Re: [Chimera-users] Problem with DelPhi in chimera
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@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@hu.edu.et Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de
On Tuesday, December 24, 2019, 08:13:52 AM GMT+3, sintaspirulina@gmail.com <sintaspirulina@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@cgl.ucsf.edu> wrote:
In case you didn’t see it, another user says this:
Begin forwarded message:
From: Boaz Shaanan <bshaanan@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@cgl.ucsf.edu" <chimera-users@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
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@hu.edu.et Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de On Tuesday, December 24, 2019, 07:34:25 PM GMT+3, Elaine Meng <meng@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@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@hu.edu.et Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de
On Tuesday, December 24, 2019, 08:13:52 AM GMT+3, sintaspirulina@gmail.com <sintaspirulina@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@cgl.ucsf.edu> wrote:
In case you didn’t see it, another user says this:
Begin forwarded message:
From: Boaz Shaanan <bshaanan@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@cgl.ucsf.edu" <chimera-users@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
Hello, I would like to clarify that in Chimera, you can indeed color a molecular surface by the electrostatic potential in a cube file. I haven’t tried that many examples, but in the few I tried, the resulting appearance seemed reasonable, making me think it should be fine to use newer versions of DelPhi. When you open the cube file in Chimera, it shows as isosurfaces because that format is also used for orbitals. But if you just hide the isosurfaces (for example by clicking the “eye” icon in Volume Viewer, to the right of the “step” setting), you can still color the molecular surface by the values in the cube file, the same way as for a phi file or dx file. I had both a dx file and a cube file for 2gbp. I got the cube file using the DelPhi web server. <http://compbio.clemson.edu/sapp/delphi_webserver/> Below are screen shots showing using Surface Color with the “electrostatic potential” option for both of those map formats. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco see also Coulombic Surface Coloring <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html> and the Surface Properties image tutorial <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
On Dec 24, 2019, at 8:34 AM, Elaine Meng <meng@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@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@hu.edu.et Sintayehu.M.Shenkutie@bot3.bio.uni-giessen.de
On Tuesday, December 24, 2019, 08:13:52 AM GMT+3, sintaspirulina@gmail.com <sintaspirulina@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@cgl.ucsf.edu> wrote:
In case you didn’t see it, another user says this:
Begin forwarded message:
From: Boaz Shaanan <bshaanan@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@cgl.ucsf.edu" <chimera-users@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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