pymol-users Mailing List for PyMOL Molecular Graphics System

On 30 May 2014, at 14:05, Takanori Nakane <tn...@ca...> wrote:
> However, showing intact spheres above the clip plane for the surface
> can be difficult. I am not sure if it is possible to set different
> clipping planes to each object.

no this is not possible, but has been requested many times. Maybe that would be a nice PyMOL Open-Source Fellowship project?

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi,

This page would be useful:
http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#cut

However, showing intact spheres above the clip plane for the surface
can be difficult. I am not sure if it is possible to set different
clipping planes to each object.

Best regards,

Takanori Nakane


(2014/05/30 2:09), Yarrow Madrona wrote:
> Hello,
>
> I have previously cut my protein in half with a solid cross section using a
> series of steps (including photoshop) but I am wondering if there is
> something simpler.
>
> I would like to make a figure similar to this:
>
> https://www.dropbox.com/s/bxpz6v4xly5fsee/MMI_7243_f6.gif
>
> This can be done pretty easily in Chimera, but I already have everything in
> Pymol and would like not to have to repeat it all. Thank you.
>
>
>
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Hello,

I have previously cut my protein in half with a solid cross section using a
series of steps (including photoshop) but I am wondering if there is
something simpler.

I would like to make a figure similar to this:

https://www.dropbox.com/s/bxpz6v4xly5fsee/MMI_7243_f6.gif

This can be done pretty easily in Chimera, but I already have everything in
Pymol and would like not to have to repeat it all. Thank you.

Hi,

Unfortunately, no.

PyMOL simply skips these lines and does not store
them in memory.

Best regards,

Takanori Nakane

On 2014-05-27 21:20, Lesburg, Charles wrote:
> Hi PyMOLers,
> 
> Does anyone know if it's possible to access the REMARK (and other non
> ATOM/HETATM) lines of a PDB file *after* the molecule has been loaded?
> 
> Chip
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Hello,

I've been working through different tabs of the AD plugin, trying to find
out what works with PyMOL v.1.7.1.3. The radio buttons on the grid tab are
not working, but the biggest hurdle I've come against to this point is on
the receptor tab. The plugin will correctly import the receptor file I have
loaded into pymol, but when I click on "Generate Receptor", the following
error message pops up:

Error: 1
<type 'exceptions.WindowsError'> Exception in Tk callback
  Function: <bound method Autodock.generate_receptor of
<pmg_tk.startup.autodock_plugin.Autodock instance at 0x000000000A4F42C8>>
(type: <type 'instancemethod'>)
  Args: ()
Traceback (innermost last):
  File "C:\Python27\lib\site-packages\Pmw\Pmw_1_3\lib\PmwBase.py", line
1747, in __call__
    return apply(self.func, args)
  File
"C:/Python27/Lib/site-packages/pymol/pymol_path/Pymol-Scripts-Pymol-script-repo/plugins\autodock_plugin.py",
line 1952, in generate_receptor
    result, output = getstatusoutput(command)
  File
"C:/Python27/Lib/site-packages/pymol/pymol_path/Pymol-Scripts-Pymol-script-repo/plugins\autodock_plugin.py",
line 54, in getstatusoutput
    p = Popen(command.split(), stdout=PIPE, stderr=STDOUT, env=env)
  File "C:\Python27\lib\subprocess.py", line 709, in __init__
    errread, errwrite)
  File "C:\Python27\lib\subprocess.py", line 957, in _execute_child
    startupinfo)
<type 'exceptions.WindowsError'>: [Error 2] The system cannot find the file
specified

I'm not a python expert, but as far as I can tell the error lies with the
AD plugin not being able to find subprocess.py. I DO have subprocess.py in
my python 2.7 directory, but there is a slight difference my path name --
the actual location is "\Python27\Lib", whereas the AD plugin is looking
for subprocess.py in "\Python27\lib".

I don't know where in the autodock_plugin.py script it specifies the path
for locating subprocess.py, otherwise I would have fixed this by now. Any
help would be greatly appreciated, as I'm not sure if Seeliger is actively
maintaining the plugin anymore.

Blake

Hi PyMOLers,

Does anyone know if it's possible to access the REMARK (and other non ATOM/HETATM) lines of a PDB file *after* the molecule has been loaded?

Chip
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Hi I-Ji -

You say the superimposed atoms are still there; that seems like normal behavior to me.  If you disable one of the objects, can you see the other one, and vice versa?

If the two structures are nearly identical, you may not be able to differentiate them visually after alignment.  If that is the case, you may wish to use different representations and/or colors for the two objects.

Cheers,
Jared

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






On May 26, 2014, at 6:58 PM, I-Ji Jung <u52...@an...<mailto:u52...@an...>> wrote:

Hi,

I'm trying to superimpose a small structure to a residue of a protein.
When I use align or pair_fit to do this, the superposition works, but for some weird reason I can't see my small structure anymore. Like it's whole structure disappears. The superimposed atoms are there - but then those are overlapped by the same atoms of the residue, so you can't see them anyway. I've tried pair_fit some while ago and I recall using it without a problem. Why am I suddenly having this problem?
Can somebody help me?

Thanks,

I-Ji
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Hi,

And you can use get_raw_distances script at
http://www.pymolwiki.org/index.php/Get_raw_distances
to get detailed information about contacts.

Best regards,

Takanori Nakane

On 2014-05-27 15:24, Sampson, Jared wrote:
> Hi Merlin -
> 
> Try limiting the distances shown to those between atoms in specific
> selections using the `distance` command. For example, to show H-bonds
> to solvent, disable the “my_obj_pol_conts” object created by the
> technical preset and use the command:
> 
> distance my_dist, my_obj and not solvent, my_obj and solvent,
> cutoff=3.5
> 
> Make sure to specify a cutoff or you’ll get every pair of polar
> atoms between your selections.
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
>  --
>  Jared Sampson
>  Xiangpeng Kong Lab
>  NYU Langone Medical Center
>  http://kong.med.nyu.edu/ [2]
> 
> On May 27, 2014, at 3:33 AM, 天元 <422...@qq...> wrote:
> 
>> Dear PyMol users!
>> 
>> I'm analysing polar contacts by "preset:technical". I got so many
>> yellow bar measurements that I can't count the number.
>> 
>> IS there any else way to count the number of all polar contacts ?
>> 
>> Thanks for help,
>> 
>> Merlin
>> 
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Dear Thomas,

Thank you very much for your investigation.

I agree with you. PyMOL is doing right;
SCALEn should be the identity matrix, or CRYST1 expanded.

CRYST1 is defined to be "1 1 1 90 90 90" for
structures determined by non-crystallographic methods.
Thanks to the increased resolution of cryo EM, people are
starting to use refinement software for crystallography.
In this case, authors might submit files with CRYST1 and SCALEn
based on the (pseudo-)cell used during the refinement, and
annotators in PDB edit CRYST1 only, thus leading to the inconsistency.

I talked to one of the authors of the structure and
he said he will talk to PDB on the issue.

Best regards,

Takanori Nakane

On 2014-05-27 14:35, Thomas Holder wrote:
> Hi Takanori,
> 
> PyMOL uses SCALEn to transform into fractional coordinates, and then 
> the
> unit cell parameters (CRYST1) to transform back into cartesian
> coordinates. The PDB spec says: "The unit cell parameters are used to
> calculate SCALE". For 1VW3, CRYST1 defines a unit cube, so I assume
> SCALEn should be the identity matrix, but it's not.
> 
> You can skip this back-and-forth transformation with a setting:
> 
> PyMOL> set pdb_insure_orthogonal, off
> 
> I assume PyMOL is doing the right thing here. If we want to know more
> about the intended interplay of CRYST1, ORIGXn and SCALEn, we might 
> want
> to crosspost the topic to the CCP4BB list.
> 
> Cheers,
>   Thomas
> 
> Takanori Nakane wrote, On 05/24/14 03:48:
>> Dear all,
>> 
>> I noticed a strange behaviour in the handling of SCALEn
>> records in PDB files.
>> 
>> When I load 1VW3, all atomic coordinates are scaled down
>> to one thousandth and therefore all atoms get connected.
>> The fact that the coordinates are incorrectly transformed
>> can be confirmed by saving the loaded model again.
>> 
>> This is probably due to the presence of SCALEn records:
>> 
>>> SCALE1      0.001000  0.000000  0.000000        0.00000
>>> SCALE2      0.000000  0.001000  0.000000        0.00000
>>> SCALE3      0.000000  0.000000  0.001000        0.00000
>> 
>> When they are deleted, the model can be loaded correctly.
>> 
>> According to the PDB format specification
>> http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#SCALEn ,
>> SCALEn records should not affect real space (orthogonal) coordinates.
>> 
>> Best regards,
>> 
>> Takanori Nakane
> 
> --
> Thomas Holder
> PyMOL
> Schrödinger, Inc.
> 
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Hi Merlin -

Try limiting the distances shown to those between atoms in specific selections using the `distance` command.  For example, to show H-bonds to solvent, disable the “my_obj_pol_conts” object created by the technical preset and use the command:

distance my_dist, my_obj and not solvent, my_obj and solvent, cutoff=3.5

Make sure to specify a cutoff or you’ll get every pair of polar atoms between your selections.

Hope that helps.

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






On May 27, 2014, at 3:33 AM, 天元 <422...@qq...<mailto:422...@qq...>> wrote:


Dear PyMol users!


I'm analysing polar contacts by "preset:technical". I got so many yellow bar measurements that I can't count the number.

IS there any else way to count the number of all polar contacts ?

Thanks for help,


Merlin

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=================================

Hi Takanori,

PyMOL uses SCALEn to transform into fractional coordinates, and then the
unit cell parameters (CRYST1) to transform back into cartesian
coordinates. The PDB spec says: "The unit cell parameters are used to
calculate SCALE". For 1VW3, CRYST1 defines a unit cube, so I assume
SCALEn should be the identity matrix, but it's not.

You can skip this back-and-forth transformation with a setting:

PyMOL> set pdb_insure_orthogonal, off

I assume PyMOL is doing the right thing here. If we want to know more
about the intended interplay of CRYST1, ORIGXn and SCALEn, we might want
to crosspost the topic to the CCP4BB list.

