pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Albert,

Such a property transfer can be done with iterate and alter:

stored.colors = {}
iterate obj1, stored.colors[chain,resi,name] = color
alter obj2, color = stored.colors.get((chain,resi,name), color)
recolor

Hope that helps.

Cheers,
  Thomas

On 28 Aug 2015, at 10:03, Albert <mai...@gm...> wrote:

> Hello:
> 
> I've colored object1 in various color in different regions. I am just 
> wondering how can we copy the color scheme for object1 to object2? 
> Object 2 is the same protein with object1 but with different conformations.
> 
> Thank you very much
> 
> Albert

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello:

I've colored object1 in various color in different regions. I am just 
wondering how can we copy the color scheme for object1 to object2? 
Object 2 is the same protein with object1 but with different conformations.

Thank you very much

Albert

Hi Celestine,

Welcome to the PyMOL community!

I am not sure what is your problem, could you please provide more details?

Cheers,
Osvaldo.





On Fri, Aug 28, 2015 at 6:00 AM, Chi Celestine <
chi...@ph...> wrote:

>
> Hi,
> I am very new in pymol and will like to know how know the display in the
> lower command line works. However, i can see how to make it active. I have
> pymol v1.7.6.4
> Thanks
> Celestine
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

What version of PyMol are you using?

> On Aug 27, 2015, at 7:50 AM, Christian Trindler <chr...@un...> wrote:
> 
> Hello,
>  
> I’ve been trying to make a pseudoatom/sphere simply by typing:
> pseudoatom name
> into the command line of Pymol, but it only gives me the following error message instead of the pseudoatom:
>  
> Traceback (most recent call last):
>   File "C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 370, in parse
>     exec(com2[nest]+"\n",pymol_names,pymol_names)
>   File "<string>", line 1
>      pseudoatom name
>                   ^
> SyntaxError: invalid syntax
>  
> What is the error? What do I have to change?
>  
> Thanks for your help,
> Christian
>  
> ------------------------------------------------------------------------------
> _______________________________________________
> 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,
I am very new in pymol and will like to know how know the display in the lower command line works. However, i can see how to make it active. I have pymol v1.7.6.4
Thanks
Celestine

Dear Pymolers,
I am looking forward to make a movie for a nucleic acid where I would like
to show the opening/bond breaking of several base pairs and interaction
with another protein. Is it possible to do this in pymol? Any help
regarding this is highly appreciated!


Regards
Ravi

*Department of Pharmacological Sciences at **Stony Brook University  *

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Hi Dirk,

cmd.iterate is actually the most efficient function to access atom properties. If you want a wrapper which directly gets b and q for one atom, it could look like this (returns a dictionary):

from pymol import cmd
@cmd.extend
def get_signle_atom_props(selection, props=['b', 'q'], quiet=1):
    if isinstance(props, basestring):
        props = cmd.safe_list_eval(props)
    expr = ','.join((repr(k) + ':' + k) for k in props)
    expr = '_r.update({' + expr + '})'
    r = {}
    n = cmd.iterate(selection, expr, space={'_r': r})
    if n > 1:
        print ' Warning: selections spans more than one atom'
    if not int(quiet):
        print r
    return r

You can use the "first" operator to limit your selection to one atom:
print get_single_atom_props('first polymer')

Cheers,
  Thomas

On 27 Aug 2015, at 06:27, Dirk Kostrewa <kos...@ge...> wrote:

> Dear PyMOLers,
> 
> I have trouble to find out, which command I could use in a python script 
> to get the b-factor and occupancy of a single atom.
> In the script library, I only found examples getting b-factors iterating 
> over a selection.
> Although, I could iterate over one atom, only, is there a more elegant 
> way of getting the b-factor and occupancy of a single atom?
> 
> Best regards,
> 
> Dirk.
> 
> -- 
> 
> *******************************************************
> Dirk Kostrewa
> Gene Center Munich, A5.07
> Department of Biochemistry
> Ludwig-Maximilians-Universität München
> Feodor-Lynen-Str. 25
> D-81377 Munich
> Germany
> Phone:  +49-89-2180-76845
> Fax:    +49-89-2180-76999
> E-mail: kos...@ge...
> WWW:    www.genzentrum.lmu.de
> *******************************************************

