[Chimera-users] any aid for dock3.5 score?

[Elaine Meng]

Hi Francesco,
As far as we know, DelPhiController works with the current version of  
DelPhi
(the academic version obtained from the Honig lab, not the one in  
commercial
packages).  Although DelPhiController was created several years ago,
we have maintained it, and Chimera users have been using it this whole  
time.
I have tried it with a version of DelPhi downloaded from the Honig  
website
in summer or fall 2008, but don't remember the exact date or the version
number. The most direct way to answer this question is to try it  
yourself,
which seems faster than sending mail and waiting for an answer.

I tried to explain previously, but perhaps it wasn't clear, that
DelPhi/DelPhiController do not use the charges assigned by Chimera.
DelPhi only looks in the delphi charge parameter file, which is one
of the inputs to DelPhiController.  I believe the Honig lab supplies
one or more example charge parameter files.  I don't remember how  
capping
groups are handled, and I'm sure it depends which charge file you use,
but you can look in the charge file (and radius file, also from Honig  
lab)
using a text-editor, and change/add whatever parameters you want.  The
DelPhiController manual page links to file descriptions at the Honig  
site:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/delphicontroller/delphicontroller.html 
 >

As to APBS, the current situation is you have to run APBS yourself, and
then you can open the resulting potential map in Chimera for display.
There is no tool for running APBS in Chimera.  We have discussed this,  
but
given the available manpower, I believe there are no specific plans
to create such a tool.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



On May 9, 2009, at 12:47 AM, Francesco Pietra wrote:

> Hi Elaine:
> Do you know if standard capping groups (ACE NME) pose special
> problems, or are you aware if there is a charge assignment for them in
> relation to delphi? At any event, should their charge be adjusted so
> that the total charge of the protein is unitary?
>
> As the chimera tool is old, any idea if it faces problems with current
> version 4 of delphi?
>
> Any plan to make use of apbs in this context?
>
> thanks
> francesco
>
> On Thu, May 7, 2009 at 2:20 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hi Francesco,
>> If by "the grid" you mean the potential map from DelPhi:
>>
>> If you have the academic version of DelPhi from the Honig Lab, you  
>> can run
>> it with the Chimera tool DelPhiController (under Tools... Surface/ 
>> Binding
>> Analysis):
>> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/delphicontroller/delphicontroller.html 
>> >
>>
>> This allows entering all the DelPhi run parameters and input/output
>> filenames into a GUI instead of the text files needed to run DelPhi
>> "manually."  However, it does not help you make sure parameters are
>> correctly assigned; you are still responsible for figuring out  
>> which DelPhi
>> charge and radius files (also from the Honig lab) to use and making  
>> sure the
>> atoms in your structure are named correctly to match with the  
>> parameters in
>> these files.
>>
>> Also, DelPhiController is one of our older tools and may not be  
>> very easy to
>> use.
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>                      http://www.cgl.ucsf.edu/home/meng/index.html
>>
>> On May 6, 2009, at 10:14 AM, Francesco Pietra wrote:
>>
>>> Hi:
>>> I am considering to use dock3.5 score in DOCK6.2, which makes use of
>>> Delphi. Is any aid in chimera for builing the grid?
>>> thanks
>>> francesco
>>>
>>
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