Cheers,
  Thomas

Takanori Nakane wrote, On 05/24/14 03:48:
> Dear all,
> 
> I noticed a strange behaviour in the handling of SCALEn
> records in PDB files.
> 
> When I load 1VW3, all atomic coordinates are scaled down
> to one thousandth and therefore all atoms get connected.
> The fact that the coordinates are incorrectly transformed
> can be confirmed by saving the loaded model again.
> 
> This is probably due to the presence of SCALEn records:
> 
>> SCALE1      0.001000  0.000000  0.000000        0.00000                         
>> SCALE2      0.000000  0.001000  0.000000        0.00000                         
>> SCALE3      0.000000  0.000000  0.001000        0.00000 
> 
> When they are deleted, the model can be loaded correctly.
> 
> According to the PDB format specification
> http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#SCALEn ,
> SCALEn records should not affect real space (orthogonal) coordinates.
> 
> Best regards,
> 
> Takanori Nakane

-- 
Thomas Holder
PyMOL
Schrödinger, Inc.

Dear PyMol users! I'm analysing polar contacts by "preset:technical". I got so many yellow bar measurements that I can't count the number.  IS there any else way to count the number of all polar contacts ? Thanks for help, Merlin

Hi,


I'm trying to superimpose a small structure to a residue of a protein.

When I use align or pair_fit to do this, the superposition works, but for some weird reason I can't see my small structure anymore. Like it's whole structure disappears. The superimposed atoms are there - but then those are overlapped by the same atoms of the residue, so you can't see them anyway. I've tried pair_fit some while ago and I recall using it without a problem. Why am I suddenly having this problem?

Can somebody help me?


Thanks,


I-Ji

Solved it. Apparently something is seriously broken in the latest mesa
on MacPorts (8.0.5). Reverting to 8.0.4 fixes the problem.

Enjoy!

Matteo

2014-05-23 19:07 GMT+02:00 Matteo Tiberti <mat...@gm...>:
> Errata corrige: the actual ticket for the PyMOL bug is:
>
> https://trac.macports.org/ticket/43802
>
> Cheers,
>
> Matteo
>
> 2014-05-23 18:50 GMT+02:00 Matteo Tiberti <mat...@gm...>:
>> Hi Thomas,
>>
>> thanks a lot, good to know that it's not just me, I was getting mad
>> over this. I have opened a ticket at macports and put you in cc in
>> case you'd like to follow the issue (
>> https://trac.macports.org/ticket/42860 ).
>> Talking about macports, just for you and everybody on the list to
>> know, I have adapted the 1.6.0 patches to work for version 1.7.1 (
>> https://trac.macports.org/ticket/42860 ). I've been using this version
>> for few months now and looks fine to me, and may be helpful in case
>> anybody needs a more recent PyMOL on macports. Just don't update it
>> right now or everything will screw up :) let's hope this gets fixed
>> quickly.
>>
>> Thanks again for your help
>>
>> Matteo
>>
>> 2014-05-23 18:00 GMT+02:00 Thomas Holder <tho...@sc...>:
>>> Hi Matteo,
>>>
>>> I can confirm this. It only happens if I build PyMOL in the macports environment and it's not related to any recent changes to PyMOL. So I wonder what they screwed up in macports...
>>>
>>> Cheers,
>>>   Thomas
>>>
>>> On 22 May 2014, at 14:25, Matteo Tiberti <mat...@gm...> wrote:
>>>
>>>> Dear PyMOL users,
>>>> I'm trying to use PyMOL (open source version) 1.6.0 on Mac OSX
>>>> Mavericks, installed through MacPorts. The same happens with pymol
>>>> 1.7.1 as well.
>>>> Up to yesterday everything was working perfectly fine. As far as I can
>>>> remember nothing changed, but now when I run pymol I get this:
>>>>
>>>> http://pastebin.com/uFyvYQCz
>>>>
>>>> Detected OpenGL version 2.0 or greater. Shaders available.
>>>> CShaderPrg_New-Error: vertex shader compilation failed
>>>> name='default'; log follows.
>>>> infoLog=ERROR: 0:1: '' :  #version required and missing.
>>>> ERROR: 0:1: 'attribute' : syntax error syntax error
>>>>
>>>> I also tried this:
>>>> And then PyMOL crashes. I have then tried the following:
>>>>
>>>> - reinstalled PyMOL 1.6.0
>>>> - removed PyMOL 1.6.0 and installed 1.7.1
>>>> - updated the XQuartz X server to the latest version
>>>> - reinstalled the XQuartz X server to an older version
>>>> - wiped MacPorts and reinstalled PyMOL and its prerequisites from scratch
>>>> - installed the gfxCardStatus program and tried both using the
>>>> integrated gpu and the discrete one
>>>> - searched on the internet (of course :) )
>>>>
>>>> Any idea of where this problem might come from or how I could solve it?
>>>>
>>>> Thank you
>>>>
>>>> Matteo
>>>
>>> --
>>> Thomas Holder
>>> PyMOL Developer
>>> Schrödinger, Inc.
>>>

Dear all,

I noticed a strange behaviour in the handling of SCALEn
records in PDB files.

When I load 1VW3, all atomic coordinates are scaled down
to one thousandth and therefore all atoms get connected.
The fact that the coordinates are incorrectly transformed
can be confirmed by saving the loaded model again.

This is probably due to the presence of SCALEn records:

> SCALE1      0.001000  0.000000  0.000000        0.00000                         
> SCALE2      0.000000  0.001000  0.000000        0.00000                         
> SCALE3      0.000000  0.000000  0.001000        0.00000 

When they are deleted, the model can be loaded correctly.

According to the PDB format specification
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#SCALEn ,
SCALEn records should not affect real space (orthogonal) coordinates.

Best regards,

Takanori Nakane

Errata corrige: the actual ticket for the PyMOL bug is:

https://trac.macports.org/ticket/43802

Cheers,

Matteo

2014-05-23 18:50 GMT+02:00 Matteo Tiberti <mat...@gm...>:
> Hi Thomas,
>
> thanks a lot, good to know that it's not just me, I was getting mad
> over this. I have opened a ticket at macports and put you in cc in
> case you'd like to follow the issue (
> https://trac.macports.org/ticket/42860 ).
> Talking about macports, just for you and everybody on the list to
> know, I have adapted the 1.6.0 patches to work for version 1.7.1 (
> https://trac.macports.org/ticket/42860 ). I've been using this version
> for few months now and looks fine to me, and may be helpful in case
> anybody needs a more recent PyMOL on macports. Just don't update it
> right now or everything will screw up :) let's hope this gets fixed
> quickly.
>
> Thanks again for your help
>
> Matteo
>
> 2014-05-23 18:00 GMT+02:00 Thomas Holder <tho...@sc...>:
>> Hi Matteo,
>>
>> I can confirm this. It only happens if I build PyMOL in the macports environment and it's not related to any recent changes to PyMOL. So I wonder what they screwed up in macports...
>>
>> Cheers,
>>   Thomas
>>
>> On 22 May 2014, at 14:25, Matteo Tiberti <mat...@gm...> wrote:
>>
>>> Dear PyMOL users,
>>> I'm trying to use PyMOL (open source version) 1.6.0 on Mac OSX
>>> Mavericks, installed through MacPorts. The same happens with pymol
>>> 1.7.1 as well.
>>> Up to yesterday everything was working perfectly fine. As far as I can
>>> remember nothing changed, but now when I run pymol I get this:
>>>
>>> http://pastebin.com/uFyvYQCz
>>>
>>> Detected OpenGL version 2.0 or greater. Shaders available.
>>> CShaderPrg_New-Error: vertex shader compilation failed
>>> name='default'; log follows.
>>> infoLog=ERROR: 0:1: '' :  #version required and missing.
>>> ERROR: 0:1: 'attribute' : syntax error syntax error
>>>
>>> I also tried this:
>>> And then PyMOL crashes. I have then tried the following:
>>>
>>> - reinstalled PyMOL 1.6.0
>>> - removed PyMOL 1.6.0 and installed 1.7.1
>>> - updated the XQuartz X server to the latest version
>>> - reinstalled the XQuartz X server to an older version
>>> - wiped MacPorts and reinstalled PyMOL and its prerequisites from scratch
>>> - installed the gfxCardStatus program and tried both using the
>>> integrated gpu and the discrete one
>>> - searched on the internet (of course :) )
>>>
>>> Any idea of where this problem might come from or how I could solve it?
>>>
>>> Thank you
>>>
>>> Matteo
>>
>> --
>> Thomas Holder
>> PyMOL Developer
>> Schrödinger, Inc.
>>

Hi Thomas,

thanks a lot, good to know that it's not just me, I was getting mad
over this. I have opened a ticket at macports and put you in cc in
case you'd like to follow the issue (
https://trac.macports.org/ticket/42860 ).
Talking about macports, just for you and everybody on the list to
know, I have adapted the 1.6.0 patches to work for version 1.7.1 (
https://trac.macports.org/ticket/42860 ). I've been using this version
for few months now and looks fine to me, and may be helpful in case
anybody needs a more recent PyMOL on macports. Just don't update it
right now or everything will screw up :) let's hope this gets fixed
quickly.

Thanks again for your help

Matteo

2014-05-23 18:00 GMT+02:00 Thomas Holder <tho...@sc...>:
> Hi Matteo,
>
> I can confirm this. It only happens if I build PyMOL in the macports environment and it's not related to any recent changes to PyMOL. So I wonder what they screwed up in macports...
>
> Cheers,
>   Thomas
>
> On 22 May 2014, at 14:25, Matteo Tiberti <mat...@gm...> wrote:
>
>> Dear PyMOL users,
>> I'm trying to use PyMOL (open source version) 1.6.0 on Mac OSX
>> Mavericks, installed through MacPorts. The same happens with pymol
>> 1.7.1 as well.
>> Up to yesterday everything was working perfectly fine. As far as I can
>> remember nothing changed, but now when I run pymol I get this:
>>
>> http://pastebin.com/uFyvYQCz
>>
>> Detected OpenGL version 2.0 or greater. Shaders available.
>> CShaderPrg_New-Error: vertex shader compilation failed
>> name='default'; log follows.
>> infoLog=ERROR: 0:1: '' :  #version required and missing.
>> ERROR: 0:1: 'attribute' : syntax error syntax error
>>
>> I also tried this:
>> And then PyMOL crashes. I have then tried the following:
>>
>> - reinstalled PyMOL 1.6.0
>> - removed PyMOL 1.6.0 and installed 1.7.1
>> - updated the XQuartz X server to the latest version
>> - reinstalled the XQuartz X server to an older version
>> - wiped MacPorts and reinstalled PyMOL and its prerequisites from scratch
>> - installed the gfxCardStatus program and tried both using the
>> integrated gpu and the discrete one
>> - searched on the internet (of course :) )
>>
>> Any idea of where this problem might come from or how I could solve it?
>>
>> Thank you
>>
>> Matteo
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>

Hi Matteo,

I can confirm this. It only happens if I build PyMOL in the macports environment and it's not related to any recent changes to PyMOL. So I wonder what they screwed up in macports...

Cheers,
  Thomas

On 22 May 2014, at 14:25, Matteo Tiberti <mat...@gm...> wrote:

> Dear PyMOL users,
> I'm trying to use PyMOL (open source version) 1.6.0 on Mac OSX
> Mavericks, installed through MacPorts. The same happens with pymol
> 1.7.1 as well.
> Up to yesterday everything was working perfectly fine. As far as I can
> remember nothing changed, but now when I run pymol I get this:
> 
> http://pastebin.com/uFyvYQCz
> 
> Detected OpenGL version 2.0 or greater. Shaders available.
> CShaderPrg_New-Error: vertex shader compilation failed
> name='default'; log follows.
> infoLog=ERROR: 0:1: '' :  #version required and missing.
> ERROR: 0:1: 'attribute' : syntax error syntax error
> 
> I also tried this:
> And then PyMOL crashes. I have then tried the following:
> 
> - reinstalled PyMOL 1.6.0
> - removed PyMOL 1.6.0 and installed 1.7.1
> - updated the XQuartz X server to the latest version
> - reinstalled the XQuartz X server to an older version
> - wiped MacPorts and reinstalled PyMOL and its prerequisites from scratch
> - installed the gfxCardStatus program and tried both using the
> integrated gpu and the discrete one
> - searched on the internet (of course :) )
> 
> Any idea of where this problem might come from or how I could solve it?
> 
> Thank you
> 
> Matteo

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Rongjin,

does your map have the same name like your molecule (like test.pdb and test.phi)? If yes, load them with unique names:

PyMOL> load test.pdb, molobj
PyMOL> load test.phi, mapobj

I used delphi successfully with PyMOL a while back.

Cheers,
  Thomas

On 23 May 2014, at 11:12, rjguan <rj...@gm...> wrote:

> Dear Pymol users
>  
> I am trying to make an electrostatic surface with delphi in pymol.
> I loaded my protein structure and showed the surface, and then loaded the .phi file as emap,
> But, once I loaded the .phi file, my molecule disappeared immediately, without any
> error message. Everything seems normal, but my protein molecule is not shown.
>  
> Has anyone using Delphi in pymol seen this before?
>  
> Thank you
> Rongjin Guan

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Dear Pymol users

I am trying to make an electrostatic surface with delphi in pymol. 
I loaded my protein structure and showed the surface, and then loaded the .phi file as emap,
But, once I loaded the .phi file, my molecule disappeared immediately, without any
error message. Everything seems normal, but my protein molecule is not shown. 

Has anyone using Delphi in pymol seen this before? 

Thank you
Rongjin Guan 

Dear PyMOL users,
I'm trying to use PyMOL (open source version) 1.6.0 on Mac OSX
Mavericks, installed through MacPorts. The same happens with pymol
1.7.1 as well.
Up to yesterday everything was working perfectly fine. As far as I can
remember nothing changed, but now when I run pymol I get this:

http://pastebin.com/uFyvYQCz

 Detected OpenGL version 2.0 or greater. Shaders available.
 CShaderPrg_New-Error: vertex shader compilation failed
name='default'; log follows.
infoLog=ERROR: 0:1: '' :  #version required and missing.
ERROR: 0:1: 'attribute' : syntax error syntax error

I also tried this:
And then PyMOL crashes. I have then tried the following:

- reinstalled PyMOL 1.6.0
- removed PyMOL 1.6.0 and installed 1.7.1
- updated the XQuartz X server to the latest version
- reinstalled the XQuartz X server to an older version
- wiped MacPorts and reinstalled PyMOL and its prerequisites from scratch
- installed the gfxCardStatus program and tried both using the
integrated gpu and the discrete one
- searched on the internet (of course :) )

Any idea of where this problem might come from or how I could solve it?

Thank you

Matteo

|
NameDorothyLujah
pap...@12...
Organization: China Pharmaceutical University
Address:No.639 Longmian Avenue Jiangning district Nanjing
Telephone:15195873287
QQ:1393803136
|

扫描该二维码，可以将电子名片迅速保存到手机 使用帮助

|



At 2014-05-22 00:08:55, pym...@li... wrote:
>Send PyMOL-users mailing list submissions to
>	pym...@li...
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	https://lists.sourceforge.net/lists/listinfo/pymol-users
>or, via email, send a message with subject or body 'help' to
>	pym...@li...
>
>You can reach the person managing the list at
>	pym...@li...
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of PyMOL-users digest..."
>
>
>Today's Topics:
>
>   1. Re: morph command questions (Thomas Holder)
>   2. Re: disable all screen output (Osvaldo Martin)
>   3. Re: Bugfix release 1.7.0.5 (Abhinav Kumar)
>   4. Re: Bugfix release 1.7.0.5 (Abhinav Kumar)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 20 May 2014 17:04:27 -0400
>From: Thomas Holder <tho...@sc...>
>Subject: Re: [PyMOL] morph command questions
>To: "Dr. Mark Mayer" <ma...@ma...>
>Cc: pym...@li...
>Message-ID: <716...@sc...>
>Content-Type: text/plain; charset=iso-8859-1
>
>Hi Mark,
>
>both the labels and the distance lines should be visible in all states. Here a working example, tested with 1.7.0.0 and 1.7.0.5:
>
>fetch 1akeA 4akeA, async=0
>align 1akeA, 4akeA
>morph mobj, 1akeA, 4akeA
>as ribbon
>enable 1akeA
>select sele1, resi 148 & guide
>label sele1, resi
>distance dobj, mobj & sele1, 1akeA  & sele1
>mplay
>
>Feel free to share your script (if possible), then we can figure out if there is a problem.
>
>Cheers,
>  Thomas
>
>On 20 May 2014, at 16:14, Dr. Mark Mayer <ma...@ma...> wrote:
>
>> I have two questions about the morph command in PyMOL 1.7
>> 
>> 1) Is it possible to keep atom label text displayed throughout the 
>> morph? I've run a script morphing from mol1 to mol2 with text 
>> associated with mol1, but the label disappears at the start of the 
>> morph.
>> 
>> 2) Is it possible to have the distance vector between identical atom 
>> selections in mol1 and mol2
>> displayed to indicate the change in distance during the morph.  I've 
>> run a script morphing from mol1 to mol2 with text associated with 
>> mol1, but the line disappears at the start of the morph.
>> 
>> Thanks,
>> 
>> Mark
>
>-- 
>Thomas Holder
>PyMOL Developer
>Schr?dinger, Inc.
>
>
>
>
>------------------------------
>
>Message: 2
>Date: Tue, 20 May 2014 18:16:17 -0300
>From: Osvaldo Martin <alo...@gm...>
>Subject: Re: [PyMOL] disable all screen output
>To: Thomas Holder <tho...@sc...>
>Cc: "pym...@li..."
>	<PyM...@li...>
>Message-ID:
>	<CAG...@ma...>
>Content-Type: text/plain; charset="utf-8"
>
>Thanks Thomas,
>
>You are right. I just have added a couple of links to the "suspend_updates"
>setting in the wiki to make that option easier to find.
>
>Cheers,
>Osvaldo.
>
>
>On Tue, May 20, 2014 at 5:46 PM, Thomas Holder <
>tho...@sc...> wrote:
>
>> Hi Osvaldo,
>>
>> I think you are looking for the "suspend_updates" setting.
>>
>> Cheers,
>>   Thomas
>>
>> On 19 May 2014, at 15:10, Osvaldo Martin <alo...@gm...> wrote:
>>
>> > Hello everyone!
>> >
>> > I working on a PyMOL plugin that performs a lot of selections and
>> operations. I would like to avoid updating the screen until the script
>> finish (mainly to increase the performance of the plugin)
>> >
>> > I tried with something like this
>> >
>> > cmd.disable('all')
>> > "Some code"
>> > cmd.enable('all')
>> >
>> > The problem is that the "disable" command only toggles off the display
>> of the currently visible representations of an object. If "Some code"
>> creates a new object then this new object will be visible. On possible
>> solution will be to repeat the "cmd.disable('all')" command any time a new
>> object is created, but I will prefer a cleaner solution (if possible).
>> >
>> > Thanks in advance,
>> >
>> > Osvaldo.
>>
>> --
>> Thomas Holder
>> PyMOL Developer
>> Schr?dinger, Inc.
>>
>>
>-------------- next part --------------
>An HTML attachment was scrubbed...
>
>------------------------------
>
>Message: 3
>Date: Wed, 21 May 2014 08:26:47 -0700
>From: Abhinav Kumar <abh...@sl...>
>Subject: Re: [PyMOL] Bugfix release 1.7.0.5
>To: <pym...@li...>
>Message-ID: <537...@sl...>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi,
>
>I installed pymol ( pymol-v1.7.0.5-Linux-x86_64.tar.bz2) on my ubuntu 
>(12.04 LTS) desktop and this was working fine.
>Later, I upgraded my Ubuntu to 14.04 LTS and now pymol has become 
>extremely sluggish. Even rotating a small molecule like ATP takes a while.
>
>Any suggestions on how to fix this?
>
>Coot and rasmol are not affected by this Ubuntu upgrade.
>
>Thanks,
>Abhinav
>______________________________________
>Abhinav Kumar, Ph.D.
>The Joint Center for Structural Genomics
>MS99, SLAC National Accelerator Laboratory
>2575 Sand Hill Rd, Menlo Park, CA 94025
>(650) 926-2992
>
>
>On 05/13/2014 10:43 AM, Thomas Holder wrote:
>> Greetings,
>>
>> We'd like to announce the release of Incentive PyMOL 1.7.0.5, which is a bugfix release. Applicable bugfixes have also been pushed to the sourceforge SVN repository as Open-Source PyMOL 1.7.1.3 (SVN rev 4076).
>>
>> Fixed bugs include:
>>
>> Incentive PyMOL (for licensed users):
>>   - don't disable all shaders if geometry shaders are not available
>>   - many z-depth issues for labels and connectors in immediate, shader, and
>>     ray tracing (all renderings should now look almost exactly the same)
>>   - background in front of text with use_shaders=0
>>   - label picking broken with use_shaders=0
>>   - character rendering in ray tracing
>>   - clipped text in multi-line labels (shader on and off)
>>
>> Open Source and Incentive PyMOL:
>>   - cartoon memory leak
>>   - CGO colors ignored with ALPHA
>>   - hidden groups flash in scene based movies
>>   - "A > find > polar contact > just intra-side chain" broken
>>   - "scene auto, update" broken
>>   - small solvent_radius crashes Surface generation
>>   - grid_mode support for volumes
>>
>> Some of these changes have been in the SVN repository for a couple of weeks.
>>
>> Download:
>> Installers for Incentive PyMOL: http://pymol.org/dsc/ip/
>> Open Source: http://sourceforge.net/p/pymol/
>>
>> Cheers,
>>    The PyMOL Team at Schr?dinger
>>
>
>-------------- next part --------------
>An HTML attachment was scrubbed...
>
>------------------------------
>
>Message: 4
>Date: Wed, 21 May 2014 09:08:27 -0700
>From: Abhinav Kumar <abh...@sl...>
>Subject: Re: [PyMOL] Bugfix release 1.7.0.5
>To: Clotilde LowKam <clo...@um...>, pymol-users
>	<pym...@li...>
>Message-ID: <537...@sl...>
>Content-Type: text/plain; charset="utf-8"
>
>Thanks Clotilde again.
>
>I switched the graphics card driver and it has fixed the problem.
>The switch I made was from Nouveau display driver to Nvidia dreiver.
>
>Thanks,
>Abhinav
>______________________________________
>Abhinav Kumar, Ph.D.
>The Joint Center for Structural Genomics
>MS99, SLAC National Accelerator Laboratory
>2575 Sand Hill Rd, Menlo Park, CA 94025
>(650) 926-2992
>
>
>On 05/21/2014 08:44 AM, Clotilde LowKam wrote:
>> Hello,
>> probably a driver/graphic card problem. Maybe trying the legacy driver 
>> for your card could help.
>> Clotilde
>>
>>
>> 2014-05-21 11:26 GMT-04:00 Abhinav Kumar <abh...@sl... 
>> <mailto:abh...@sl...>>:
>>
>>     Hi,
>>
>>     I installed pymol ( pymol-v1.7.0.5-Linux-x86_64.tar.bz2) on my
>>     ubuntu (12.04 LTS) desktop and this was working fine.
>>     Later, I upgraded my Ubuntu to 14.04 LTS and now pymol has become
>>     extremely sluggish. Even rotating a small molecule like ATP takes
>>     a while.
>>
>>     Any suggestions on how to fix this?
>>
>>     Coot and rasmol are not affected by this Ubuntu upgrade.
>>
>>     Thanks,
>>     Abhinav
>>     ______________________________________
>>     Abhinav Kumar, Ph.D.
>>     The Joint Center for Structural Genomics
>>     MS99, SLAC National Accelerator Laboratory
>>     2575 Sand Hill Rd, Menlo Park, CA 94025
>>     (650) 926-2992 <tel:%28650%29%20926-2992>
>>
>>
>>     On 05/13/2014 10:43 AM, Thomas Holder wrote:
>>>     Greetings,
>>>
>>>     We'd like to announce the release of Incentive PyMOL 1.7.0.5, which is a bugfix release. Applicable bugfixes have also been pushed to the sourceforge SVN repository as Open-Source PyMOL 1.7.1.3 (SVN rev 4076).
>>>
>>>     Fixed bugs include:
>>>
>>>     Incentive PyMOL (for licensed users):
>>>       - don't disable all shaders if geometry shaders are not available
>>>       - many z-depth issues for labels and connectors in immediate, shader, and
>>>         ray tracing (all renderings should now look almost exactly the same)
>>>       - background in front of text with use_shaders=0
>>>       - label picking broken with use_shaders=0
>>>       - character rendering in ray tracing
>>>       - clipped text in multi-line labels (shader on and off)
>>>
>>>     Open Source and Incentive PyMOL:
>>>       - cartoon memory leak
>>>       - CGO colors ignored with ALPHA
>>>       - hidden groups flash in scene based movies
>>>       - "A > find > polar contact > just intra-side chain" broken
>>>       - "scene auto, update" broken
>>>       - small solvent_radius crashes Surface generation
>>>       - grid_mode support for volumes
>>>
>>>     Some of these changes have been in the SVN repository for a couple of weeks.
>>>
>>>     Download:
>>>     Installers for Incentive PyMOL:http://pymol.org/dsc/ip/
>>>     Open Source:http://sourceforge.net/p/pymol/
>>>
>>>     Cheers,
>>>        The PyMOL Team at Schr?dinger
>>>
>>
>>
>>     ------------------------------------------------------------------------------
>>     "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>     Instantly run your Selenium tests across 300+ browser/OS combos.
>>     Get unparalleled scalability from the best Selenium testing
>>     platform available
>>     Simple to use. Nothing to install. Get started now for free."
>>     http://p.sf.net/sfu/SauceLabs
>>     _______________________________________________
>>     PyMOL-users mailing list (PyM...@li...
>>     <mailto:PyM...@li...>)
>>     Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>     Archives:
>>     http://www.mail-archive.com/pym...@li...
>>
>>
>
>-------------- next part --------------
>An HTML attachment was scrubbed...
>
>------------------------------
>
>------------------------------------------------------------------------------
>"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>Instantly run your Selenium tests across 300+ browser/OS combos.
>Get unparalleled scalability from the best Selenium testing platform available
>Simple to use. Nothing to install. Get started now for free."
>http://p.sf.net/sfu/SauceLabs
>
>------------------------------
>
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>End of PyMOL-users Digest, Vol 96, Issue 12
>*******************************************

|
NameDorothyLujah
pap...@12...
Organization: China Pharmaceutical University
Address:No.639 Longmian Avenue Jiangning district Nanjing
Telephone:15195873287
QQ:1393803136
|

扫描该二维码，可以将电子名片迅速保存到手机 使用帮助

|

Thanks Clotilde again.

I switched the graphics card driver and it has fixed the problem.
The switch I made was from Nouveau display driver to Nvidia dreiver.

Thanks,
Abhinav
______________________________________
Abhinav Kumar, Ph.D.
The Joint Center for Structural Genomics
MS99, SLAC National Accelerator Laboratory
2575 Sand Hill Rd, Menlo Park, CA 94025
(650) 926-2992


On 05/21/2014 08:44 AM, Clotilde LowKam wrote:
> Hello,
> probably a driver/graphic card problem. Maybe trying the legacy driver 
> for your card could help.
> Clotilde
>
>
> 2014-05-21 11:26 GMT-04:00 Abhinav Kumar <abh...@sl... 
> <mailto:abh...@sl...>>:
>
>     Hi,
>
>     I installed pymol ( pymol-v1.7.0.5-Linux-x86_64.tar.bz2) on my
>     ubuntu (12.04 LTS) desktop and this was working fine.
>     Later, I upgraded my Ubuntu to 14.04 LTS and now pymol has become
>     extremely sluggish. Even rotating a small molecule like ATP takes
>     a while.
>
>     Any suggestions on how to fix this?
>
>     Coot and rasmol are not affected by this Ubuntu upgrade.
>
>     Thanks,
>     Abhinav
>     ______________________________________
>     Abhinav Kumar, Ph.D.
>     The Joint Center for Structural Genomics
>     MS99, SLAC National Accelerator Laboratory
>     2575 Sand Hill Rd, Menlo Park, CA 94025
>     (650) 926-2992 <tel:%28650%29%20926-2992>
>
>
>     On 05/13/2014 10:43 AM, Thomas Holder wrote:
>>     Greetings,
>>
>>     We'd like to announce the release of Incentive PyMOL 1.7.0.5, which is a bugfix release. Applicable bugfixes have also been pushed to the sourceforge SVN repository as Open-Source PyMOL 1.7.1.3 (SVN rev 4076).
>>
>>     Fixed bugs include:
>>
>>     Incentive PyMOL (for licensed users):
>>       - don't disable all shaders if geometry shaders are not available
>>       - many z-depth issues for labels and connectors in immediate, shader, and
>>         ray tracing (all renderings should now look almost exactly the same)
>>       - background in front of text with use_shaders=0
>>       - label picking broken with use_shaders=0
>>       - character rendering in ray tracing
>>       - clipped text in multi-line labels (shader on and off)
>>
>>     Open Source and Incentive PyMOL:
>>       - cartoon memory leak
>>       - CGO colors ignored with ALPHA
>>       - hidden groups flash in scene based movies
>>       - "A > find > polar contact > just intra-side chain" broken
>>       - "scene auto, update" broken
>>       - small solvent_radius crashes Surface generation
>>       - grid_mode support for volumes
>>
>>     Some of these changes have been in the SVN repository for a couple of weeks.
>>
>>     Download:
>>     Installers for Incentive PyMOL:http://pymol.org/dsc/ip/
>>     Open Source:http://sourceforge.net/p/pymol/
>>
>>     Cheers,
>>        The PyMOL Team at Schrödinger
>>
>
>
>     ------------------------------------------------------------------------------
>     "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>     Instantly run your Selenium tests across 300+ browser/OS combos.
>     Get unparalleled scalability from the best Selenium testing
>     platform available
>     Simple to use. Nothing to install. Get started now for free."
>     http://p.sf.net/sfu/SauceLabs
>     _______________________________________________
>     PyMOL-users mailing list (PyM...@li...
>     <mailto:PyM...@li...>)
>     Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>     Archives:
>     http://www.mail-archive.com/pym...@li...
>
>