[Chimera-users] Chimera and DelphiController

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 31 10:19:50 PDT 2006

Hi Nihshanka,
(1) the issue with trying to get the charge and size parameters to  
match all your atoms is very common in electrostatics and energy  
calculations, and depends on the names of the atoms and residues in  
your input file.   This is more of a DelPhi issue than a Chimera  
issue.  In your input file, the atoms/residues might be incorrectly  
named, or they might be nonstandard residues (like some inhibitor  
molecule or ion).  Incorrect names include names that look correct  
but are in the wrong columns of a PDB file.  If the atom is a carbon,  
"C" in the name should be in column 14 even though the name can fill  
columns 13-16.   (For more discussion of PDB format, see http:// 
www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.pdf )
  If the atoms/residues are really nonstandard, you could make your  
own copies of the size and charge files with lines added including  
parameters for those atoms (or decide it is OK for those atoms to  
have zero charge).  The DelPhi parameter files are just plain text,  
the default ones are quite short, and it is easy to add new lines.   
Looking at the default charge file, I see that Lys and Arg should  
come out as +1.  Those are the only positive charges added by this  
file, so I don't see how you could get other residues with a positive  
charge.  There might be more information and suggestions at the  
DelPhi web site,

(2) the parameters you enter into DelPhi via DelPhiController only  
affect the surface used in the electrostatic calculations.  You could  
see this surface by designating output of a Grasp surface in  
DelPhiController (in the Parameter section) and then opening that  
surface in Chimera.  The surface used by Delphi is a solvent-excluded  
surface, also known as a Connolly surface, also known as as a  
molecular surface (Richards definition).  The surface shown with  
Actions->Surface->Show is also a molecular surface (Richards  
definition).  However, it will differ from the one used by DelPhi  
because it will be based on the radii in Chimera rather than the ones  
in the *.siz DelPhi parameter file, and also you could have used a  
different probe radius and resolution (spacing of points).  The  
differences generally won't be huge, but if you display both surfaces  
together you can see that they are different.

I hope this helps,

On Jul 28, 2006, at 10:35 AM, Nihshanka Debroy wrote:

> Hi,
>      My name is Nihshanka Debroy, and I am a graduate student at  
> Duke University. I recently joined this mailing list. I was  
> wondering if I could ask a couple of questions about the software.
>      The first one is more related to Delphi. I have been using the  
> Delphi Controller tool in Chimera, and I have been getting warnings  
> that certain radii records are missing from my .siz file, and some  
> residues have a net positive charge. I used the default files  
> provided when installing Delphi. I was wondering if anyone has  
> faced this problem before. Is there an online database where I  
> could get the missing radii and charge values for atoms and residues ?
>      Secondly, I am trying to generate the Connolly surface for  
> certain proteins. What I have been doing so far is running Delphi  
> Controller and assigning a probe radius of 1.4 Angstroms in the  
> Parameter section. I just wanted to make sure that this is  
> different from the molecular surface (MS) that is generated when  
> simply choosing Actions->Surface->Show.
> Thank you for your time.
> Sincerely,
> Nihshanka
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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