pymol-users Mailing List for PyMOL Molecular Graphics System

Hi,
thanks Jason.
It's not native but the script is simple enough to be included with every surface.
Alex
----- Ursprüngliche Mail -----
> Von: "Jason Vertrees" <jas...@sc...>
> An: "Alexander Rose" <ale...@we...>
> CC: "pymol-users" <pym...@li...>
> Gesendet: Freitag, 27. September 2013 15:41:39
> Betreff: Re: [PyMOL] load surface
> 
> 
> Hi Alexander,
> 
> 
> See http://www.pymolwiki.org/index.php/Wfmesh .
> 
> 
> Cheers,
> 
> 
> -- Jason
> 
> 
> 
> On Fri, Sep 27, 2013 at 3:05 PM, Alexander Rose <
> ale...@we... > wrote:
> 
> 
> Hi,
> 
> I have create a surface (vertices and faces) in some external program
> and am now looking for a format to convert it to so that PyMOL can
> natively load it. Any suggestion is much appreciated.
> 
> 
> Best
> Alexander
> 
> ------------------------------------------------------------------------------
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> 
> 
> 
> 
> --
> 
> Jason Vertrees, PhD
> Director of Core Modeling Products
> Schrödinger, Inc.
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Hi Alexander,
See http://www.pymolwiki.org/index.php/Wfmesh.
Cheers,
-- Jason
On Fri, Sep 27, 2013 at 3:05 PM, Alexander Rose <ale...@we...
> wrote:
> Hi,
>
> I have create a surface (vertices and faces) in some external program and
> am now looking for a format to convert it to so that PyMOL can natively
> load it. Any suggestion is much appreciated.
>
>
> Best
> Alexander
>
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most
> from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk
> _______________________________________________
> 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
Director of Core Modeling Products
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi,
I have create a surface (vertices and faces) in some external program and am now looking for a format to convert it to so that PyMOL can natively load it. Any suggestion is much appreciated.
Best
Alexander

Hi,
http://www.pymolwiki.org/index.php/Label would help.
Zhijian Xu
On 09/26/2013 10:40 AM, xfc_2013 wrote:
> Dear everybody,
> I'm a new user of pymol and have come with some questions about label. The two main progroms are as following:
> 1. I have labeled residue names of a receptor protein around its ligand (Syntax:Pymol> label near, ("%s/%s") % (resn, resi)#("%s/%s")). While, how to write the syntax to make one residue with only a single name.
> 2. Could anyone tell me how to label residues in protein-protein docking results?
> Thank you so much.
> Best wishes!
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> xfc_2013
>
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
> the latest Intel processors and coprocessors. See abstracts and register>
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Dear everybody,
I'm a new user of pymol and have come with some questions about label. The two main progroms are as following:
1. I have labeled residue names of a receptor protein around its ligand (Syntax:Pymol> label near, ("%s/%s") % (resn, resi)#("%s/%s") ). While, how to write the syntax to make one residue with only a single name.
2. Could anyone tell me how to label residues in protein-protein docking results?
Thank you so much.
Best wishes! 
xfc_2013

do you have numpy and psico installed?
http://www.pymolwiki.org/index.php/Psico
Psico has that particular command.
Jordan
On Sep 21, 2013, at 8:45 AM, Ananya Chatterjee <ana...@ya...> wrote:
> Dear all,
> 
> After simulation of my protein I have aligned the initial and the final structure and I could see movement in one domain, now to measure the angle between the domain I used the following lines,
> 
> Select d1, Structure1 and resi 1-160
> Select d2, Structure2 and resi 1-160
> angle_between_domains d1, d2
> 
> and then I am geting following error,
> 
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 464, in parse
> exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
> File "<string>", line 1
> angle_between_domains d1, d2
> ^
> SyntaxError: invalid syntax
> 
> Can any one tell me where am I getting wrong and also is there any other way to measure the angle between the domain moved.
> 
> Thanks in advance
> 
> Ananya
> 
> ------------------------------------------------------------------------------
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Dear all,
After simulation of my protein I have aligned the initial and the final structure and I could see movement in one domain, now to measure the angle between the domain I used the following lines,
Select d1, Structure1 and resi 1-160
Select d2, Structure2 and resi 1-160
angle_between_domains d1, d2
and then I am geting following error,
Traceback (most recent call last):
 File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 464, in parse
  exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
 File "<string>", line 1
  angle_between_domains d1, d2
              ^
SyntaxError: invalid syntax
Can any one tell me where am I getting wrong and also is there any other way to measure the angle between the domain moved.
Thanks in advance
Ananya

