date:20160119

Re: [PyMOL] pdb edition

2016-01-19 Thread Tsjerk Wassenaar

Hi Edward,

Oh, I read over the moving part. Well, what I meant to convey is that you
can use CONECT records to draw additional bonds, but for the rest
bondedness is inferred from distance. So you can only remove bonds if the
particles are further apart than the cutoff AND have a CONECT record.

But moving and saving is possible ofcourse. There's the possibility to edit
wit the mouse and you can use commands alter_state, translate and rotate.
To save the new coordinates, well... use 'save'.

Hope it helps,

Tsjerk
On Jan 19, 2016 22:59, "Edward A. Berry"  wrote:

>
>
> On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote:
>
>> Hi Pascual,
>>
>> The PDB file does not really have information on bonds. If atoms are
>> closer than some cutoff a bond is drawn. Unbonding and saving will not
>> change the distance, so the bond will be drawn again when loaded again.
>> What is your aim?
>>
>> Cheers,
>>
>
> (Actually of course the PDB file format does (or did) have a way to specify
> bonds, but i guess no programs ever used it)
> But the poster did specify moving atoms (to) break bonds and separate
> atoms,
> so maybe that is where the help is needed- how do you move atoms in Pymol?
> Or since this is probably a RTFM-type question, perhaps a pointer
> to chapter and verse in the wiki would be more appropriate?
> And then to save the modified pdb: I suppose file:save:molecule, and
> it will be obvious which molecule to save?
>
>>
>> Tsjerk
>>
>> On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta <
>> pascual.lahue...@uv.es > wrote:
>>
>> I am new user of Pymol and I would like to use this program for a
>> very simple task that I describe here in three steps:
>>
>> 1. Start with a simple structure (structure 1.pdb1) either loaded or
>> created with the editor.
>> 2. The second task will be to change the position of the atoms in
>> structure 1, breaking bonds and separating atoms.
>> 3. The third step will be to save the resulting structure as
>> structure2.pdb file.
>>
>> I wonder if  pymol allows me to perform this task.  iI hope someone
>> can guide me in this task.
>>
>> Thanks in advance
>>
>> Pascual
>> =
>>
>>
>> Pascual Lahuerta
>> Universitat de Valencia
>> Dep. Q. Inorganica
>> Edificio Investigación 3.36
>> Dr. Moliner 50
>> 46100 Burjassot-Valencia
>> Despacho 96 354 3147
>> Movil 617 188 331
>> lahue...@uv.es 
>>
>>
>>
>>
>> --
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>>
>>
>> --
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Re: [PyMOL] pdb edition

2016-01-19 Thread Edward A. Berry

Thanks, David!
My take- Pymol is a very powerful tool for creating beautiful and insightful
figures of molecules, with myriad features for displaying aspects of interest
to structural biologists, such as different surfaces, electrostatic potential,
H-bonds and other inter-atomic interactions, secondary structure, B-factor;
but for extensive graphical editing of the structures ("rebuilding at the 
graphics machine",
the crystallographers say), one would be better off using a program that was 
designed
for that, such as coot, or "O".
Then, when you get the model you want, come back to pymol (or ccp4MG, or 
chimera) to
make figures and movies.
Ed

