
I get an error saying
set() got an unexpected keyword argument 'size'
I get the error wether 'size' is a string or an integer. What am I missing?
Thanks,
Bradley
-- 
Bradley J. Hintze
Graduate Student
Duke University
School of Medicine
801-712-8799
------------------------------------------------------------------------------
Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
_______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...

Hi all,
I have a question regarding the changing of sphere size in a PyMOL API. When
I use the command as presented on the PyMOLwiki, namely:
cmd.set ("sphere_scale", size=1, selection='', state=0, updates=1, log=0,
quiet=1)
I get an error saying
set() got an unexpected keyword argument 'size'
I get the error wether 'size' is a string or an integer. What am I missing?
Thanks,
Bradley
-- 
Bradley J. Hintze
Graduate Student
Duke University
School of Medicine
801-712-8799

Hi PyMOLers,
I was wondering if anybody had a solution for independent when using grid_mode=on. I want to be able to show, side-by-side, the same structure where one structure is "zoomed in" on a specific part on the biomolecule and the other object is "zoomed out" (viewing the entire molecule). And as I turn one of the two structures, the other one turns accordingly. I think this would be useful when trying to keep track of the orientation of the biomolecule or for docking.
Any suggestions would be greatly appreciated.
Sean
> From: pym...@li...
> Subject: PyMOL-users Digest, Vol 56, Issue 9
> To: pym...@li...
> Date: 2011年1月24日 22:11:17 +0000
> 
> Send PyMOL-users mailing list submissions to
> 	pym...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
> 
> You can reach the person managing the list at
> 	pym...@li...
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
> 1. Re: Faster way to find polymer chains? (Tsjerk Wassenaar)
> 2. Re: Faster way to find polymer chains? (Thomas Holder)
> 3. unable to open the file (wang_qi)
> 4. Re: unable to open the file (Christoph Gohlke)
> 5. Re: Faster way to find polymer chains? (Seth Harris)
> 6. dialogs in pyMOL (rv...@li...)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: 2011年1月23日 10:48:20 +0100
> From: Tsjerk Wassenaar <ts...@gm...>
> Subject: Re: [PyMOL] Faster way to find polymer chains?
> To: Seth Harris <se...@gm...>
> Cc: pym...@li...
> Message-ID:
> 	<AAN...@ma...>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Oops... That should've been:
> 
> polychains = set([i.chain for i in cmd.get_model('polymer').atom])
> 
> Sorry for that. :p
> 
> Tsjerk
> 
> On Sun, Jan 23, 2011 at 10:32 AM, Tsjerk Wassenaar <ts...@gm...> wrote:
> > Hi Seth,
> >
> > So you just want to have all unique chain identifiers for the
> > 'polymer' selection? Does the following give what you want?:
> >
> > polychains = set([i.chain for i in cmd.get_model('polymer')])
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris <se...@gm...> wrote:
> >> Hi All,
> >> I am script-plowing through PDB files and extracting unique chain
> >> identifiers only for "polymers" using PyMOL's polymer selection. Right now
> >> my code is a kind of brute force thing like this:
> >> <code>
> >> ??cmd.create ("justpolys","polymer")
> >> ??polymer_chains=[]
> >> ??for a in cmd.index("justpolys"):
> >> ?? ?q_sel = "%s`%d"%a
> >> ?? ?#print q_sel+":",
> >> ?? ?cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
> >> ?? ?#cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
> >> ?? ?#print
> >> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
> >> ?? ?# Track any unique chains by adding to polymer_chains list if not
> >> already there
> >> ?? ?# first reformat to get rid of flanking ' marks
> >> ?? ?thischain=`stored.qry_info[0]`
> >> ?? ?thischain=thischain.replace("'","")
> >> ?? ?if thischain not in polymer_chains:
> >> ?? ? ?polymer_chains.append(thischain)
> >> </code>
> >> This works, but is quite slow as it iterates over every atom in every pdb
> >> just to get out the chain so it is quite redundant.