Hi Nils,
Thomas will soon fix the return values of the get command for color to
properly contain the "0x" prefixes. In the meantime, please add them
yourself if this is causing lots of problems:
# prepend the result with 0x
x = "0x%s" % (cmd.get("bg_rgb_top"))
# set the color
cmd.set("bg_rgb_bottom", x)
Cheers,
-- Jason
On Fri, Sep 20, 2013 at 11:36 AM, Nils NN <N-...@gm...> wrote:
>
>
> Hi Jason,
> thanks for the reply.
> Your method works well for the single color background.
> For the gradient BG however the problem still remains:
> PyMOL>set bg_gradient, 1
> PyMOL>get bg_rgb_top
> -> this returns '00004d', which seems to be the hex-value.
>
> However when I try to set the bg_rgb_top/bottom value (regardless if I use
> hex or rgb-list) I still get an endless output of:
> Setting-Error: type read mismatch (color) 663
> Setting-Error: type read mismatch (color) 663
> Setting-Error: type read mismatch (color) 663
> Setting-Error: type read mismatch (color) 663
> Setting-Error: type read mismatch (color) 663
> ...
>
> This message keeps flooding the output shell until I close the program. I
> guess this is rather a bug than intended?
>
> Best,
> Nils
>
>
>
> Gesendet: Donnerstag, 19. September 2013 um 17:39 Uhr
> Von: "Jason Vertrees" <jas...@sc...>
> An: "Nils NN" <N-...@gm...>
> Cc: "pym...@li..." <pym...@li...
> >
> Betreff: Re: [PyMOL] Background colors in PyMOL 1.6
>
> Hi Nils,
>
> We've updated how PyMOL stores colors in sessions. You can try,
>
> cmd.get_color_tuple(cmd.get("bg_rgb"))
>
> or if you need it as a list:
>
> list(cmd.get_color_tuple(cmd.get("bg_rgb")))
>
> Cheers,
>
> -- Jason
>
> On Thu, Sep 19, 2013 at 5:17 PM, Nils NN <N-...@gm...> wrote:
>
> Hello,
>
> I recently installed PyMOL 1.6 on my Debian machine. I have noticed that
> the description of the background colors has somehow changed. The command
> "get bg_color" returns [R,G,B] values in all previous versions, while since
> 1.6 it only returns values like "black" (which messes up some of my
> plugins and scripts). I'm not sure if this some kind of bug or a new way of
> handling colors...
> When I try to set the background gradient colors (set bg_rgb_top/bottom) I
> get an endless output of "Setting-Error: type read mismatch (color) 664" -
> I have to kill and restart the program to get rid of the message. Same
> happens with my scripts using cmd...
> Can someone confirm these problems? Perhaps I'm doing something wrong here.
>
> Thanks in advance,
> Nils
>
>
>
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...[
> PyM...@li...])
> Info Page:
> https://lists.sourceforge.net/lists/listinfo/pymol-users[https://lists.sourceforge.net/lists/listinfo/pymol-users]
> Archives:
> http://www.mail-archive.com/pym...@li...[http://www.mail-archive.com/pym...@li...]
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Products
> Schrödinger, Inc.
>
> (e) Jas...@sc...[Jas...@sc...]
> (o) +1 (603) 374-7120
>
-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Jason,
thanks for the reply.
Your method works well for the single color background.
For the gradient BG however the problem still remains:
PyMOL>set bg_gradient, 1
PyMOL>get bg_rgb_top
-> this returns '00004d', which seems to be the hex-value.
However when I try to set the bg_rgb_top/bottom value (regardless if I use hex or rgb-list) I still get an endless output of:
Setting-Error: type read mismatch (color) 663
Setting-Error: type read mismatch (color) 663
Setting-Error: type read mismatch (color) 663
Setting-Error: type read mismatch (color) 663
Setting-Error: type read mismatch (color) 663
...
This message keeps flooding the output shell until I close the program. I guess this is rather a bug than intended?
Best,
Nils
 
 
Gesendet: Donnerstag, 19. September 2013 um 17:39 Uhr
Von: "Jason Vertrees" <jas...@sc...>
An: "Nils NN" <N-...@gm...>
Cc: "pym...@li..." <pym...@li...>
Betreff: Re: [PyMOL] Background colors in PyMOL 1.6
Hi Nils,
 
