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PyMOL Molecular Graphics System

PyMOL is an OpenGL based molecular visualization system

Brought to you by: herc111, speleo3

Re: [PyMOL] Clashes cut off

Re: [PyMOL] Clashes cut off

From: Thomas Holder <speleo3@us...> - 2012-05-21 07:13:26

Hi Arne,

this works for any kind of molecule.

Cheers,
   Thomas

Arne Dieckmann wrote, On 05/20/12 22:56:
> Hi Thomas, 
> 
> is this a general purpose script or does it only work for proteins/amino 
> acids? 
> 
> 
> Cheers, 
> Arne
> 
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
> - - - - - - - - - - - - - 
> Dr. Arne Dieckmann
> Houk Research Lab | University of California, Los Angeles
> 
> On May 20, 2012, at 1:15 PM, Thomas Holder wrote:
> 
>> Hi Doran,
>>
>> there is a script on the PyMOLWiki that shows VDW clashes:
>>
>> http://pymolwiki.org/index.php/Show_bumps
>>
>> There are several sculpt_vdw_vis_* settings which control the 
>> visualization:
>>
>> sculpt_vdw_vis_max
>> sculpt_vdw_vis_mid
>> sculpt_vdw_vis_min
>>
>> Cheers,
>>   Thomas
>>
>> doranhen@... wrote, On 05/20/12 18:26:
>>> Hi,
>>> I want to make pymol show me clashes between residues vdw spheres only  
>>> if the clashes are above a certain clash cut off, say if the clashing  
>>> residues overlap by x square angstrom than its o.k, but if they  
>>> overlap by more then x it's should show as a clash.
>>> Does anyone know of a way to do it in pymol?
>>>
>>> Thank you,
>>> Doran

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Thread view

[PyMOL] Clashes cut off

From: <doranhen@po...> - 2012-05-20 17:02:00

Hi,
I want to make pymol show me clashes between residues vdw spheres only  
if the clashes are above a certain clash cut off, say if the clashing  
residues overlap by x square angstrom than its o.k, but if they  
overlap by more then x it's should show as a clash.
Does anyone know of a way to do it in pymol?

Thank you,
Doran

Re: [PyMOL] Clashes cut off

From: Thomas Holder <speleo3@us...> - 2012-05-20 20:15:14

Hi Doran,

there is a script on the PyMOLWiki that shows VDW clashes:

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

There are several sculpt_vdw_vis_* settings which control the visualization:

sculpt_vdw_vis_max
sculpt_vdw_vis_mid
sculpt_vdw_vis_min

Cheers,
   Thomas

doranhen@... wrote, On 05/20/12 18:26:
> Hi,
> I want to make pymol show me clashes between residues vdw spheres only  
> if the clashes are above a certain clash cut off, say if the clashing  
> residues overlap by x square angstrom than its o.k, but if they  
> overlap by more then x it's should show as a clash.
> Does anyone know of a way to do it in pymol?
> 
> Thank you,
> Doran

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Re: [PyMOL] Clashes cut off

From: Arne Dieckmann <adieckma@go...> - 2012-05-20 20:56:58

Attachments: Message as HTML

Hi Thomas, 

is this a general purpose script or does it only work for proteins/amino acids? 


Cheers, 
Arne

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Dr. Arne Dieckmann
Houk Research Lab | University of California, Los Angeles

On May 20, 2012, at 1:15 PM, Thomas Holder wrote:

> Hi Doran,
> 
> there is a script on the PyMOLWiki that shows VDW clashes:
> 
> http://pymolwiki.org/index.php/Show_bumps
> 
> There are several sculpt_vdw_vis_* settings which control the visualization:
> 
> sculpt_vdw_vis_max
> sculpt_vdw_vis_mid
> sculpt_vdw_vis_min
> 
> Cheers,
>   Thomas
> 
> doranhen@... wrote, On 05/20/12 18:26:
>> Hi,
>> I want to make pymol show me clashes between residues vdw spheres only  
>> if the clashes are above a certain clash cut off, say if the clashing  
>> residues overlap by x square angstrom than its o.k, but if they  
>> overlap by more then x it's should show as a clash.
>> Does anyone know of a way to do it in pymol?
>> 
>> Thank you,
>> Doran
> 
> -- 
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
> 
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> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...

Re: [PyMOL] Clashes cut off

From: Thomas Holder <speleo3@us...> - 2012-05-21 07:13:26

Hi Arne,

this works for any kind of molecule.

Cheers,
   Thomas

Arne Dieckmann wrote, On 05/20/12 22:56:
> Hi Thomas, 
> 
> is this a general purpose script or does it only work for proteins/amino 
> acids? 
> 
> 
> Cheers, 
> Arne
> 
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
> - - - - - - - - - - - - - 
> Dr. Arne Dieckmann
> Houk Research Lab | University of California, Los Angeles
> 
> On May 20, 2012, at 1:15 PM, Thomas Holder wrote:
> 
>> Hi Doran,
>>
>> there is a script on the PyMOLWiki that shows VDW clashes:
>>
>> http://pymolwiki.org/index.php/Show_bumps
>>
>> There are several sculpt_vdw_vis_* settings which control the 
>> visualization:
>>
>> sculpt_vdw_vis_max
>> sculpt_vdw_vis_mid
>> sculpt_vdw_vis_min
>>
>> Cheers,
>>   Thomas
>>
>> doranhen@... wrote, On 05/20/12 18:26:
>>> Hi,
>>> I want to make pymol show me clashes between residues vdw spheres only  
>>> if the clashes are above a certain clash cut off, say if the clashing  
>>> residues overlap by x square angstrom than its o.k, but if they  
>>> overlap by more then x it's should show as a clash.
>>> Does anyone know of a way to do it in pymol?
>>>
>>> Thank you,
>>> Doran

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Re: [PyMOL] Clashes cut off

From: <doranhen@po...> - 2012-05-21 07:49:16

Hi Thomas,
Thank you for your reply.

I tried running the show_bumps.py script I copied from PymolWiki using  
@,however pymol gives me the following error :
NameError: name 'show_bumps' is not defined
How can I define it?
Also, do you know what are the values that sculpt_vdw_vis_max, mid and  
min are set to by default?

Thank you,
Doran
Quoting Thomas Holder <speleo3@...>:

> Hi Doran,
>
> there is a script on the PyMOLWiki that shows VDW clashes:
>
> http://pymolwiki.org/index.php/Show_bumps
>
> There are several sculpt_vdw_vis_* settings which control the visualization:
>
> sculpt_vdw_vis_max
> sculpt_vdw_vis_mid
> sculpt_vdw_vis_min
>
> Cheers,
>   Thomas
>
> doranhen@... wrote, On 05/20/12 18:26:
>> Hi,
>> I want to make pymol show me clashes between residues vdw spheres  
>> only  if the clashes are above a certain clash cut off, say if the  
>> clashing  residues overlap by x square angstrom than its o.k, but  
>> if they  overlap by more then x it's should show as a clash.
>> Does anyone know of a way to do it in pymol?
>>
>> Thank you,
>> Doran
>
> -- 
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen

Re: [PyMOL] Clashes cut off

From: Thomas Holder <speleo3@us...> - 2012-05-21 08:50:47

Hi Doran,

this is a python script, so you must load it with "run".

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

Use the "get" command to query default values of settings:

PyMOL>get sculpt_vdw_vis_max
  get: sculpt_vdw_vis_max = 0.30000

So the complete procedure should look like this:

run show_bumps_wikiscript.py
load yourmolecule.pdb
set sculpt_vdw_vis_min, 0
set sculpt_vdw_vis_mid, 0.2
set sculpt_vdw_vis_max, 0.4
show_bumps all

Cheers,
   Thomas

doranhen@... wrote, On 05/21/12 09:49:
> Hi Thomas,
> Thank you for your reply.
> 
> I tried running the show_bumps.py script I copied from PymolWiki using 
> @,however pymol gives me the following error :
> NameError: name 'show_bumps' is not defined
> How can I define it?
> Also, do you know what are the values that sculpt_vdw_vis_max, mid and 
> min are set to by default?
> 
> Thank you,
> Doran
> Quoting Thomas Holder <speleo3@...>:
> 
>> Hi Doran,
>>
>> there is a script on the PyMOLWiki that shows VDW clashes:
>>
>> http://pymolwiki.org/index.php/Show_bumps
>>
>> There are several sculpt_vdw_vis_* settings which control the 
>> visualization:
>>
>> sculpt_vdw_vis_max
>> sculpt_vdw_vis_mid
>> sculpt_vdw_vis_min
>>
>> Cheers,
>>   Thomas
>>
>> doranhen@... wrote, On 05/20/12 18:26:
>>> Hi,
>>> I want to make pymol show me clashes between residues vdw spheres 
>>> only  if the clashes are above a certain clash cut off, say if the 
>>> clashing  residues overlap by x square angstrom than its o.k, but if 
>>> they  overlap by more then x it's should show as a clash.
>>> Does anyone know of a way to do it in pymol?
>>>
>>> Thank you,
>>> Doran

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen