Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

[Lukáš P. <xp...@nc...>]

Which version of PyMOL do you have? Mine is 1.7.4 and it is working just fine. So in case you have and older version(< 1.3 I guess) it might not work properly.

 

Lukas

 

From: Brenton Horne [mailto:bre...@ym...] 
Sent: Friday, March 20, 2015 12:02 AM
To: Lukáš Pravda
Subject: Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

 

Thanks for ya help but I'm afraid this isn't working. See it saves the fetched file as .sf format which it then fails to recognize. 




PyMOL>fetch 4V7Y, type = cif
 please wait ...
PyMOL>as cartoon
 CmdLoad: ".\4v7y.sf" loaded as "4V7Y".

 

On 19/03/2015 9:31 PM, Lukáš Pravda wrote:

Hi Brenton,

 

fetch 4v7y, type=cif 

 

is the command you are looking for

 

All the best

 

Lukas Pravda

---

CEITEC - Central European Institute of Technology

Masaryk University

Brno, Czech Republic

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From: Brenton Horne [mailto:bre...@ym...] 
Sent: Thursday, March 19, 2015 4:55 AM
To: pym...@li... <mailto:pym...@li...> 
Subject: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

 

Hi,

I have noticed that for some PDBs wwPDB doesn't contain PDB files (e.g., 4V7Y <http://www.rcsb.org/pdb/explore/explore.do?structureId=4V7Y> ), but rather they have mmCIF files instead and I was wondering if it was possible to get the fetch command to fetch these mmCIFs instead of PDBs. Now to be clear, I do understand how to load mmCIFs that I have downloaded manually from wwPDB by going to File->Open... but I'd like to know how to get PyMOL to fetch these files from wwPDB and load them. 

Thanks for your time,
Brenton