[Chimera-users] Problem with DelPhi in chimera

[sintaspirulina at gmail.com]

HiThank you very much. Every thing is working fine but DelPhi; It isn't because I didn't wait too long. I was only doing the tutorial before I analyze my PDB 6TC5. I also used DelPhi web server. kindest regards,
Sintayehu M. Shenkutie, Dr. rer. nat. Assistant Professor of Biochemistry. Department of Chemistry
Hawassa UniversityEthiopiaMobile: +251902432925Email: dr.sintayehu at hu.edu.et Sintayehu.M.Shenkutie at bot3.bio.uni-giessen.de

 

    On Tuesday, December 24, 2019, 07:34:25 PM GMT+3, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 
 Hello,
That sounds like a problem with your DelPhi setup, or you didn’t wait long enough for the calculation to finish.  Sometimes it takes several minutes.

Instead of DelPhi, you could try using PDB2PQR and then (on the resulting pqr file) using APBS.  Chimera has interfaces to both of these:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>

…or you can use their web server directly, outside of Chimera:
<http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/>
<https://apbs-pdb2pqr.readthedocs.io/en/latest/downloads.html#web-servers>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 23, 2019, at 9:45 PM, sintaspirulina at gmail.com wrote:
> 
> FYI
> I tried DelPhi for windows F95 v6 as suggested by Boaz S. but in my case the out put .phi is empty file not even truncated. 
> regards,
> Sintayehu M. Shenkutie, Dr. rer. nat. 
> Assistant Professor of Biochemistry. 
> Department of Chemistry
> Hawassa University
> Ethiopia
> Mobile: +251902432925
> Email: dr.sintayehu at hu.edu.et 
> Sintayehu.M.Shenkutie at bot3.bio.uni-giessen.de
> 
> On Tuesday, December 24, 2019, 08:13:52 AM GMT+3, sintaspirulina at gmail.com <sintaspirulina at gmail.com> wrote:
> 
> Hello again,
> Thank you very much for your reply.
> For the bug report, my bad I might have attached the wrong file. I repeated the same thing with the .phi file. The email from another user, that is probably helpful. I will see if I can get the old DelPhi version.
> kindest regards,
> 
> 
> On Tuesday, December 24, 2019, 12:27:54 AM GMT+3, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 
> In case you didn’t see it, another user says this:
> 
>> Begin forwarded message:
>> 
>> From: Boaz Shaanan <bshaanan at bgu.ac.il>
>> Subject: Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18
>> Date: December 23, 2019 at 1:21:35 PM PST
>> To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
>> 
>> Hi,
>> 
>> I ran into this Chimera/Delphi problem a few months ago (and discussed it with the Chimera/Delphi people). The latest Delphi version that I tried (8.4) produced a cube format file which formally can be read and contoured in the Chimera volume viewer. I hated the way the electrostatic surface produced that way looked and abandoned it. Delphi v. 6 which I have (and which I think Elaine used 3 years ago) produced the good old .phi which is file properly displayed in Chimera . I think one can still get hold of V.6  from the Delphi distribution site. 
>> 
>> To avoid this mess I used the APBS interface of Chimera which worked fine and produced a nice, familiar style, looking electrostatic surface (see for example Fig. S10 in the supplementary of doi: 10.1093/nar/gkz604).
>> 
>> Regards,
>>            Boaz
>> 




  
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