pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Martin,
So it seems I was right :D
ID is an atomic property, read from the PDB file, whereas index is an
'internal' identifier. Following Jasons comments, ID is not changed upon
additions/deletions, whereas index does.
For your purpose, you probably want to make sure that the IDs are identical
for corresponding atoms.
Hope it helps,
Tsjerk
On Oct 31, 2010 3:35 PM, "Martin Hediger" <ma...@bl...> wrote:
Hey, Thanks for your earlier response on the issue.
Its quite important to me right now, since I am trying to interpolate
between two states of the same structure and therefore (let me call it
'physical') atom numbering has to be perfectly identical.
I looked into it but i cant quite get my following observation into
agreement with what you said.
I have a PDB file with 920 atoms. Starting from the top, with no 'TER' or
'MODEL' or other PDB syntax elements, on line 909 of that file an ATOM is
stated (hydrogen), with the number '909' at the "line-909".split()[1]
position.
When I open the file in PyMOL and let it display LABELS>ATOM_IDENTIFIERS>ID,
I get '909' displayed in the model. Changing the value at '909' in the PDB
file to 950, reloading and redisplaying the 'ID' labels, presents '950' also
in the PyMOL viewer, even if the ATOM is still on line 909 in the PDB file.
How can this behavior be explained with regard to what we were talking about
previously? What label-type is required to display the actual,
non-label-dependent index of the atom in the system? Does the functionality
depend on whether there are more detailed atom descriptors available, like
residue type or chain id?
Thanks one more time for any help on this.
Martin
Am 25.10.10 17:03, schrieb Jason Vertrees:
> > Hi Martin& Tsjerk, > > There is a another difference between the two
aside from the > off-by-o...

Hey, Thanks for your earlier response on the issue.
Its quite important to me right now, since I am trying to interpolate 
between two states of the same structure and therefore (let me call it 
'physical') atom numbering has to be perfectly identical.
I looked into it but i cant quite get my following observation into 
agreement with what you said.
I have a PDB file with 920 atoms. Starting from the top, with no 'TER' 
or 'MODEL' or other PDB syntax elements, on line 909 of that file an 
ATOM is stated (hydrogen), with the number '909' at the 
"line-909".split()[1] position.
When I open the file in PyMOL and let it display 
LABELS>ATOM_IDENTIFIERS>ID, I get '909' displayed in the model. Changing 
the value at '909' in the PDB file to 950, reloading and redisplaying 
the 'ID' labels, presents '950' also in the PyMOL viewer, even if the 
ATOM is still on line 909 in the PDB file. How can this behavior be 
explained with regard to what we were talking about previously? What 
label-type is required to display the actual, non-label-dependent index 
of the atom in the system? Does the functionality depend on whether 
there are more detailed atom descriptors available, like residue type or 
chain id?
Thanks one more time for any help on this.
Martin
Am 25.10.10 17:03, schrieb Jason Vertrees:
> Hi Martin& Tsjerk,
>
> There is a another difference between the two aside from the
> off-by-one characteristic. PyMOL has to keep track of atoms, so a
> simple 'index' could work. But, then when the user removes an atom
> from the middle of a structure, do we shift indices above it down?
> (This could make bonds point to new places!) Leave them as is? (But
> there aren't N-atoms anymore, there's N-1.) So, PyMOL has two
> indices, one tracks the absolute numbering (ID) and doesn't change
> between (molecular) object builds, and the other tracks the atom's
> relative position from the first atom found. This could be confusing,
> so how about some code:
>
> # create an alanine fragment
> frag ala
>
> # now read the label on the ALA`2/HA; C-alpha's hydrogen
> # it should read, '7-9'
> label *, "%s-%s" % (index,ID)
>
> [.. read the label before copying and pasting below ..]
>
> # Now, remove the alpha carbon; subsequent commands
> # will need to rebuild the connection table, generating
> # new numbers for index
> remove 2/CA
>
> # hide the labels
> hide labels
>
> # now read the label on the 2/HA atom ("6-9")
> label *, "%s-%s" % (index,ID)
>
> Cheers,
>
> -- Jason
>
>
>
>
> On Mon, Oct 25, 2010 at 6:49 AM, Tsjerk Wassenaar<ts...@gm...> wrote:
>> Never get used to that only-reply-to-sender policy...
>>
>>
>> ---------- Forwarded message ----------
>> From: Tsjerk Wassenaar<ts...@gm...>
>> Date: Mon, Oct 25, 2010 at 12:30 PM
>> Subject: Re: [PyMOL] What is the difference between Atom ID and Index
>> To: Martin Hediger<ma...@bl...>
>>
>>
>> Hi Martin,
>>
>> ID is indeed the atom id from the coordinate (PDB) file. Index, AFAIK,
>> is the atom index in the model, starting from 1.
>>
>> Probably you should get yourself acquainted with the command line and
>> with python, as it will help you to solve these and other problems.
>> For example, you can access properties from the atoms easily through
>> constructions like these:
>>
>> x = [ at.id for at in cmd.get_model(selection).atom ]
>> y = [ at.index for at in cmd.get_model(selection).atom ]
>>
>> That will first build a selection/model object, with a list of atoms
>> (.atom), over which you can iterate to extract some properties. To
>> check whether the index is indeed a straightforward list of increasing
>> numbers, you can then look at the output of
>>
>> print y == range(1,len(y)+1)
>>
>> Hope it helps :)
>>
>> Tsjerk
>>
>> On Mon, Oct 25, 2010 at 10:55 AM, Martin Hediger<ma...@bl...> wrote:
>>> Dear All
>>> I'm trying to figure out for myself, what the two labels 'Label> Atom
>>> Identifiers> ID' and 'Label> Atom Identifiers> index' mean, or what
>>> the respective difference between the two is. For sure, the numerical
>>> value is very different when I show the labels in a structure. ID seems
>>> to be the index of the atom in the list of atom-descriptor lines in the
>>> PDB input file. But I cant figure out what 'index' is referring to.
>>>
>>> Any help on this would be very welcome.
>>>
>>> Martin
>>>
>>> ------------------------------------------------------------------------------
>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>> Create new apps& games for the Nokia N8 for consumers in U.S. and Canada
>>> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>> http://p.sf.net/sfu/nokia-dev2dev
>>> _______________________________________________
>>> 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
>>
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps& games for the Nokia N8 for consumers in U.S. and Canada
>> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