We've updated how PyMOL stores colors in sessions. You can try,
 
cmd.get_color_tuple(cmd.get("bg_rgb"))
 
or if you need it as a list:
 
list(cmd.get_color_tuple(cmd.get("bg_rgb")))
 
Cheers,
 
-- Jason
 
On Thu, Sep 19, 2013 at 5:17 PM, Nils NN <N-...@gm...> wrote:
Hello,
 
I recently installed PyMOL 1.6 on my Debian machine. I have noticed that the description of the background colors has somehow changed. The command "get bg_color" returns [R,G,B] values in all previous versions, while since 1.6 it only returns values like "black" (which messes up some of my plugins and scripts). I'm not sure if this some kind of bug or a new way of handling colors...
When I try to set the background gradient colors (set bg_rgb_top/bottom) I get an endless output of "Setting-Error: type read mismatch (color) 664" - I have to kill and restart the program to get rid of the message. Same happens with my scripts using cmd...
Can someone confirm these problems? Perhaps I'm doing something wrong here.
 
Thanks in advance,
Nils
 
 
 
 
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 --
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) Jas...@sc...[Jas...@sc...]
(o) +1 (603) 374-7120

Hi Raul,
I don't think the bond guessing routine is exposed to the python API.
This would actually be very useful, so I take this as a feature request.
Meanwhile, I guess you need some workaround like dumping to PDB format
and loading as PDB again. Have a look at cmd.get_pdbstr and cmd.read_pdbstr.
Cheers,
 Thomas
Raúl Mera Adasme wrote, On 09/17/13 19:15:
> Hi all,
> 
> I want to load a chempy model into PyMOL. Unfortunately, the model has
> all the coordinate information, but not bonds defined.
> I know PyMOL can guess the bonds from the distances, but it does not
> do it if I just use cmd.load_model, and I could not find a way of
> doing it.
> 
> Does anyone know how can I achieve this?
> 
> Thanks!
> 
> Raul
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Jacob,
saving to mol2 format is only fully supported in incentive PyMOL. It
uses a proprietary library for the atom type assignment, which is not
available in open-source PyMOL.
Cheers,
 Thomas
Jacob Pessin wrote, On 09/19/13 00:05:
> Hi,
> 
> I've come across an issue saving .mol2 ( @<TRIPOS> ) files.
> MGL tools' PMV/ADT won't read them, babel/open babel issues a set of
> complaint and read errors.
> 
> If I am reading the format correctly then ...
> 
> In the atom content the columnation appears to be off after the X Y Z
> coordinates, the question marks under atom_type seem to throw a lot of
> scripts (not surprising).
> 
> I'm not quite sure what the issue is, but it occurs when saving peptides
> and molecules built by a mouse or script as well as RCSB downloaded
> structures. seems the same on all builds and machines I've tried (listed
> at bottom)
> 
> thanks for your time
> 
> jacob
> 
> # created with PyMOL
> @<TRIPOS>MOLECULE
> untitled
> 57 57 0 0 0
> PROTEIN
> USER_CHARGES
> @<TRIPOS>ATOM
> 1 N 0.394 -2.167 -1.142 ?? 1.000
> 2 CA 0.891 -0.794 -1.142 ?? 1.000
> 3 C 2.400 -0.765 -1.142 ?? 1.000
> 4 O 3.074 -1.654 -0.600 ?? 1.000
> 5 CB 0.286 0.038 0.061 ?? 1.000
> 6 CG1 -1.272 -0.010 0.168 ?? 1.000
> 
> ...
> 
> saved from pymol 1.6 https://www.dropbox.com/s/jlpwa2lsub5ez8g/IPR.mol2
> babel pipes https://www.dropbox.com/s/ruh23hcxfmbv0z8/babelmol2_mol2.txt
> babel
> out https://www.dropbox.com/s/3p41lkvybdlwhwc/IPR_mol2mol2_babeled.mol2
> <https://www.dropbox.com/s/3p41lkvybdlwhwc/IPR_mol2mol2_babeled.mol2>
> tripos mol2 format pdf http://www.tripos.com/data/support/mol2.pdf
> 
> hardware
> dell T3600 e5-1650
> w/ quadro 600 xUbuntu 13.04 pymol 1.6.0 from source w/build_seq.py and
> seq_convert.py
> 1.5.2 from package (and lots of plugins)
> 
> lenovo t420 nvs 400
> windows 7 1.4.? (not sitting at it while typing) pre-built many plugins
> also xUbuntu 12.04 1.4 from package and 1.6 from source
> (w/nvidia-bumblebee, and just intel graphics)
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Nils,
We've updated how PyMOL stores colors in sessions. You can try,
cmd.get_color_tuple(cmd.get("bg_rgb"))
or if you need it as a list:
list(cmd.get_color_tuple(cmd.get("bg_rgb")))
Cheers,
-- Jason
On Thu, Sep 19, 2013 at 5:17 PM, Nils NN <N-...@gm...> wrote:
> Hello,
>
> I recently installed PyMOL 1.6 on my Debian machine. I have noticed that
> the description of the background colors has somehow changed. The command
> "get bg_color" returns [R,G,B] values in all previous versions, while since
> 1.6 it only returns values like "black" (which messes up some of my
> plugins and scripts). I'm not sure if this some kind of bug or a new way of
> handling colors...
> When I try to set the background gradient colors (set bg_rgb_top/bottom) I
> get an endless output of "Setting-Error: type read mismatch (color) 664" -
> I have to kill and restart the program to get rid of the message. Same
> happens with my scripts using cmd...
> Can someone confirm these problems? Perhaps I'm doing something wrong here.
>
> Thanks in advance,
> Nils
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> LIMITED TIME SALE - Full Year of Microsoft Training For Just 49ドル.99!
> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8,
> SharePoint
> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack
> includes
> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk
> _______________________________________________
> 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
Director of Core Modeling Products
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>Hello,</div>
<div>&nbsp;</div>
<div>I recently installed PyMOL 1.6 on my Debian machine. I have noticed that the description of the background colors has somehow changed. The command &quot;get bg_color&quot; returns [R,G,B] values in all previous versions, while since 1.6 it only returns values &nbsp;like&nbsp;&quot;black&quot; (which messes up some of my plugins and scripts). I&#39;m not sure if this some kind of bug or a new way of handling colors...</div>
<div>When I try to set the background gradient colors (set bg_rgb_top/bottom) I get an endless output of &quot;Setting-Error: type read mismatch (color) 664&quot; - I have to kill and restart the program to get rid of the message. Same happens with my scripts using cmd...</div>
<div>Can someone confirm these problems? Perhaps I&#39;m doing something wrong here.</div>
<div>&nbsp;</div>
<div>Thanks in advance,</div>
<div>Nils</div>
<div>&nbsp;</div>
<div>&nbsp;</div>
<div>&nbsp;</div>
<div>&nbsp;</div></div></body></html>

Hi,
I've come across an issue saving .mol2 ( @<TRIPOS> ) files.
MGL tools' PMV/ADT won't read them, babel/open babel issues a set of complaint and read errors.
If I am reading the format correctly then ...
In the atom content the columnation appears to be off after the X Y Z coordinates, the question marks under atom_type seem to throw a lot of scripts (not surprising).
I'm not quite sure what the issue is, but it occurs when saving peptides and molecules built by a mouse or script as well as RCSB downloaded structures. seems the same on all builds and machines I've tried (listed at bottom)
thanks for your time
jacob
# created with PyMOL
@<TRIPOS>MOLECULE
untitled
57 57 0 0 0
PROTEIN
USER_CHARGES
@<TRIPOS>ATOM
1 N 0.394 -2.167 -1.142 ?? 1.000
2 CA 0.891 -0.794 -1.142 ?? 1.000
3 C 2.400 -0.765 -1.142 ?? 1.000
4 O 3.074 -1.654 -0.600 ?? 1.000
5 CB 0.286 0.038 0.061 ?? 1.000
6 CG1 -1.272 -0.010 0.168 ?? 1.000
...
saved from pymol 1.6 https://www.dropbox.com/s/jlpwa2lsub5ez8g/IPR.mol2
babel pipes https://www.dropbox.com/s/ruh23hcxfmbv0z8/babelmol2_mol2.txt
babel out https://www.dropbox.com/s/3p41lkvybdlwhwc/IPR_mol2mol2_babeled.mol2<https://www.dropbox.com/s/3p41lkvybdlwhwc/IPR_mol2mol2_babeled.mol2>
tripos mol2 format pdf http://www.tripos.com/data/support/mol2.pdf
hardware
dell T3600 e5-1650
w/ quadro 600 xUbuntu 13.04 pymol 1.6.0 from source w/build_seq.py and seq_convert.py
1.5.2 from package (and lots of plugins)
lenovo t420 nvs 400
windows 7 1.4.? (not sitting at it while typing) pre-built many plugins
also xUbuntu 12.04 1.4 from package and 1.6 from source (w/nvidia-bumblebee, and just intel graphics)

hi,
i have a PDB with a morph of an RNA molecule in about 30 states.
when i display each state separately the cartoons are smooth.
however when i load the morph and display it in cartoon rectangle 
it will have occasional 'twists'.
this is also true for oval,arrow and dumbbell.
is there some setting i can use to get rid of these twists ?
thanks
jpd
 

Hi all,
I want to load a chempy model into PyMOL. Unfortunately, the model has
all the coordinate information, but not bonds defined.
I know PyMOL can guess the bonds from the distances, but it does not
do it if I just use cmd.load_model, and I could not find a way of
doing it.
Does anyone know how can I achieve this?
Thanks!
Raul

Dear PyMOL user,
 
we would like to inform you that there's a new PyMOL plugin available. The
plugin incorporates a functionality of the new tool MOLE 2.0 for detection
and analysis of channels, pores and cavities in biomacromolecules. Further
information with appropriate links to the publication and other details of
this tool can be found at the pymolwiki here
<http://pymolwiki.org/index.php/MOLE_2.0:_advanced_approach_for_analysis_of_
biomacromolecular_channels> .
 
Best Regards 
 
MOLE 2.0 authors

Hi,
> The lines produced by the measurement wizard are barely visible, how does one increase the line's visibility e.g. thickness.
set dash_width, XX
(default is 2.5)
 
> Moreover, how does one draw lines (thick) on the surface of a protein?
set mesh_width, XX
(default is 1.0)
You might need to ray-trace your scene to see the effect.
Best regards,
Takanori Nakane

Hi,
> I want to dump a loaded pdb file to a string, the inverse of the function
> read_pdbstr(). There is such a function available?
cmd.get_pdbstr() will do the job.
Best regards,
Takanori Nakane

Thanks!
Sent from my iPad
On 17 Sep 2013, at 00:04, Takanori Nakane <t.n...@ma...> wrote:
> Hi,
> 
>> The lines produced by the measurement wizard are barely visible, how does one increase the line's visibility e.g. thickness.
> 
> set dash_width, XX
> (default is 2.5)
> 
>> Moreover, how does one draw lines (thick) on the surface of a protein?
> 
> set mesh_width, XX
> (default is 1.0)
> 
> You might need to ray-trace your scene to see the effect.
> 
> Best regards,
> 
> Takanori Nakane

Thanks a lot!
Osvaldo.
On Mon, Sep 16, 2013 at 8:01 PM, Takanori Nakane <
t.n...@ma...> wrote:
> Hi,
>
> > I want to dump a loaded pdb file to a string, the inverse of the function
> > read_pdbstr(). There is such a function available?
>
> cmd.get_pdbstr() will do the job.
>
> Best regards,
>
> Takanori Nakane
>

Oh! Just noticed the set width command....
Cheers,
Sent from my iPad
On 16 Sep 2013, at 23:56, James Rutley <jam...@gm...> wrote:
> 
> The lines produced by the measurement wizard are barely visible, how does one increase the line's visibility e.g. thickness.
> 
> Moreover, how does one draw lines (thick) on the surface of a protein?
> 
> Thanks,
> 
> Sent from my iPad
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The lines produced by the measurement wizard are barely visible, how does one increase the line's visibility e.g. thickness.
Moreover, how does one draw lines (thick) on the surface of a protein?
Thanks,
Sent from my iPad

Hi,
I want to dump a loaded pdb file to a string, the inverse of the function
read_pdbstr(). There is such a function available?
Thanks in advance.

I have Debian Testing/Jessie installed in a VMware Player v-6.0 on my 64 
bit Laptop as a testbed before installing apps on my native Linux 
production computer.
I have installed the Debian package from the Jessie repository, but it 
crashes when I try to open it. The run log is attached. If anyone has 
encountered this problem I would appreciate some pointers towards a 
solution.
Thinks in advance.