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

1. Make the subunits into separate objects

2. Command

set cartoon_cylindrical_helices, on, [object name]

for the one you want to have cylinders

Shane Caldwell
McGill University

On Thu, Aug 27, 2015 at 4:01 AM, Smith Liu <smi...@16...> wrote:

> Dear All,
>
> Suppose a protein contains 2 subunits. Will you please introduce to me by
> pymol how to represent helix in one subunit as cylindrical helix, and helix
> in another subunit as regular helix?
>
> Best regards.
>
> Smith
>
>
> 夏日畅销榜大牌美妆只要1元
> <" rel="nofollow">http://r.mail.163.com/r.jsp?url=http%3A%2F%2F1.163.com%2Fhd%2Foneact%2Fhdframe.do%3Fid%3D21%26from%3Dfooter_beauty&sign=817593681&_r_ignore_statId=7_13_79_48&_r_...@16...>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hello,

I've been trying to make a pseudoatom/sphere simply by typing:
pseudoatom name
into the command line of Pymol, but it only gives me the following error message instead of the pseudoatom:

Traceback (most recent call last):
  File "C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 370, in parse
    exec(com2[nest]+"\n",pymol_names,pymol_names)
  File "<string>", line 1
     pseudoatom name
                  ^
SyntaxError: invalid syntax

What is the error? What do I have to change?

Thanks for your help,
Christian

Dear PyMOLers,

I have trouble to find out, which command I could use in a python script 
to get the b-factor and occupancy of a single atom.
In the script library, I only found examples getting b-factors iterating 
over a selection.
Although, I could iterate over one atom, only, is there a more elegant 
way of getting the b-factor and occupancy of a single atom?

Best regards,

Dirk.

-- 

*******************************************************
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:    +49-89-2180-76999
E-mail: kos...@ge...
WWW:    www.genzentrum.lmu.de
*******************************************************

Dear All,


Suppose a protein contains 2 subunits. Will you please introduce to me by pymol how to represent helix in one subunit as cylindrical helix, and helix in another subunit as regular helix?


Best regards.


Smith

set cartoon_cylindrical_helices, on

http://www.pymolwiki.org/index.php/Cartoon_Helix_Settings

Shane Caldwell
McGill University

On Wed, Aug 26, 2015 at 10:38 AM, Smith Liu <smi...@16...> wrote:

> Dear All,
>
> Will you please tell me how to process so that a long helix will be shown
> as a long rod (pr long bar） by pymol?
>
> Best regards.
>
> Smith
>
>
> 夏日畅销榜大牌美妆只要1元
> <" rel="nofollow">http://r.mail.163.com/r.jsp?url=http%3A%2F%2F1.163.com%2Fhd%2Foneact%2Fhdframe.do%3Fid%3D21%26from%3Dfooter_beauty&sign=817593681&_r_ignore_statId=7_13_79_48&_r_...@16...>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> 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 All,


Will you please tell me how to process so that a long helix will be shown as a long rod (pr long bar） by pymol?


Best regards.


Smith

Thanks Osvaldo for your suggestion .

I will work it out and let you know if any issues raises  .

Regards


On Mon, Aug 24, 2015 at 5:17 PM, Osvaldo Martin <alo...@gm...>
wrote:

