Re: [Apbs-users] ligands in APBS

[Leonid S. <sa...@mr...>]

Dear Warren,

Thanks for tip - it did solve the visualisation problem. However, I am 
not sure if APBS actually includes HETATMs in calculations, as the 
number of atoms listed by APBS at the start of calculations does not 
include HETATMs. Could anybody  clarify this?


Warren DeLano wrote:

>Leonid,
>
>Are you sure that those residues aren't in the map?  I'm guessing they
>were, but that PyMOL just isn't displaying a surface on those atoms.
>
>set surface_mode, 1
>
>in order to put surfaces on HETATMs too.  By default, PyMOL only
>surfaces ATOMs...
>
>Cheers,
>Warren
>
>--
>Warren L. DeLano, Ph.D.                     
>Principal Scientist
>
>. DeLano Scientific LLC  
>. 400 Oyster Point Blvd., Suite 213           
>. South San Francisco, CA 94080 USA   
>. Biz:(650)-872-0942  Tech:(650)-872-0834     
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> 
>
>  
>
>>-----Original Message-----
>>From: apb...@li... 
>>[mailto:apb...@li...] On Behalf Of 
>>Leonid Sazanov
>>Sent: Monday, March 27, 2006 6:29 AM
>>To: apb...@li...
>>Subject: [Apbs-users] ligands in APBS
>>
>>Hi, I am using APBS through PYMOL plug-in, with PQR file 
>>generated externally, by PDB2PQR. I have supplied the user 
>>file with parameters for the ligand, and so PDB2PQR 
>>recognizes it and writes out HETATM data for my non-standard 
>>residue, with all charges and radii. However, after APBS 
>>processing of PQR file, this data is ignored in the resulting 
>>map, and only standard protein residues are included in the 
>>map. APBS does not give any error messages.
>>Any help in resolving this greatly appreciated!
>>
>>--
>>Dr. Leonid A. Sazanov
>>Research group leader
>>Medical Research Council
>>Dunn Human Nutrition Unit
>>Wellcome Trust / MRC Building
>>Hills Road
>>Cambridge
>>CB2 2XY
>>WEB: www.mrc-dunn.cam.ac.uk
>>Tel: +44-1223-252910
>>Fax: +44-1223-252915
>>
>>
>>
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>>
>>    
>>

-- 
Dr. Leonid A. Sazanov
Research group leader
Medical Research Council
Dunn Human Nutrition Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge
CB2 2XY
WEB: www.mrc-dunn.cam.ac.uk
Tel: +44-1223-252910
Fax: +44-1223-252915