I have been thinking about getting a multicore remote server to run 
Autodock, do rendering, etc. It would be convenient to run PyMol 
directly on the server, tunneling the connection to an X-server running 
on my desktop. However, there is a long response-time delay when using 
PyMol 1.2r1 (x86_64) on CentOS 5 , an issue I have been ascribing to 
network latency. Am I correct in this assumption?
I note that there was a short discussion thread last year on 
master/slave pymol sessions, using XML-RPC.
http://www.mail-archive.com/pym...@li.../msg06984.html
I'm completely unfamiliar with this, and do not know how to implement it 
(my desktop runs PyMol 1.2r1 on Windows XP). Would this be an 
appropriate solution? Would it work to call remote plugins?
Jed
-- 
------------------------
Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Woods Hole, MA 02543

Dear Bryan,
Curiously the escape key will switch back for you. It's been this way
forever I think.
When asking questions please specify some details on your version of
PyMOL. In my version (1.2) the figure in the main window does not
disappear when invoking the help command.
Hope this helps!
Best regards,
Folmer Fredslund
2010年10月29日 Prince, D Bryan <DBr...@as...>:
> Dear PyMOL users:
>
>
>
> I have been working my way through a tutorial on how to use PyMOL, and
> working primarily from the command line. Being somewhat schooled in UNIX, I
> ran into a problem and typed >help show on the command line. I got the
> information much like I would have from a UNIX terminal, but I was not able
> to figure out how to return to the model I had been working on. I randomly
> tried to hide all and show all, but nothing happened. Is there a way to get
> back to the figure after invoking help on the command line?
>
>
>
> Many thanks,
>
>
>
> Bryan
>
> ________________________________
>
> Confidentiality Notice: This message is private and may contain confidential
> and proprietary information. If you have received this message in error,
> please notify us and remove it from your system and note that you must not
> copy, distribute or take any action in reliance on it. Any unauthorized use
> or disclosure of the contents of this message is not permitted and may be
> unlawful.
>
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear PyMOL users:
 
I have been working my way through a tutorial on how to use PyMOL, and
working primarily from the command line. Being somewhat schooled in
UNIX, I ran into a problem and typed >help show on the command line. I
got the information much like I would have from a UNIX terminal, but I
was not able to figure out how to return to the model I had been working
on. I randomly tried to hide all and show all, but nothing happened. Is
there a way to get back to the figure after invoking help on the command
line?
 
Many thanks,
 
Bryan
--------------------------------------------------------------------------
Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.
 