> Dear Vinod,
>
>
> One option is to call PyMOL function from Python script.
>
> import __main__
> __main__.pymol_argv = ['pymol','-qc']
> import pymol
> from pymol import cmd, stored
> pymol.finish_launching()
>
> cmd.set('dot_solvent', 1)
> cmd.set('dot_density', 3)
>
> cmd.load('pdb.file') # use the name of your pdb file
> stored.residues = []
> cmd.iterate('name ca', 'stored.residues.append(resi)')
>
> sasa_per_residue = []
> for i in stored.residues:
>     sasa_per_residue.append(cmd.get_area('resi %s' % i))
>
> print sum(sasa_per_residue)
> print cmd.get_area('all')  # just to check that the sum of sasa per
> residue equals the total area
>
>
> Please let us know if you have doubts about the above script.
>
> Cheers,
> Osvaldo.
>
> On Mon, Aug 24, 2015 at 3:46 AM, Vinod Devaraji <
> vin...@sc...> wrote:
>
>> Hi All
>>
>> I doing one task with pymol where I need to calculate Solvent Accessible
>> Surface Area for individual residues numbers.
>>
>> I tried with get_area command but little confused on how to put it for
>> individual residues .
>>
>>
>> Could any one  please suggest command or script to do it  ?
>>
>> Any suggestions or comments would be highly appreciated .
>>
>>
>> Regards
>>
>>
>> --
>> Please feel free to call me or mail me
>>
>> Thanks and Regards
>>
>> Vinod.D M.Pharm.
>> Junior Applications Scientist
>> Mobile no:+91-9900090044
>>
>> http://www.schrodinger.com/
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>


-- 
Please feel free to call me or mail me

Thanks and Regards

Vinod.D M.Pharm.
Junior Applications Scientist
Mobile no:+91-9900090044

http://www.schrodinger.com/

Dear Vinod,


One option is to call PyMOL function from Python script.

import __main__
__main__.pymol_argv = ['pymol','-qc']
import pymol
from pymol import cmd, stored
pymol.finish_launching()

cmd.set('dot_solvent', 1)
cmd.set('dot_density', 3)

cmd.load('pdb.file') # use the name of your pdb file
stored.residues = []
cmd.iterate('name ca', 'stored.residues.append(resi)')

sasa_per_residue = []
for i in stored.residues:
    sasa_per_residue.append(cmd.get_area('resi %s' % i))

print sum(sasa_per_residue)
print cmd.get_area('all')  # just to check that the sum of sasa per residue
equals the total area


Please let us know if you have doubts about the above script.

Cheers,
Osvaldo.

On Mon, Aug 24, 2015 at 3:46 AM, Vinod Devaraji <
vin...@sc...> wrote:

> Hi All
>
> I doing one task with pymol where I need to calculate Solvent Accessible
> Surface Area for individual residues numbers.
>
> I tried with get_area command but little confused on how to put it for
> individual residues .
>
>
> Could any one  please suggest command or script to do it  ?
>
> Any suggestions or comments would be highly appreciated .
>
>
> Regards
>
>
> --
> Please feel free to call me or mail me
>
> Thanks and Regards
>
> Vinod.D M.Pharm.
> Junior Applications Scientist
> Mobile no:+91-9900090044
>
> http://www.schrodinger.com/
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> 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 doing one task with pymol where I need to calculate Solvent Accessible
Surface Area for individual residues numbers.

I tried with get_area command but little confused on how to put it for
individual residues .


Could any one  please suggest command or script to do it  ?

Any suggestions or comments would be highly appreciated .


Regards


-- 
Please feel free to call me or mail me

Thanks and Regards

Vinod.D M.Pharm.
Junior Applications Scientist
Mobile no:+91-9900090044

http://www.schrodinger.com/

Hi Pymol-Users list,

I'm trying to ray-trace images using ray_trace_mode = 1 (solid surfaces,
with black lines at the borders of elements).

I would like to have this tracing on elements of the image except for
meshes, which get really ugly because they shouldn't have a border.

Is there any way to selectively trace different objects with different
modes? Or am I better off tracing the objects into different files and
overlaying them in image processing software?

Shane Caldwell
McGill University

Thanks Jared,
I have tried the transformations.py script, and here is what I've got:
- I get a quaternions from external source (a 3d manipulator) in a
classical form: [x,y,z,w]
- I use function: quaternion_matrix(quaternion) from transformations.py
script:

m = quaternion_matrix([x, y, z, w])    # m is an array of an arrays (4x4)
M = [m[0,0], m[0,1], m[0,2], m[0,3], m[1,0], m[1,1], m[1,2], m[1,3],
m[2,0], m[2,1], m[2,2], m[2,3], m[3,0], m[3,1], m[3,2], m[3,3]]   # so i
need to convert it to a vector 16x1
cmd.transform_selection("all", M, homogenous=1)  # its time to apply the
vector into a transform_selection function; homogenous=0 also doesn't work
print M # print works fine ;)

But the function transform_selection does not work and I don't really know
why, rotation doesn't occur.
Maybe it's because the selection is wrong? On the scene I have a CGO (an
arrow) and even when I change the selection string from "all" to "arrow" it
doesn't rotate either.
What exactly is the "selection", could this be a CGO?