On 01/19/2016 05:48 PM, David Hall wrote:
> Well, yes, programs do use the CONECT records, including pymol
>
> http://pymolwiki.org/index.php/Connect_mode
>
> Removing bonds is http://pymolwiki.org/index.php/Unbond
>
> Atoms can be translated using the command line 
> http://pymolwiki.org/index.php/Editing_atoms#Get_coordinates_from_Python
>
> Or in edit mode 
> http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#move
>
> And then save http://pymolwiki.org/index.php/Save
>
>
> But honestly, the description sounds like something that would be infinitely 
> easier to do using some plain python code rather than in pymol.
>
> -David
>
>
>> On Jan 19, 2016, at 4:59 PM, Edward A. Berry > > wrote:
>>
>>
>>
>> On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote:
>>> Hi Pascual,
>>>
>>> The PDB file does not really have information on bonds. If atoms are closer 
>>> than some cutoff a bond is drawn. Unbonding and saving will not change the 
>>> distance, so the bond will be drawn again when loaded again. What is your 
>>> aim?
>>>
>>> Cheers,
>>
>> (Actually of course the PDB file format does (or did) have a way to specify
>> bonds, but i guess no programs ever used it)
>> But the poster did specify moving atoms (to) break bonds and separate atoms,
>> so maybe that is where the help is needed- how do you move atoms in Pymol?
>> Or since this is probably a RTFM-type question, perhaps a pointer
>> to chapter and verse in the wiki would be more appropriate?
>> And then to save the modified pdb: I suppose file:save:molecule, and
>> it will be obvious which molecule to save?
>>>
>>> Tsjerk
>>>
>>> On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta >> > wrote:
>>>
>>>I am new user of Pymol and I would like to use this program for a very 
>>> simple task that I describe here in three steps:
>>>
>>>1. Start with a simple structure (structure 1.pdb1) either loaded or 
>>> created with the editor.
>>>2. The second task will be to change the position of the atoms in 
>>> structure 1, breaking bonds and separating atoms.
>>>3. The third step will be to save the resulting structure as 
>>> structure2.pdb file.
>>>
>>>I wonder if  pymol allows me to perform this task.  iI hope someone can 
>>> guide me in this task.
>>>
>>>Thanks in advance
>>>
>>>Pascual
>>>=
>>>
>>>
>>>Pascual Lahuerta
>>>Universitat de Valencia
>>>Dep. Q. Inorganica
>>>Edificio Investigación 3.36
>>>Dr. Moliner 50
>>>46100 Burjassot-Valencia
>>>Despacho 96 354 3147
>>>Movil 617 188 331
>>> lahue...@uv.es 
>>>
>>>
>>>
>>>
>>> --
>>>Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>Monitor end-to-end web transactions and take corrective actions now
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>>>___
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>>> )
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>>>
>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>>
>>>
>>> --
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>
>> -

Re: [PyMOL] pdb edition

2016-01-19 Thread Ezra Peisach

CONECT records are not used for peptide bonds for standard amino acid and
nucleic acid links.  These are assumed. In addition, for these standard
chemical component, CONECT records are not used to internal bonds - they
are "known."

Non standard amino/nucleic acids used CONECT records for all atoms present.

On Tue, Jan 19, 2016 at 5:48 PM, David Hall  wrote:

> Well, yes, programs do use the CONECT records, including pymol
>
> http://pymolwiki.org/index.php/Connect_mode
>
> Removing bonds is http://pymolwiki.org/index.php/Unbond
>
> Atoms can be translated using the command line
> http://pymolwiki.org/index.php/Editing_atoms#Get_coordinates_from_Python
>
> Or in edit mode
> http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#move
>
> And then save http://pymolwiki.org/index.php/Save
>
>
> But honestly, the description sounds like something that would be
> infinitely easier to do using some plain python code rather than in pymol.
>
> -David
>
>
> On Jan 19, 2016, at 4:59 PM, Edward A. Berry  wrote:
>
>
>
> On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote:
>
> Hi Pascual,
>
> The PDB file does not really have information on bonds. If atoms are
> closer than some cutoff a bond is drawn. Unbonding and saving will not
> change the distance, so the bond will be drawn again when loaded again.
> What is your aim?
>
> Cheers,
>
>
> (Actually of course the PDB file format does (or did) have a way to specify
> bonds, but i guess no programs ever used it)
> But the poster did specify moving atoms (to) break bonds and separate
> atoms,
> so maybe that is where the help is needed- how do you move atoms in Pymol?
> Or since this is probably a RTFM-type question, perhaps a pointer
> to chapter and verse in the wiki would be more appropriate?
> And then to save the modified pdb: I suppose file:save:molecule, and
> it will be obvious which molecule to save?
>
>
> Tsjerk
>
> On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta   > wrote:
>
>I am new user of Pymol and I would like to use this program for a very
> simple task that I describe here in three steps:
>
>1. Start with a simple structure (structure 1.pdb1) either loaded or
> created with the editor.
>2. The second task will be to change the position of the atoms in
> structure 1, breaking bonds and separating atoms.
>3. The third step will be to save the resulting structure as
> structure2.pdb file.
>
>I wonder if  pymol allows me to perform this task.  iI hope someone can
> guide me in this task.
>
>Thanks in advance
>
>Pascual
>=
>
>
>Pascual Lahuerta
>Universitat de Valencia
>Dep. Q. Inorganica
>Edificio Investigación 3.36
>Dr. Moliner 50
>46100 Burjassot-Valencia
>Despacho 96 354 3147
>Movil 617 188 331
>lahue...@uv.es 
>
>
>
>
>
> --
>Site24x7 APM Insight: Get Deep Visibility into Application Performance
>APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>Monitor end-to-end web transactions and take corrective actions now
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> mailto:PyMOL-users@lists.sourceforge.net
> >)
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>Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
>
>
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
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>
>
>
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>
>
>
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Re: [PyMOL] pdb edition

2016-01-19 Thread David Hall

Well, yes, programs do use the CONECT records, including pymol

http://pymolwiki.org/index.php/Connect_mode

Removing bonds is http://pymolwiki.org/index.php/Unbond

Atoms can be translated using the command line 
http://pymolwiki.org/index.php/Editing_atoms#Get_coordinates_from_Python

Or in edit mode 
http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#move

And then save http://pymolwiki.org/index.php/Save


But honestly, the description sounds like something that would be infinitely 
easier to do using some plain python code rather than in pymol.

-David


> On Jan 19, 2016, at 4:59 PM, Edward A. Berry  wrote:
> 
> 
> 
> On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote:
>> Hi Pascual,
>> 
>> The PDB file does not really have information on bonds. If atoms are closer 
>> than some cutoff a bond is drawn. Unbonding and saving will not change the 
>> distance, so the bond will be drawn again when loaded again. What is your 
>> aim?
>> 
>> Cheers,
> 
> (Actually of course the PDB file format does (or did) have a way to specify
> bonds, but i guess no programs ever used it)
> But the poster did specify moving atoms (to) break bonds and separate atoms,
> so maybe that is where the help is needed- how do you move atoms in Pymol?
> Or since this is probably a RTFM-type question, perhaps a pointer
> to chapter and verse in the wiki would be more appropriate?
> And then to save the modified pdb: I suppose file:save:molecule, and
> it will be obvious which molecule to save?
>> 
>> Tsjerk
>> 
>> On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta >  > >> wrote:
>> 
>>I am new user of Pymol and I would like to use this program for a very 
>> simple task that I describe here in three steps:
>> 
>>1. Start with a simple structure (structure 1.pdb1) either loaded or 
>> created with the editor.
>>2. The second task will be to change the position of the atoms in 
>> structure 1, breaking bonds and separating atoms.
>>3. The third step will be to save the resulting structure as 
>> structure2.pdb file.
>> 
>>I wonder if  pymol allows me to perform this task.  iI hope someone can 
>> guide me in this task.
>> 
>>Thanks in advance
>> 
>>Pascual
>>=
>> 
>> 
>>Pascual Lahuerta
>>Universitat de Valencia
>>Dep. Q. Inorganica
>>Edificio Investigación 3.36
>>Dr. Moliner 50
>>46100 Burjassot-Valencia
>>Despacho 96 354 3147
>>Movil 617 188 331
>>lahue...@uv.es  > >
>> 
>> 
>> 
>>
>> --
>>Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>Monitor end-to-end web transactions and take corrective actions now
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>>  
>> > >)
>>Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> 
>> 
>> 
>> 
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> 
>> 
>> 
>> --
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Re: [PyMOL] pdb edition

2016-01-19 Thread Edward A. Berry



On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote:
> Hi Pascual,
>
> The PDB file does not really have information on bonds. If atoms are closer 
> than some cutoff a bond is drawn. Unbonding and saving will not change the 
> distance, so the bond will be drawn again when loaded again. What is your aim?
>
> Cheers,

(Actually of course the PDB file format does (or did) have a way to specify
bonds, but i guess no programs ever used it)
But the poster did specify moving atoms (to) break bonds and separate atoms,
so maybe that is where the help is needed- how do you move atoms in Pymol?
Or since this is probably a RTFM-type question, perhaps a pointer
to chapter and verse in the wiki would be more appropriate?
And then to save the modified pdb: I suppose file:save:molecule, and
it will be obvious which molecule to save?
>
> Tsjerk
>
> On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta  > wrote:
>
> I am new user of Pymol and I would like to use this program for a very 
> simple task that I describe here in three steps:
>
> 1. Start with a simple structure (structure 1.pdb1) either loaded or 
> created with the editor.
> 2. The second task will be to change the position of the atoms in 
> structure 1, breaking bonds and separating atoms.
> 3. The third step will be to save the resulting structure as 
> structure2.pdb file.
>
> I wonder if  pymol allows me to perform this task.  iI hope someone can 
> guide me in this task.
>
> Thanks in advance
>
> Pascual
> =
>
>
> Pascual Lahuerta
> Universitat de Valencia
> Dep. Q. Inorganica
> Edificio Investigación 3.36
> Dr. Moliner 50
> 46100 Burjassot-Valencia
> Despacho 96 354 3147
> Movil 617 188 331
> lahue...@uv.es 
>
>
>
> 
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
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> )
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
>
> --
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Re: [PyMOL] pdb edition

2016-01-19 Thread Tsjerk Wassenaar

Hi Pascual,

The PDB file does not really have information on bonds. If atoms are closer
than some cutoff a bond is drawn. Unbonding and saving will not change the
distance, so the bond will be drawn again when loaded again. What is your
aim?

Cheers,

Tsjerk

On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta 
wrote:

> I am new user of Pymol and I would like to use this program for a very
> simple task that I describe here in three steps:
>
> 1. Start with a simple structure (structure 1.pdb1) either loaded or
> created with the editor.
> 2. The second task will be to change the position of the atoms in
> structure 1, breaking bonds and separating atoms.
> 3. The third step will be to save the resulting structure as
> structure2.pdb file.
>
> I wonder if  pymol allows me to perform this task.  iI hope someone can
> guide me in this task.
>
> Thanks in advance
>
> Pascual
> =
>
>
> Pascual Lahuerta
> Universitat de Valencia
> Dep. Q. Inorganica
> Edificio Investigación 3.36
> Dr. Moliner 50
> 46100 Burjassot-Valencia
> Despacho 96 354 3147
> Movil 617 188 331
> lahue...@uv.es
>
>
>
>
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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-- 
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[PyMOL] segmentation fault

2016-01-19 Thread henry tang

Dear developer,

I had this segmentation fault problem whenever using plugin like apbs or
autodock etc. it crashes when I click button "APBS binary location" etc,
Tried both pymol 1.7.4 and 1.8.0 and gave the same error. Any help would be
greatly appreciated.

Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 4.50.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: GeForce GTX 850M/PCIe/SSE2
  GL_VERSION:  4.5.0 NVIDIA 352.68
 Detected 4 CPU cores.  Enabled multithreaded rendering.

/pymol: line 3: 20414 Segmentation fault  (core dumped)
"/usr/bin/python" "/home/protein/pymol/lib/python/pymol/__init__.py" "$@"

Henry
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[PyMOL] pdb edition

2016-01-19 Thread Pascual Lahuerta

I am new user of Pymol and I would like to use this program for a very simple 
task that I describe here in three steps:

1. Start with a simple structure (structure 1.pdb1) either loaded or created 
with the editor.  
2. The second task will be to change the position of the atoms in structure 1, 
breaking bonds and separating atoms. 
3. The third step will be to save the resulting structure as structure2.pdb 
file.

I wonder if  pymol allows me to perform this task.  iI hope someone can guide 
me in this task. 

Thanks in advance

Pascual
=


Pascual Lahuerta
Universitat de Valencia
Dep. Q. Inorganica
Edificio Investigación 3.36
Dr. Moliner 50
46100 Burjassot-Valencia
Despacho 96 354 3147
Movil 617 188 331
lahue...@uv.es



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Re: [PyMOL] pdb edition

Re: [PyMOL] pdb edition

Re: [PyMOL] pdb edition

Re: [PyMOL] pdb edition

Re: [PyMOL] pdb edition

Re: [PyMOL] pdb edition

[PyMOL] segmentation fault

[PyMOL] pdb edition

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