PyMOLers,
Work on bringing PyMOL's code up to a newer openGL standard has begun.
 This will bring us access to new openGL features. We're taking a
poll of which openGL version your systems support.
To cast your vote please visit: http://pymol.org/poll
Cheers,
-- Jason
-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Saif,
I checked the same file in PyMOL and Coot. You're right, there are
some differences at the boundaries, but they still look insignificant.
 Maybe you can point out a residue with a large deviation. For this
map, Coot shows large blocks of red/green mesh indicating differences
in the observed and calculated densities. The resolution of that map
is 3.0 Ang. So, I'm not surprised to see slight variations in the
mesh due to algorithmic differences, especially at that resolution
near boundaries.
Cheers,
-- Jason
On Wed, Oct 27, 2010 at 2:29 PM, S. Saif Hasan <ss...@pu...> wrote:
> Hello,
>
> The structure is PDB2E74 and I downloaded the 2Fo-Fc and Fo-Fc maps in the CCP4
> format from the EDS website (http://eds.bmc.uu.se/eds/) and named the former map
> 2e74a.
>
> Once I open the 2e74.pdb file (downloaded from the PDB) and the 2Fo-Fc map in
> PyMol, I selected the lipid (OPC, part of chain H) and used this command in
> PyMol- "isomesh msh1, 2e74a, 2.0, sele, carve=2"
>
> Thanks.
>
> --
> S. Saif Hasan
>
> Graduate Student
> Department of Biological Sciences
> Hockmeyer Hall of Structural Biology
> Purdue University
> 240 S. Martin Jischke Drive
> West Lafayette, IN 47907
>
>
>
> Quoting Jason Vertrees <jas...@sc...>:
>
>> Hi Saif,
>>
>> Can you please show us the commands you used in PyMOL to load the data
>> and generate the map? (Also, can you send me a copy of the map and
>> structure?) Has anyone else seen this problem?
>>
>> I've looked over a few CCP4 maps in PyMOL, Maestro, and Coot
>> side-by-side, and at various contours, they all look virtually
>> identical. There are slight differences, probably due to algorithmic
>> deviations, but they look good to me.
>>
>> In PyMOL:
>> # mimic Coot
>> set orthoscopic
>> set line_width, 5
>>
>> # get the data
>> fetch 1cll, async=0
>> fetch 1cll, type=2fofc, async=0
>>
>> # create the map; carve 2.5 Ang from the polymer
>> isomesh 1cll_map,1cll_2fofc, 1.06, poly, carve=2.5
>>
>> # find example residue
>> orient i. 78
>>
>> # color
>> color magenta, e. N
>> color tv_yellow, e. C
>>
>>
>> In Coot:
>>  * Fetch 1CLL and its map from EDS
>>  * zoom to residue 78
>>  * scroll to 1.06 sigma
>>
>> What do you see here?
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>> On Tue, Oct 26, 2010 at 9:50 AM, S. Saif Hasan <ss...@pu...> wrote:
>> > Hello,
>> >
>> > I am trying to carve a 2Fo-Fc map around a lipid molecule. The electron
>> density
>> > at 2 sigma is much smaller in PyMol than in Coot (the map at 1 sigma in
>> PyMol
>> > is similar to the 2 sigma level map in Coot). I used the "unset
>> > normalize_ccp4_maps" command but that stops the carved map from being
>> > generated. What should I do to solve this problem ?
>> >
>> > Thank you.
>> > --
>> > Saif Hasan
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Nokia and AT&T present the 2010 Calling All Innovators-North America
>> contest
>> > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
>> > 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in
>> marketing
>> > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> > http://p.sf.net/sfu/nokia-dev2dev
>> > _______________________________________________
>> > 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,
The tutorial states that the quality needs to be increased prior to
ray-tracing. But it seems to me that the {sphere,stick}_quality
settings apply to the OpenGL rendering, whereas the raytracer uses
'real' spheres and cylinders. Even when setting sphere_quality to 0,
'ray' will still give (near) perfect spheres.
Cheers,
Tsjerk
On Wed, Oct 27, 2010 at 11:27 PM, Jason Vertrees
<jas...@sc...> wrote:
> Hi Xiao-Ping,
>
> If you want the _best_ sphere quality, then try,
>
> set sphere_mode, 5
>
> This is pixel-perfect rendering of spheres in PyMOL using openGL
> shaders. Otherwise, these quality settings in PyMOL are typically
> limited to how much memory your machine has; also, these settings are
> usually quadratic or exponential in their use of memory.
>
> That tutorial looks good, but needs updating to make better use of
> PyMOL's features.
>
> Cheers,
>
> -- Jason
>
> On Wed, Oct 27, 2010 at 5:09 PM, Xiao-Ping Zhang <xp...@uc...> wrote:
>> Hi, PyMol users,
>>
>> I have noticed that Justin Lorieau
>> (http://www.lorieau.com/methods-and-reference/molecular-viewers/30-pymol--ball-and-stick-figures.html) can use +ACI-set sphere+AF8-quality, 10+ACI to generate a ball+AF8-stick picture. When I tried to use the same command, PyMol crashed. The default sphere+AF8-quality is 1, 3 is the maximum value that I can use. I am curious what is the maximum value. I am running PyMol 1.3 on Fedora 13.
>> Thank you for your help.
>>
>> Xiao-Ping
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
>> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> _______________________________________________
>> 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
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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

Dear Jason,
Thank you for your reply. I tried sphere_mode command on two machines. 
On Fedora 13, PyMol 1.3
set sphere_mode, 5 
disabled sphere display.
set sphere_mode, 4, 3, or 2 can show sphere, but it looks terrible. 
One Fedora 8, PyMol 1.3
set sphere_mode, 5
also disabled sphere display. But 4 gives a beautiful sphere view.
It seems that I need to fix OpenGL on Fedora 13. 
Best regards,
Xiao-Ping
 
On Wed, 2010年10月27日 at 17:27 -0400, Jason Vertrees wrote:
> Hi Xiao-Ping,
> 
> If you want the _best_ sphere quality, then try,
> 
> set sphere_mode, 5
> 
> This is pixel-perfect rendering of spheres in PyMOL using openGL
> shaders. Otherwise, these quality settings in PyMOL are typically
> limited to how much memory your machine has; also, these settings are
> usually quadratic or exponential in their use of memory.
> 
> That tutorial looks good, but needs updating to make better use of
> PyMOL's features.
> 
> Cheers,
> 
> -- Jason
> 
> On Wed, Oct 27, 2010 at 5:09 PM, Xiao-Ping Zhang <xp...@uc...> wrote:
> > Hi, PyMol users,
> >
> > I have noticed that Justin Lorieau
> > (http:www.lorieau.commethods-and-referencemolecular-viewers30-pymol--ball-and-stick-figures.html) can use +ACI-set sphere+AF8-quality, 10+ACI to generate a ball+AF8-stick picture. When I tried to use the same command, PyMol crashed. The default sphere+AF8-quality is 1, 3 is the maximum value that I can use. I am curious what is the maximum value. I am running PyMol 1.3 on Fedora 13.
> > Thank you for your help.
> >
> > Xiao-Ping
> >
> >
> >
> >
> > ------------------------------------------------------------------------------
> > Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> > 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> > http:p.sf.netsfunokia-dev2dev
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https:lists.sourceforge.netlistslistinfopymol-users
> > Archives: http:www...@li...
> >
> 
> 
> 

Dear Roger Rowlett,
Thank you for your reply. I did run "set stick_ball, on" before "set
sphere_quality, xx". 
Sincerely,
Xiao-Ping
 
On Wed, 2010年10月27日 at 17:20 -0400, Roger Rowlett wrote:
> See http:www.pymolwiki.orgindex.phpSphere_quality.
> 
> On 10272010 5:09 PM, Xiao-Ping Zhang wrote: 
> > Hi, PyMol users,
> > 
> > I have noticed that Justin Lorieau
> > (http:www.lorieau.commethods-and-referencemolecular-viewers30-pymol--ball-and-stick-figures.html) can use "set sphere_quality, 10" to generate a ball_stick picture. When I tried to use the same command, PyMol crashed. The default sphere_quality is 1, 3 is the maximum value that I can use. I am curious what is the maximum value. I am running PyMol 1.3 on Fedora 13. 
> > Thank you for your help. 
> > 
> > Xiao-Ping
> > 
> > 
> > 
> > 
> > ------------------------------------------------------------------------------
> > Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> > 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store 
> > http:p.sf.netsfunokia-dev2dev
> > 
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https:lists.sourceforge.netlistslistinfopymol-users
> > Archives: http:www...@li...

Hi Xiao-Ping,
If you want the _best_ sphere quality, then try,
 set sphere_mode, 5
This is pixel-perfect rendering of spheres in PyMOL using openGL
shaders. Otherwise, these quality settings in PyMOL are typically
limited to how much memory your machine has; also, these settings are
usually quadratic or exponential in their use of memory.
That tutorial looks good, but needs updating to make better use of
PyMOL's features.
Cheers,
-- Jason
On Wed, Oct 27, 2010 at 5:09 PM, Xiao-Ping Zhang <xp...@uc...> wrote:
> Hi, PyMol users,
>
> I have noticed that Justin Lorieau
> (http://www.lorieau.com/methods-and-reference/molecular-viewers/30-pymol--ball-and-stick-figures.html) can use +ACI-set sphere+AF8-quality, 10+ACI to generate a ball+AF8-stick picture. When I tried to use the same command, PyMol crashed. The default sphere+AF8-quality is 1, 3 is the maximum value that I can use. I am curious what is the maximum value. I am running PyMol 1.3 on Fedora 13.
> Thank you for your help.
>
> Xiao-Ping
>
>
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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, PyMol users,
I have noticed that Justin Lorieau
(http:www.lorieau.commethods-and-referencemolecular-viewers30-pymol--ball-and-stick-figures.html) can use "set sphere_quality, 10" to generate a ball_stick picture. When I tried to use the same command, PyMol crashed. The default sphere_quality is 1, 3 is the maximum value that I can use. I am curious what is the maximum value. I am running PyMol 1.3 on Fedora 13. 
Thank you for your help. 
Xiao-Ping

Yehudi,
What happens when you click on the mouse mode matrix? Also, are you
stuck inside a Wizard? Last, what happens when you type,
mouse three_button_viewing
at the command line?
Cheers,
-- Jason
On Tue, Oct 26, 2010 at 7:00 PM, Yehudi Bloch <yeh...@ug...> wrote:
> Hy,
>
> Whilst working on a project, suddenly the "3-button editing" mouse mode
> got stuck in atoms (and joints) picking. I can no longer select any
> other picking mode. In viewing mode all selecting modes are still available.
>
> This is so for all my files (both old and new). For PyMol in Windows 7
> (1.3 edu) and Ubuntu 10.10 (1.3 edu and 1.2r2). Reinstalling doesn't
> help. Computers at university can handle home made "stuck" files just fine.
>
> Any help would be great.
>
> Cheers,
> Yehudi
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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

Hy,
Whilst working on a project, suddenly the "3-button editing" mouse mode 
got stuck in atoms (and joints) picking. I can no longer select any 
other picking mode. In viewing mode all selecting modes are still available.
This is so for all my files (both old and new). For PyMol in Windows 7 
(1.3 edu) and Ubuntu 10.10 (1.3 edu and 1.2r2). Reinstalling doesn't 
help. Computers at university can handle home made "stuck" files just fine.
Any help would be great.
Cheers,
Yehudi

Hi Saif,
Can you please show us the commands you used in PyMOL to load the data
and generate the map? (Also, can you send me a copy of the map and
structure?) Has anyone else seen this problem?
I've looked over a few CCP4 maps in PyMOL, Maestro, and Coot
side-by-side, and at various contours, they all look virtually
identical. There are slight differences, probably due to algorithmic
deviations, but they look good to me.
In PyMOL:
# mimic Coot
set orthoscopic
set line_width, 5
# get the data
fetch 1cll, async=0
fetch 1cll, type=2fofc, async=0
# create the map; carve 2.5 Ang from the polymer
isomesh 1cll_map,1cll_2fofc, 1.06, poly, carve=2.5
# find example residue
orient i. 78
# color
color magenta, e. N
color tv_yellow, e. C
In Coot:
 * Fetch 1CLL and its map from EDS
 * zoom to residue 78
 * scroll to 1.06 sigma
What do you see here?
Cheers,
-- Jason
On Tue, Oct 26, 2010 at 9:50 AM, S. Saif Hasan <ss...@pu...> wrote:
> Hello,
>
> I am trying to carve a 2Fo-Fc map around a lipid molecule. The electron density
> at 2 sigma is much smaller in PyMol than in Coot (the map at 1 sigma in PyMol
> is similar to the 2 sigma level map in Coot). I used the "unset
> normalize_ccp4_maps" command but that stops the carved map from being
> generated. What should I do to solve this problem ?
>
> Thank you.
> --
> Saif Hasan
>
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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