I have also noticed, that function cmd.rotate(...) works for my CGO "arrow"
when I set property object="arrow" and I put some arbitrary "hardcoded"
parameters (axis and angle).
Maybe the better way would be use this function?
But I'm not really sure which function from transformations.py script
should I use to convert quaternions to axis and angle params required by
cmd.rotate() function...
any ideas?

Cheers,
Pawel T.





2015-08-13 18:34 GMT+02:00 Sampson, Jared <Jar...@ny...>:

> Hi Paweł -
>
> Honestly, if you prefer to use matrices, I'd say just go ahead and use
> get_object_matrix; I doubt it's going away any time soon.  You may want to
> use this in combination with transform_selection
> <." rel="nofollow">http://www.pymolwiki.org/index.php/Transform_selection>.
>
> Also maybe check out Christoph Gohlke's transformations.py script
> <." rel="nofollow">http://www.pymolwiki.org/index.php/Transformations>.  It offers several
> tools for manipulating quaternions, matrices, and angle/axis operations.  I
> think there's also a newer version on his website, which is linked from the
> wiki page.
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
>
>
>
> On Aug 6, 2015, at 4:04 AM, Paweł Tomaszewski <cro...@gm...> wrote:
>
> Hello,
> I've created a CGO in pymol script (a cone) and I need to make some
> transformations on it. I've found that it is easier for me to modify a TTT
> matrix rather than using translate/rotate functions.
>
> Documentation says [http://www.pymolwiki.org/index.php/Get_object_matrix]
> get_object_matrix is unsupported operation. So how to get/set TTT?
>
> The problem is, that I get (from external source) position in quaternions
> and now I need to make my CGO position equal to those quaternion. How can I
> make it work?
>
> Thanks
> Paweł Tomaszewski
>
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
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Thanks for the quick fix! I would love to get a hotfix if possible.

The PDBe API is a nice solution. I think that detecting CA traces will fix
90% of the cases. There are still a few edge cases besides CA which don't
have a cartoon mode (e.g. 1hzs, which has a polydeoxyribonucleotide polymer
type but lacks phosphate atoms needed for cartoon), but these are rare
enough to be handled individually.

-Spencer

On Mon, Aug 17, 2015 at 7:54 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Spencer,
>
> Thank you for the bug report. We could reproduce and fix the crash, if you
> want I can send you a hotfix build. I will also push the fix to the open
> source SVN repository soon.
>
> I second John's suggestions to query the "ca_p_only" property from the
> PDBe API. Also, the next PyMOL version will read that property from the
> mmCIF file and automatically set the cartoon_trace_atoms and
> ribbon_trace_atoms settings.
>
> Cheers,
>   Thomas
>
> On 17 Aug 2015, at 10:58, John Berrisford <jm...@eb...> wrote:
>
> > Dear Spencer
> > It is possible to work this out using the PDBe API.
> > for our interactive API see:
> > http://www.ebi.ac.uk/pdbe/api/doc/
> > The molecules url will give you this information:
> > http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1a1q
> > entity 1 has "ca_p_only": true,
> > which means cartoon will not work for this chain - so we use ribbon
> instead with the command
> > pymol.cmd.set("ribbon_trace_atoms", 1)
> > This test allows us to make images such as those shown on the entry page
> for 1a1q at PDBe
> > http://www.ebi.ac.uk/pdbe/entry/pdb/1a1q
> > The images are made with pymol (currently 1.6, but also works in 1.7)
> > Regards
> > John
> > PDBe
> > On Monday 17 August 2015 15:40:14 Spencer Bliven wrote:
> > > We have a pipeline that uses pymol to create images using the headless
> > > command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at
> > > least) crash if you try to ray-trace an empty viewport.
> > >
> > > Example:
> > >
> > > pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray'
> > >
> > > This particular example only has CA atoms, so the cartoon mode doesn't
> show
> > > anything. In interactive mode I would `set cartoon_trace_atoms,1` but
> when
> > > batch processing there isn't a good way of detecting whether anything
> is
> > > showing or not.
> > >
> > > The error is:
> > >
> > > *** glibc detected ***
> > > /home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or
> > > corruption (out): 0x00007f11f8744f40 ***
> > >
> > > I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL
> 1.7.4.1
> > > through 1.7.6.3.
> > >
> > > Attached is a stack trace.
> > >
> > >
> > > Any suggestions on ensuring that there are some polygons in frame would
> > > also be appreciated. Say, if there was a way to detect that cartoon
> would
> > > fail so that I can switch to a lines or nonbonded representation (I
> wish
> > > that was the default fallback for cartoon).
> > >
> > > Thanks,
> > > Spencer
> > >
> > --
> > John Berrisford
> > PDBe
> > European Bioinformatics Institute (EMBL-EBI)
> > European Molecular Biology Laboratory
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge CB10 1SD UK
> > Tel: +44 1223 492529
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> 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 Spencer,