> >> Is there any way to iterate in a 'chain by chain' fashion? This q_sel stuff
> >> is recycled from something Warren suggested for a different purpose years
> >> ago, and I only have a loose idea of how that is interacting with the
> >> cmd.index part. Maybe there's a way to get just the chain from the get-go
> >> instead of all the individual atoms? Any reminders on that one or better
> >> method suggestions?
> >> Thanks,
> >> Seth
> >>
> >> ------------------------------------------------------------------------------
> >> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> >> Finally, a world-class log management solution at an even better price-free!
> >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> >> February 28th, so secure your free ArcSight Logger TODAY!
> >> http://p.sf.net/sfu/arcsight-sfd2d
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >>
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> >
> > post-doctoral researcher
> > Molecular Dynamics Group
> > * Groningen Institute for Biomolecular Research and Biotechnology
> > * Zernike Institute for Advanced Materials
> > University of Groningen
> > The Netherlands
> >
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> 
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: 2011年1月23日 14:58:17 +0100
> From: Thomas Holder <sp...@us...>
> Subject: Re: [PyMOL] Faster way to find polymer chains?
> To: Seth Harris <se...@gm...>
> Cc: pym...@li...
> Message-ID: <4D3...@us...>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi Seth,
> 
> I think this one-liner will do the job for you:
> 
> print cmd.get_chains('polymer')
> 
> Cheers,
> Thomas
> 
> Seth Harris wrote, On 01/23/11 10:04:
> > Hi All,
> > 
> > I am script-plowing through PDB files and extracting unique chain 
> > identifiers only for "polymers" using PyMOL's polymer selection. Right 
> > now my code is a kind of brute force thing like this:
> > <code>
> > 
> > cmd.create ("justpolys","polymer")
> > 
> > polymer_chains=[]
> > 
> > for a in cmd.index("justpolys"):
> > q_sel = "%s`%d"%a
> > #print q_sel+":",
> > cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
> > #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
> > #print 
> > stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
> > # Track any unique chains by adding to polymer_chains list if not 
> > already there
> > # first reformat to get rid of flanking ' marks
> > thischain=`stored.qry_info[0]`
> > thischain=thischain.replace("'","")
> > if thischain not in polymer_chains:
> > polymer_chains.append(thischain)
> > </code>
> > 
> > This works, but is quite slow as it iterates over every atom in every 
> > pdb just to get out the chain so it is quite redundant. 
> > 
> > Is there any way to iterate in a 'chain by chain' fashion? This q_sel 
> > stuff is recycled from something Warren suggested for a different 
> > purpose years ago, and I only have a loose idea of how that is 
> > interacting with the cmd.index part. Maybe there's a way to get just the 
> > chain from the get-go instead of all the individual atoms? Any reminders 
> > on that one or better method suggestions?
> > 
> > Thanks,
> > Seth
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: 2011年1月23日 23:02:17 +0800
> From: "wang_qi" <wan...@gm...>
> Subject: [PyMOL] unable to open the file
> To: "pymol-users" <pym...@li...>
> Message-ID: <201...@gm...>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hello, everyone,
> 
> I have downloaded the pymol of version 1.3. and installed it on windows XP successfully. But when selecting "file-open" to load my file, it doesn't work and displays that the file is unable to be opend. Dose anyone meet this problem? Ana how how can i solve it?
> 
> Thanks.
> 
> Qi Wang
> 
> 2011年01月23日 
> 
> 
> 
> wang_qi 
> -------------- next part --------------
> An HTML attachment was scrubbed...
> 
> ------------------------------
> 
> Message: 4
> Date: 2011年1月23日 08:27:33 -0800
> From: Christoph Gohlke <cg...@uc...>
> Subject: Re: [PyMOL] unable to open the file
> To: pym...@li...
> Message-ID: <4D3...@uc...>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> You can try the attached patch. It fixes three issues:
> 
> * is_string() returns False in case of unicode filenames
> * Python/Tk bug http://bugs.python.org/issue5712
> * filenames containing whitespace
> 
> Christoph
> 
> On 1/23/2011 7:02 AM, wang_qi wrote:
> > Hello, everyone,
> > I have downloaded the pymol of version 1.3. and installed it on windows
> > XP successfully. But when selecting "file-open" to load my file, it
> > doesn't work and displays that the file is unable to be opend. Dose
> > anyone meet this problem? Ana how how can i solve it?
> > Thanks.
> > Qi Wang
> > 2011年01月23日
> > wang_qi
> >
> >
> 
> 
> -------------- next part --------------
> An embedded and charset-unspecified text was scrubbed...
> Name: pymol-fileopen.diff
> 
> ------------------------------
> 
> Message: 5
> Date: 2011年1月23日 12:14:17 -0800
> From: Seth Harris <se...@gm...>
> Subject: Re: [PyMOL] Faster way to find polymer chains?
> To: Thomas Holder <sp...@us...>
> Cc: pym...@li...
> Message-ID:
> 	<AAN...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Thanks Thomas and Tsjerk for pointing me back to the path...from my
> quicksand and brambles where I knew I was off! Brilliant. Seems to be an
> unfortunate habit I have in scripting where it's like "Why use a simple,
> elegant one-liner when a mess of impenetrable hack-arounds would do?" I had
> forgotten about those get_<goodstuff> commands.
> 
> Much appreciated!
> -Seth
> 
> 
> 
> On Sun, Jan 23, 2011 at 5:58 AM, Thomas Holder <
> sp...@us...> wrote:
> 
> > Hi Seth,
> >
> > I think this one-liner will do the job for you:
> >
> > print cmd.get_chains('polymer')
> >
> > Cheers,
> > Thomas
> >
> > Seth Harris wrote, On 01/23/11 10:04:
> >
> > Hi All,
> >>
> >> I am script-plowing through PDB files and extracting unique chain
> >> identifiers only for "polymers" using PyMOL's polymer selection. Right now
> >> my code is a kind of brute force thing like this:
> >> <code>
> >>
> >> cmd.create ("justpolys","polymer")
> >>
> >> polymer_chains=[]
> >>
> >> for a in cmd.index("justpolys"):
> >> q_sel = "%s`%d"%a
> >> #print q_sel+":",
> >> cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
> >> #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
> >> #print
> >> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
> >> # Track any unique chains by adding to polymer_chains list if not
> >> already there
> >> # first reformat to get rid of flanking ' marks
> >> thischain=`stored.qry_info[0]`
> >> thischain=thischain.replace("'","")
> >> if thischain not in polymer_chains:
> >> polymer_chains.append(thischain)
> >> </code>
> >>
> >> This works, but is quite slow as it iterates over every atom in every pdb
> >> just to get out the chain so it is quite redundant.
> >> Is there any way to iterate in a 'chain by chain' fashion? This q_sel
> >> stuff is recycled from something Warren suggested for a different purpose
> >> years ago, and I only have a loose idea of how that is interacting with the
> >> cmd.index part. Maybe there's a way to get just the chain from the get-go
> >> instead of all the individual atoms? Any reminders on that one or better
> >> method suggestions?
> >>
> >> Thanks,
> >> Seth
> >>
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> 
> ------------------------------
> 
> Message: 6
> Date: 2011年1月24日 23:11:09 +0100 (CET)
> From: "rv...@li..." <rv...@li...>
> Subject: [PyMOL] dialogs in pyMOL
> To: pym...@li...
> Message-ID:
> 	<10798172.456681295907069292.JavaMail.defaultUser@defaultHost>
> Content-Type: text/plain;charset="UTF-8"
> 
> Hi to all,
> I need to open a message box dialog inside a pyMOL plug-in.
> 
> When I try the code:
> 
> import tkMessageBox
> tkMessageBox.showinfo(?title?, ?msg?)
> 
> pyMOL crashes (the window doesn?t appear and pyMOL blocks).
> 
> I am just entering pyMOL and python. I never used Tkinter before.
> 
> Could anyone help me?
> Thanks
> 
> 
> 
> ------------------------------
> 
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires 
> February 28th, so secure your free ArcSight Logger TODAY! 
> http://p.sf.net/sfu/arcsight-sfd2d
> 
> ------------------------------
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> End of PyMOL-users Digest, Vol 56, Issue 9
> ******************************************
 		 	 		 

Hi to all,
I need to open a message box dialog inside a pyMOL plug-in.
When I try the code:
import tkMessageBox
tkMessageBox.showinfo(‘title’, ‘msg’)
pyMOL crashes (the window doesn’t appear and pyMOL blocks).
I am just entering pyMOL and python. I never used Tkinter before.
Could anyone help me?
Thanks

Thanks Thomas and Tsjerk for pointing me back to the path...from my
quicksand and brambles where I knew I was off! Brilliant. Seems to be an
unfortunate habit I have in scripting where it's like "Why use a simple,
elegant one-liner when a mess of impenetrable hack-arounds would do?" I had
forgotten about those get_<goodstuff> commands.
Much appreciated!
-Seth
On Sun, Jan 23, 2011 at 5:58 AM, Thomas Holder <
sp...@us...> wrote:
> Hi Seth,
>
> I think this one-liner will do the job for you:
>
> print cmd.get_chains('polymer')
>
> Cheers,
> Thomas
>
> Seth Harris wrote, On 01/23/11 10:04:
>
> Hi All,
>>
>> I am script-plowing through PDB files and extracting unique chain
>> identifiers only for "polymers" using PyMOL's polymer selection. Right now
>> my code is a kind of brute force thing like this:
>> <code>
>>
>> cmd.create ("justpolys","polymer")
>>
>> polymer_chains=[]
>>
>> for a in cmd.index("justpolys"):
>> q_sel = "%s`%d"%a
>> #print q_sel+":",
>> cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
>> #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
>> #print
>> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
>> # Track any unique chains by adding to polymer_chains list if not
>> already there
>> # first reformat to get rid of flanking ' marks
>> thischain=`stored.qry_info[0]`
>> thischain=thischain.replace("'","")
>> if thischain not in polymer_chains:
>> polymer_chains.append(thischain)
>> </code>
>>
>> This works, but is quite slow as it iterates over every atom in every pdb
>> just to get out the chain so it is quite redundant.
>> Is there any way to iterate in a 'chain by chain' fashion? This q_sel
>> stuff is recycled from something Warren suggested for a different purpose
>> years ago, and I only have a loose idea of how that is interacting with the
>> cmd.index part. Maybe there's a way to get just the chain from the get-go
>> instead of all the individual atoms? Any reminders on that one or better
>> method suggestions?
>>
>> Thanks,
>> Seth
>>
>

You can try the attached patch. It fixes three issues:
* is_string() returns False in case of unicode filenames
* Python/Tk bug http://bugs.python.org/issue5712
* filenames containing whitespace
Christoph
On 1/23/2011 7:02 AM, wang_qi wrote:
> Hello, everyone,
> I have downloaded the pymol of version 1.3. and installed it on windows
> XP successfully. But when selecting "file-open" to load my file, it
> doesn't work and displays that the file is unable to be opend. Dose
> anyone meet this problem? Ana how how can i solve it?
> Thanks.
> Qi Wang
> 2011年01月23日
> wang_qi
>
>

Hello, everyone,
I have downloaded the pymol of version 1.3. and installed it on windows XP successfully. But when selecting "file-open" to load my file, it doesn't work and displays that the file is unable to be opend. Dose anyone meet this problem? Ana how how can i solve it?
Thanks.
Qi Wang
2011年01月23日 
wang_qi 

Hi Seth,
I think this one-liner will do the job for you:
print cmd.get_chains('polymer')
Cheers,
 Thomas
Seth Harris wrote, On 01/23/11 10:04:
> Hi All,
> 
> I am script-plowing through PDB files and extracting unique chain 
> identifiers only for "polymers" using PyMOL's polymer selection. Right 
> now my code is a kind of brute force thing like this:
> <code>
> 
> cmd.create ("justpolys","polymer")
> 
> polymer_chains=[]
> 
> for a in cmd.index("justpolys"):
> q_sel = "%s`%d"%a
> #print q_sel+":",
> cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
> #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
> #print 
> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
> # Track any unique chains by adding to polymer_chains list if not 
> already there
> # first reformat to get rid of flanking ' marks
> thischain=`stored.qry_info[0]`
> thischain=thischain.replace("'","")
> if thischain not in polymer_chains:
> polymer_chains.append(thischain)
> </code>
> 
> This works, but is quite slow as it iterates over every atom in every 
> pdb just to get out the chain so it is quite redundant. 
> 
> Is there any way to iterate in a 'chain by chain' fashion? This q_sel 
> stuff is recycled from something Warren suggested for a different 
> purpose years ago, and I only have a loose idea of how that is 
> interacting with the cmd.index part. Maybe there's a way to get just the 
> chain from the get-go instead of all the individual atoms? Any reminders 
> on that one or better method suggestions?
> 
> Thanks,
> Seth

Oops... That should've been:
polychains = set([i.chain for i in cmd.get_model('polymer').atom])
Sorry for that. :p
Tsjerk
On Sun, Jan 23, 2011 at 10:32 AM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi Seth,
>
> So you just want to have all unique chain identifiers for the
> 'polymer' selection? Does the following give what you want?:
>
> polychains = set([i.chain for i in cmd.get_model('polymer')])
>
> Hope it helps,
>
> Tsjerk
>
> On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris <se...@gm...> wrote:
>> Hi All,
>> I am script-plowing through PDB files and extracting unique chain
>> identifiers only for "polymers" using PyMOL's polymer selection. Right now
>> my code is a kind of brute force thing like this:
>> <code>
>>  cmd.create ("justpolys","polymer")
>>  polymer_chains=[]
>>  for a in cmd.index("justpolys"):
>>   q_sel = "%s`%d"%a
>>   #print q_sel+":",
>>   cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
>>   #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
>>   #print
>> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
>>   # Track any unique chains by adding to polymer_chains list if not
>> already there
>>   # first reformat to get rid of flanking ' marks
>>   thischain=`stored.qry_info[0]`
>>   thischain=thischain.replace("'","")
>>   if thischain not in polymer_chains:
>>    polymer_chains.append(thischain)
>> </code>
>> This works, but is quite slow as it iterates over every atom in every pdb
>> just to get out the chain so it is quite redundant.
>> Is there any way to iterate in a 'chain by chain' fashion? This q_sel stuff
>> is recycled from something Warren suggested for a different purpose years
>> ago, and I only have a loose idea of how that is interacting with the
>> cmd.index part. Maybe there's a way to get just the chain from the get-go
>> instead of all the individual atoms? Any reminders on that one or better
>> method suggestions?
>> Thanks,
>> Seth
>>
>> ------------------------------------------------------------------------------
>> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
>> Finally, a world-class log management solution at an even better price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
-- 
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Hi Seth,
So you just want to have all unique chain identifiers for the
'polymer' selection? Does the following give what you want?:
polychains = set([i.chain for i in cmd.get_model('polymer')])
Hope it helps,
Tsjerk
On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris <se...@gm...> wrote:
> Hi All,
> I am script-plowing through PDB files and extracting unique chain
> identifiers only for "polymers" using PyMOL's polymer selection. Right now
> my code is a kind of brute force thing like this:
> <code>
>  cmd.create ("justpolys","polymer")
>  polymer_chains=[]
>  for a in cmd.index("justpolys"):
>   q_sel = "%s`%d"%a
>   #print q_sel+":",
>   cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
>   #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
>   #print
> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
>   # Track any unique chains by adding to polymer_chains list if not
> already there
>   # first reformat to get rid of flanking ' marks
>   thischain=`stored.qry_info[0]`
>   thischain=thischain.replace("'","")
>   if thischain not in polymer_chains:
>    polymer_chains.append(thischain)
> </code>
> This works, but is quite slow as it iterates over every atom in every pdb
> just to get out the chain so it is quite redundant.
> Is there any way to iterate in a 'chain by chain' fashion? This q_sel stuff
> is recycled from something Warren suggested for a different purpose years
> ago, and I only have a loose idea of how that is interacting with the
> cmd.index part. Maybe there's a way to get just the chain from the get-go
> instead of all the individual atoms? Any reminders on that one or better
> method suggestions?
> Thanks,
> Seth
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a 49ドル USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands