Re: [PyMOL] creating a virus capsid using supercell.py

[Ezra Peisach]

The full biological unit should be available in biological assembly file.
Have you tried using the fetch command?

i.e.:

fetch 1avd, type=pdb1

set all_states, on


The first retrieves BA #1, the all_states shows the models.

If there is something wrong with the assembly file - then by all means
contact the PDB...

Ezra



On Fri, Apr 17, 2015 at 1:34 AM, Marcelo Marcet  wrote:

> Hi Everyone,
>
> I have been trying to build a virus capsid using pymol. The biological
> unit for the complete structure is not available. :(
>
> My first attempt at getting this done was by using the “rotate” and
> “translate” commands. Unfortunately, these commands can only move objects
> either relative to the main axes or the viewer’s position (not relative to
> existing objects), thus I had to calculate the rotation angles and
> translation angle/distances for every single object (not practical).
>
> I have been advised to try the ‘supercell.py’ script. Is supercell the
> right tool for the job? Any advice would be much appreciated.
>
> Marcelo
>
>
>
>
> --
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Re: [PyMOL] creating a virus capsid using supercell.py

[Marcelo Marcet]

Hi Ezra,

Capsid was a typo, I ment to say the matrix of the virus. The pdb1 file is a 
trimer of the protein. I now how the trimeric form of the protein interacts to 
form the matrix and was hoping that a script could help me build the complete 
matrix sphere.


Marcelo


> On Apr 17, 2015, at 4:53 AM, Ezra Peisach  wrote:
> 
> The full biological unit should be available in biological assembly file.  
> Have you tried using the fetch command? 
> 
> i.e.:
> 
> fetch 1avd, type=pdb1
> set all_states, on
> 
> 
> The first retrieves BA #1, the all_states shows the models.
> 
> If there is something wrong with the assembly file - then by all means 
> contact the PDB...
> 
> Ezra
> 
> 
> On Fri, Apr 17, 2015 at 1:34 AM, Marcelo Marcet  > wrote:
> Hi Everyone,
> 
> I have been trying to build a virus capsid using pymol. The biological unit 
> for the complete structure is not available. :(
> 
> My first attempt at getting this done was by using the “rotate” and 
> “translate” commands. Unfortunately, these commands can only move objects 
> either relative to the main axes or the viewer’s position (not relative to 
> existing objects), thus I had to calculate the rotation angles and 
> translation angle/distances for every single object (not practical).
> 
> I have been advised to try the ‘supercell.py’ script. Is supercell the right 
> tool for the job? Any advice would be much appreciated.
> 
> Marcelo
> 
> 
> 
> --
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- 
>  event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net 
> )
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users 
> 
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 
> 
> 

--
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF___
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