Thank you for the bug report. We could reproduce and fix the crash, if you want I can send you a hotfix build. I will also push the fix to the open source SVN repository soon.

I second John's suggestions to query the "ca_p_only" property from the PDBe API. Also, the next PyMOL version will read that property from the mmCIF file and automatically set the cartoon_trace_atoms and ribbon_trace_atoms settings.

Cheers,
  Thomas

On 17 Aug 2015, at 10:58, John Berrisford <jm...@eb...> wrote:

> Dear Spencer
> It is possible to work this out using the PDBe API. 
> for our interactive API see:
> http://www.ebi.ac.uk/pdbe/api/doc/
> The molecules url will give you this information:
> http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1a1q
> entity 1 has "ca_p_only": true, 
> which means cartoon will not work for this chain - so we use ribbon instead with the command
> pymol.cmd.set("ribbon_trace_atoms", 1)
> This test allows us to make images such as those shown on the entry page for 1a1q at PDBe
> http://www.ebi.ac.uk/pdbe/entry/pdb/1a1q
> The images are made with pymol (currently 1.6, but also works in 1.7)
> Regards
> John
> PDBe 
> On Monday 17 August 2015 15:40:14 Spencer Bliven wrote:
> > We have a pipeline that uses pymol to create images using the headless
> > command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at
> > least) crash if you try to ray-trace an empty viewport.
> > 
> > Example:
> > 
> > pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray'
> > 
> > This particular example only has CA atoms, so the cartoon mode doesn't show
> > anything. In interactive mode I would `set cartoon_trace_atoms,1` but when
> > batch processing there isn't a good way of detecting whether anything is
> > showing or not.
> > 
> > The error is:
> > 
> > *** glibc detected ***
> > /home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or
> > corruption (out): 0x00007f11f8744f40 ***
> > 
> > I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL 1.7.4.1
> > through 1.7.6.3.
> > 
> > Attached is a stack trace.
> > 
> > 
> > Any suggestions on ensuring that there are some polygons in frame would
> > also be appreciated. Say, if there was a way to detect that cartoon would
> > fail so that I can switch to a lines or nonbonded representation (I wish
> > that was the default fallback for cartoon).
> > 
> > Thanks,
> > Spencer
> > 
> -- 
> John Berrisford
> PDBe
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD UK
> Tel: +44 1223 492529

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi again, Joe -

Try saving in COLLADA<" rel="nofollow">http://www.pymolwiki.org/index.php/COLLADA> format with `save myfile.dae` (in PyMOL v1.7.3.2 or later).

If you're using Blender, you'll need to `set collada_geometry_mode, 1`, because Blender only supports polylists for COLLADA import, and not the more efficient structures like triangles, tristrips, trifans, etc.  I've never used Maya, so I'm not sure if it has any peculiarities in its COLLADA support.