Hello,
I am trying to carve a 2Fo-Fc map around a lipid molecule. The electron density 
at 2 sigma is much smaller in PyMol than in Coot (the map at 1 sigma in PyMol 
is similar to the 2 sigma level map in Coot). I used the "unset 
normalize_ccp4_maps" command but that stops the carved map from being 
generated. What should I do to solve this problem ?
Thank you.
-- 
Saif Hasan

Ahh yes that works! Thank you!
Cheers,
Tom
--
Thomas D. Grant
Graduate Research Assistant
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203
On Tue, Oct 26, 2010 at 6:28 AM, Joao Renato Carvalho Muniz <
jrc...@gm...> wrote:
> Hi Jared and Tom,
>
> Same issue here... but sorted it out following this pymolwiki tip:
>
> When using multiple displays, the OpenGL window flickers; moving the
> window between displays crashes the whole session [1]
> If you don't need stereo then start PyMOL in mono mode with
>
> pymol -M
>
> Cheers,
>
> Joao.
>
>
>
> On Mon, Oct 25, 2010 at 9:34 PM, Sampson, Jared <Jar...@ny...>
> wrote:
> > Hi Tom - I’ve also experienced this behavior, which led me to a) attempt
> to learn not to switch Spaces while using Fink-installed X11 PyMOL (other
> X11 programs, e.g. CCP4i, appear not to have the same issue); b) make all of
> my figures using .pml scripts so that if I’ve changed something it’s already
> saved before I even see it in PyMOL; and c) find and install a very handy
> (commercial - 15ドル but worth every penny) program called ForeverSave which
> will automatically backup and save your other, non-X11 files (i.e. anything
> that can be saved with Cmd-S) in case you accidentally do switch Spaces,
> which as you say is hard not to do once you’re in the habit.
> >
> > http://www.tool-forcesw.com/foreversave/
> >
> > As I recall, the behavior began to appear with the 10.6.3 update; both
> the "delta" and "combo" installs produced the same problem. (For a while I
> had reverted to 10.6.2, but then accidentally told Software Update to do its
> thing, which got me back to the same point, after which I didn’t feel like
> reinstalling everything again. 10.6.4 obviously didn’t fix the issue
> either.)
> >
> > Despite having fairly successfully worked around the issue for a good 9
> months or so, the I’d love to see this issue go away, too. Any thoughts
> from developers or other python- or X11-savvy folks? I’m afraid I’m not one
> of them.
> >
> > Jared
> >
> > --
> > Jared Sampson
> > Xiangpeng Kong Lab
> > NYU Langone Medical Center
> > New York, NY 10016
> > (212) 263-7898
> >
> >
> > On 10/25/10 2:34 PM, "Thomas Grant" <tom...@gm...> wrote:
> >
> > Hi all,
> >
> > I'm using PyMOL version 1.3 installed via Fink on my MacBook Pro with
> Snow Leopard 10.6.4. I've noticed a strange OS-specific bug when using the
> Spaces feature of my Mac while running PyMOL. If I attempt to change Space,
> my system appears to do some sort of restart, without actually restarting.
> In other words, every program quits and the even Finder relaunches and
> anything unsaved gets lost. I realize this is a fairly system specific bug,
> but I'm wondering if anyone else running Snow Leopard who uses the Spaces
> feature runs into this and if so, whether or not you've found a solution.
> Normally I would just stop using the Spaces feature, but I've gotten in the
> habit of using it and do it without thinking, and lose everything I'm
> working on. Any advice would help, but I'm hoping to not have to turn off
> the feature. Thanks.
> >
> > Tom
> >
> > --
> > Thomas D. Grant
> > Graduate Research Assistant
> > Hauptman-Woodward Medical Research Institute
> > 700 Ellicott St.
> > Buffalo, NY 14203
> >
> >
> >
> >
> >
> > ------------------------------------------------------------
> > This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The organization
> accepts no liability for any damage caused by any virus transmitted by this
> email.
> > =================================
> >
> >
> >
> ------------------------------------------------------------------------------
> > Nokia and AT&T present the 2010 Calling All Innovators-North America
> contest
> > Create new apps & games for the Nokia N8 for consumers in U.S. and
> Canada
> > 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in
> marketing
> > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> > http://p.sf.net/sfu/nokia-dev2dev
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America
> contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in
> marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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 Jared and Tom,
Same issue here... but sorted it out following this pymolwiki tip:
When using multiple displays, the OpenGL window flickers; moving the
window between displays crashes the whole session [1]
 If you don't need stereo then start PyMOL in mono mode with
 pymol -M
Cheers,
Joao.
On Mon, Oct 25, 2010 at 9:34 PM, Sampson, Jared <Jar...@ny...> wrote:
> Hi Tom - I’ve also experienced this behavior, which led me to a) attempt to learn not to switch Spaces while using Fink-installed X11 PyMOL (other X11 programs, e.g. CCP4i, appear not to have the same issue); b) make all of my figures using .pml scripts so that if I’ve changed something it’s already saved before I even see it in PyMOL; and c) find and install a very handy (commercial - 15ドル but worth every penny) program called ForeverSave which will automatically backup and save your other, non-X11 files (i.e. anything that can be saved with Cmd-S) in case you accidentally do switch Spaces, which as you say is hard not to do once you’re in the habit.
>
> http://www.tool-forcesw.com/foreversave/
>
> As I recall, the behavior began to appear with the 10.6.3 update; both the "delta" and "combo" installs produced the same problem. (For a while I had reverted to 10.6.2, but then accidentally told Software Update to do its thing, which got me back to the same point, after which I didn’t feel like reinstalling everything again. 10.6.4 obviously didn’t fix the issue either.)
>
> Despite having fairly successfully worked around the issue for a good 9 months or so, the I’d love to see this issue go away, too. Any thoughts from developers or other python- or X11-savvy folks? I’m afraid I’m not one of them.
>
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> New York, NY 10016
> (212) 263-7898
>
>
> On 10/25/10 2:34 PM, "Thomas Grant" <tom...@gm...> wrote:
>
> Hi all,
>
> I'm using PyMOL version 1.3 installed via Fink on my MacBook Pro with Snow Leopard 10.6.4. I've noticed a strange OS-specific bug when using the Spaces feature of my Mac while running PyMOL. If I attempt to change Space, my system appears to do some sort of restart, without actually restarting. In other words, every program quits and the even Finder relaunches and anything unsaved gets lost. I realize this is a fairly system specific bug, but I'm wondering if anyone else running Snow Leopard who uses the Spaces feature runs into this and if so, whether or not you've found a solution. Normally I would just stop using the Spaces feature, but I've gotten in the habit of using it and do it without thinking, and lose everything I'm working on. Any advice would help, but I'm hoping to not have to turn off the feature. Thanks.
>
> Tom
>
> --
> Thomas D. Grant
> Graduate Research Assistant
> Hauptman-Woodward Medical Research Institute
> 700 Ellicott St.
> Buffalo, NY 14203
>
>
>
>
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
> =================================
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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 Tom - I’ve also experienced this behavior, which led me to a) attempt to learn not to switch Spaces while using Fink-installed X11 PyMOL (other X11 programs, e.g. CCP4i, appear not to have the same issue); b) make all of my figures using .pml scripts so that if I’ve changed something it’s already saved before I even see it in PyMOL; and c) find and install a very handy (commercial - 15ドル but worth every penny) program called ForeverSave which will automatically backup and save your other, non-X11 files (i.e. anything that can be saved with Cmd-S) in case you accidentally do switch Spaces, which as you say is hard not to do once you’re in the habit.
http://www.tool-forcesw.com/foreversave/
As I recall, the behavior began to appear with the 10.6.3 update; both the "delta" and "combo" installs produced the same problem. (For a while I had reverted to 10.6.2, but then accidentally told Software Update to do its thing, which got me back to the same point, after which I didn’t feel like reinstalling everything again. 10.6.4 obviously didn’t fix the issue either.)
Despite having fairly successfully worked around the issue for a good 9 months or so, the I’d love to see this issue go away, too. Any thoughts from developers or other python- or X11-savvy folks? I’m afraid I’m not one of them.
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
New York, NY 10016
(212) 263-7898
On 10/25/10 2:34 PM, "Thomas Grant" <tom...@gm...> wrote:
Hi all,
I'm using PyMOL version 1.3 installed via Fink on my MacBook Pro with Snow Leopard 10.6.4. I've noticed a strange OS-specific bug when using the Spaces feature of my Mac while running PyMOL. If I attempt to change Space, my system appears to do some sort of restart, without actually restarting. In other words, every program quits and the even Finder relaunches and anything unsaved gets lost. I realize this is a fairly system specific bug, but I'm wondering if anyone else running Snow Leopard who uses the Spaces feature runs into this and if so, whether or not you've found a solution. Normally I would just stop using the Spaces feature, but I've gotten in the habit of using it and do it without thinking, and lose everything I'm working on. Any advice would help, but I'm hoping to not have to turn off the feature. Thanks.
Tom
--
Thomas D. Grant
Graduate Research Assistant
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203
------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

Hi all,
I'm using PyMOL version 1.3 installed via Fink on my MacBook Pro with Snow
Leopard 10.6.4. I've noticed a strange OS-specific bug when using the
Spaces feature of my Mac while running PyMOL. If I attempt to change Space,
my system appears to do some sort of restart, without actually restarting.
 In other words, every program quits and the even Finder relaunches and
anything unsaved gets lost. I realize this is a fairly system specific bug,
but I'm wondering if anyone else running Snow Leopard who uses the Spaces
feature runs into this and if so, whether or not you've found a solution.
 Normally I would just stop using the Spaces feature, but I've gotten in the
habit of using it and do it without thinking, and lose everything I'm
working on. Any advice would help, but I'm hoping to not have to turn off
the feature. Thanks.
Tom
--
Thomas D. Grant
Graduate Research Assistant
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203

Hi Martin,
You could think of it as what Tsjerk purported:
# pseudocode for iterate
def iterate(sel,cmd):
 for x in selection:
 return cmd(x)
where each 'function' cmd would return a value per atom.
For example,
# pseucode for an instance of iterate
def iterate(organic, 'print b')
 for x in organic:
 print_b(organic)
> The second question is related to the Edit-Mode of PyMOL. When I switch
> to Edit-Mode and click on a atom, a couple of states/objects (?) appear
> in the object list: pk1, pkmol, pkresi, pkchain, pkobject.
> What do these objects mean? What are they useful for? I'm sure there is
> a reason for them, but I cant figure it out.
PyMOL has a fully functioning molecular editor, but it's clunky and
not well-understood. In Selection Mode you 'select,' whereas in Edit
Mode, you 'pick'. In Edit Mode, (pk1) is the first atom you 'pick'
with the mouse. Common operations can be completed when you pick the
atoms on which you want to operate. For example, in edit mode, pick
two atoms and type the word "dist" at the command line. PyMOL will
measure the distance between those two atoms. Pick three and you can
calculate an angle. PyMOL supports pk1 up to pk4. pkmol is the
molecular object associated with your picks; pkresi is the residue.
The builder has lots of interesting things built into it. Pick the
correct three atoms and you can 'invert' the stereochemistry by
flipping the liganded groups.
Cheers,
-- Jason
On Sun, Oct 24, 2010 at 8:12 AM, Martin Hediger <ma...@bl...> wrote:
> Dear All
> I am trying to get behind the way 'iterate' works, since I see it quite
> frequently in PyMOL scripts.
> The example in the help page is a bit limited in the sense that I cant
> explain to myself what actually is happening.
>
> Say, if I were to write the functionality of 'iterate' using a for-loop,
> how would this for-loop look like?
> Something like this maybe?
>
> for i in selection:
>   i.expression()
>
> I'm a bit confused about what can go into 'expression'.
>
> The second question is related to the Edit-Mode of PyMOL. When I switch
> to Edit-Mode and click on a atom, a couple of states/objects (?) appear
> in the object list: pk1, pkmol, pkresi, pkchain, pkobject.
> What do these objects mean? What are they useful for? I'm sure there is
> a reason for them, but I cant figure it out.
>
> Thanks a lot for your help guys.
>
> Martin
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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 Martin & Tsjerk,
There is a another difference between the two aside from the
off-by-one characteristic. PyMOL has to keep track of atoms, so a
simple 'index' could work. But, then when the user removes an atom
from the middle of a structure, do we shift indices above it down?
(This could make bonds point to new places!) Leave them as is? (But
there aren't N-atoms anymore, there's N-1.) So, PyMOL has two
indices, one tracks the absolute numbering (ID) and doesn't change
between (molecular) object builds, and the other tracks the atom's
relative position from the first atom found. This could be confusing,
so how about some code:
# create an alanine fragment
frag ala
# now read the label on the ALA`2/HA; C-alpha's hydrogen
# it should read, '7-9'
label *, "%s-%s" % (index,ID)
[.. read the label before copying and pasting below ..]
# Now, remove the alpha carbon; subsequent commands
# will need to rebuild the connection table, generating
# new numbers for index
remove 2/CA
# hide the labels
hide labels
# now read the label on the 2/HA atom ("6-9")
label *, "%s-%s" % (index,ID)
Cheers,
-- Jason
On Mon, Oct 25, 2010 at 6:49 AM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Never get used to that only-reply-to-sender policy...
>
>
> ---------- Forwarded message ----------
> From: Tsjerk Wassenaar <ts...@gm...>
> Date: Mon, Oct 25, 2010 at 12:30 PM
> Subject: Re: [PyMOL] What is the difference between Atom ID and Index
> To: Martin Hediger <ma...@bl...>
>
>
> Hi Martin,
>
> ID is indeed the atom id from the coordinate (PDB) file. Index, AFAIK,
> is the atom index in the model, starting from 1.
>
> Probably you should get yourself acquainted with the command line and
> with python, as it will help you to solve these and other problems.
> For example, you can access properties from the atoms easily through
> constructions like these:
>
> x = [ at.id for at in cmd.get_model(selection).atom ]
> y = [ at.index for at in cmd.get_model(selection).atom ]
>
> That will first build a selection/model object, with a list of atoms
> (.atom), over which you can iterate to extract some properties. To
> check whether the index is indeed a straightforward list of increasing
> numbers, you can then look at the output of
>
> print y == range(1,len(y)+1)
>
> Hope it helps :)
>
> Tsjerk
>
> On Mon, Oct 25, 2010 at 10:55 AM, Martin Hediger <ma...@bl...> wrote:
>> Dear All
>> I'm trying to figure out for myself, what the two labels 'Label > Atom
>> Identifiers > ID' and 'Label > Atom Identifiers > index' mean, or what
>> the respective difference between the two is. For sure, the numerical
>> value is very different when I show the labels in a structure. ID seems
>> to be the index of the atom in the list of atom-descriptor lines in the
>> PDB input file. But I cant figure out what 'index' is referring to.
>>
>> Any help on this would be very welcome.
>>
>> Martin
>>
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
>> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> _______________________________________________
>> 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
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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

Thanks Tsjerk (on both occasions).
As a matter of fact, I'm kind of making a living out of writing a Python 
script once in a while, so thats no worry ;)
What I was trying to get at was that I was trying to understand how 
certain PyMOL scripts work, and naturally from that become able to 
improve my own ones.
In particular, I was trying to understand the following script:
http://pastebin.com/5mkwWJdd
Its is supposed to find hydrogen bonds within a structure and it should 
allow to monitor the change in the HB network throughout a reaction. 
Credit to the person who wrote it.
Especially, lines 61 to 69 make heavy use of iterate, but I cant quite 
follow it. Understanding 'iterate' (and naturally iterate_state, alter 
and alter_state), I believe, would help me alot in writing better scripts.
Anyway, thanks again for the support.
Martin
On 25.10.10 12:49, Tsjerk Wassenaar wrote:
> Never get used to that only-reply-to-sender policy...
>
>
> ---------- Forwarded message ----------
> From: Tsjerk Wassenaar<ts...@gm...>
> Date: Mon, Oct 25, 2010 at 12:30 PM
> Subject: Re: [PyMOL] What is the difference between Atom ID and Index
> To: Martin Hediger<ma...@bl...>
>
>
> Hi Martin,
>
> ID is indeed the atom id from the coordinate (PDB) file. Index, AFAIK,
> is the atom index in the model, starting from 1.
>
> Probably you should get yourself acquainted with the command line and
> with python, as it will help you to solve these and other problems.
> For example, you can access properties from the atoms easily through
> constructions like these:
>
> x = [ at.id for at in cmd.get_model(selection).atom ]
> y = [ at.index for at in cmd.get_model(selection).atom ]
>
> That will first build a selection/model object, with a list of atoms
> (.atom), over which you can iterate to extract some properties. To
> check whether the index is indeed a straightforward list of increasing
> numbers, you can then look at the output of
>
> print y == range(1,len(y)+1)
>
> Hope it helps :)
>
> Tsjerk
>
> On Mon, Oct 25, 2010 at 10:55 AM, Martin Hediger<ma...@bl...> wrote:
>> Dear All
>> I'm trying to figure out for myself, what the two labels 'Label> Atom
>> Identifiers> ID' and 'Label> Atom Identifiers> index' mean, or what
>> the respective difference between the two is. For sure, the numerical
>> value is very different when I show the labels in a structure. ID seems
>> to be the index of the atom in the list of atom-descriptor lines in the
>> PDB input file. But I cant figure out what 'index' is referring to.
>>
>> Any help on this would be very welcome.
>>
>> Martin
>>
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps& games for the Nokia N8 for consumers in U.S. and Canada
>> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> _______________________________________________
>> 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
>
>
>

...
---------- Forwarded message ----------
From: Tsjerk Wassenaar <ts...@gm...>
Date: Mon, Oct 25, 2010 at 12:39 PM
Subject: Re: [PyMOL] Question about Iterate and Edit-Mode
To: Martin Hediger <ma...@bl...>
Hi Martin,
Without diving into the source, I think it is more like:
for i in selection:
 execute(command, atom=i)
with execute being a function taking a string and an atom id :) and
doing something like:
eval(command, locals=locals())
Note that there will be some trickery to extend the locals dictionary
with the properties that can be included in the command (resi, ID, b,
etc.).
Hope it helps,
Tsjerk
On Sun, Oct 24, 2010 at 2:12 PM, Martin Hediger <ma...@bl...> wrote:
> Dear All
> I am trying to get behind the way 'iterate' works, since I see it quite
> frequently in PyMOL scripts.
> The example in the help page is a bit limited in the sense that I cant
> explain to myself what actually is happening.
>
> Say, if I were to write the functionality of 'iterate' using a for-loop,
> how would this for-loop look like?
> Something like this maybe?
>
> for i in selection:
>   i.expression()
>
> I'm a bit confused about what can go into 'expression'.
>
> The second question is related to the Edit-Mode of PyMOL. When I switch
> to Edit-Mode and click on a atom, a couple of states/objects (?) appear
> in the object list: pk1, pkmol, pkresi, pkchain, pkobject.
> What do these objects mean? What are they useful for? I'm sure there is
> a reason for them, but I cant figure it out.
>
> Thanks a lot for your help guys.
>
> Martin
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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

Never get used to that only-reply-to-sender policy...
---------- Forwarded message ----------
From: Tsjerk Wassenaar <ts...@gm...>
Date: Mon, Oct 25, 2010 at 12:30 PM
Subject: Re: [PyMOL] What is the difference between Atom ID and Index
To: Martin Hediger <ma...@bl...>
Hi Martin,
ID is indeed the atom id from the coordinate (PDB) file. Index, AFAIK,
is the atom index in the model, starting from 1.
Probably you should get yourself acquainted with the command line and
with python, as it will help you to solve these and other problems.
For example, you can access properties from the atoms easily through
constructions like these:
x = [ at.id for at in cmd.get_model(selection).atom ]
y = [ at.index for at in cmd.get_model(selection).atom ]
That will first build a selection/model object, with a list of atoms
(.atom), over which you can iterate to extract some properties. To
check whether the index is indeed a straightforward list of increasing
numbers, you can then look at the output of
print y == range(1,len(y)+1)
Hope it helps :)
Tsjerk
On Mon, Oct 25, 2010 at 10:55 AM, Martin Hediger <ma...@bl...> wrote:
> Dear All
> I'm trying to figure out for myself, what the two labels 'Label > Atom
> Identifiers > ID' and 'Label > Atom Identifiers > index' mean, or what
> the respective difference between the two is. For sure, the numerical
> value is very different when I show the labels in a structure. ID seems
> to be the index of the atom in the list of atom-descriptor lines in the
> PDB input file. But I cant figure out what 'index' is referring to.
>
> Any help on this would be very welcome.
>
> Martin
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> 10ドル million total in prizes - 4ドルM cash, 500 devices, nearly 6ドルM in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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