There is also VRML2, which you can get with `save myfile.wrl`, but I'm partial to the COLLADA exporter, since I wrote it.  ;)

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Aug 15, 2015, at 1:42 PM, Joseph Georgeson <jos...@we...<mailto:jos...@we...>> wrote:

Hi all,

I was wondering the best options for importing .pdb files into rendering programs like Maya or Blender. Right now I'm trying mMaya with Maya2014 but seem to have many issues. Any suggestions?

Thanks,
JoeG
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Hi Joe -

The coordinate system in the .obj file is in camera space, where (0,0,0) is the center of the viewport, positive x to the right, positive y up, and positive z out of the screen toward the viewer.  If you want to correlate them, you would need to transform the model coordinates using the view matrix or, probably more easily, set the view to coincide with model space, as specified under "Space and File saving" here<." rel="nofollow">http://www.pymolwiki.org/index.php/Model_Space_and_Camera_Space>.

FYI, there is a bug<" rel="nofollow">https://sourceforge.net/p/pymol/bugs/170/> in .obj output of spheres, which are output as a single triangle face with identical coordinates for all three points.  Needless to say, you can't see them, unless you zoom in really close.  Also, cylinders and cones are not yet implemented in .obj output, so, basically the only representation fully supported is surfaces, which are made entirely of triangle meshes.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/




On Aug 15, 2015, at 1:34 PM, Joseph Georgeson <jos...@we...<mailto:jos...@we...>> wrote:

Hi all,

I'm trying to correlate an .obj file created in PyMOL to the actual molecular coordinates of a protein from the .pdb file. Is this possible? Does anyone know how PyMOL creates the .obj file?

Thanks,
JoeG
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Dear Spencer

It is possible to work this out using the PDBe API. 
for our interactive API see:
http://www.ebi.ac.uk/pdbe/api/doc/

The molecules url will give you this information:
http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1a1q

entity 1 has "ca_p_only": true, 
which means cartoon will not work for this chain - so we use ribbon instead 
with the command
pymol.cmd.set("ribbon_trace_atoms", 1)


This test allows us to make images such as those shown on the entry page for 
1a1q at PDBe
http://www.ebi.ac.uk/pdbe/entry/pdb/1a1q

The images are made with pymol (currently 1.6, but also works in 1.7)

Regards

John
PDBe 


On Monday 17 August 2015 15:40:14 Spencer Bliven wrote:
> We have a pipeline that uses pymol to create images using the headless
> command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at
> least) crash if you try to ray-trace an empty viewport.
> 
> Example:
> 
> pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray'
> 
> This particular example only has CA atoms, so the cartoon mode doesn't show
> anything. In interactive mode I would `set cartoon_trace_atoms,1` but when
> batch processing there isn't a good way of detecting whether anything is
> showing or not.
> 
> The error is:
> 
> *** glibc detected ***
> /home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or
> corruption (out): 0x00007f11f8744f40 ***
> 
> I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL 1.7.4.1
> through 1.7.6.3.
> 
> Attached is a stack trace.
> 
> 
> Any suggestions on ensuring that there are some polygons in frame would
> also be appreciated. Say, if there was a way to detect that cartoon would
> fail so that I can switch to a lines or nonbonded representation (I wish
> that was the default fallback for cartoon).
> 
> Thanks,
> Spencer
> 

-- 
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

We have a pipeline that uses pymol to create images using the headless
command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at
least) crash if you try to ray-trace an empty viewport.

Example:

pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray'

This particular example only has CA atoms, so the cartoon mode doesn't show
anything. In interactive mode I would `set cartoon_trace_atoms,1` but when
batch processing there isn't a good way of detecting whether anything is
showing or not.

The error is:

*** glibc detected ***
/home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or
corruption (out): 0x00007f11f8744f40 ***

I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL 1.7.4.1
through 1.7.6.3.

Attached is a stack trace.


Any suggestions on ensuring that there are some polygons in frame would
also be appreciated. Say, if there was a way to detect that cartoon would
fail so that I can switch to a lines or nonbonded representation (I wish
that was the default fallback for cartoon).

Thanks,
Spencer