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

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel

E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

________________________________________ From: Chimera-users chimera-users-bounces@cgl.ucsf.edu on behalf of chimera-users-request@cgl.ucsf.edu chimera-users-request@cgl.ucsf.edu Sent: Monday, December 23, 2019 10:48 PM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 18

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Today's Topics:

1. Re: Problem with DelPhi in chimera (Elaine Meng) 2. need your assistance (Asmi Mahmood) 3. Re: Problem with DelPhi in chimera (labe boye) 4. Re: Problem with DelPhi in chimera (Elaine Meng) 5. dock prep for many ligands (Elaine Meng) 6. Re: Problem with DelPhi in chimera (sintaspirulina@gmail.com)

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Message: 1 Date: Fri, 20 Dec 2019 12:16:20 -0800 From: Elaine Meng meng@cgl.ucsf.edu To: labe boye sintaspirulina@gmail.com Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: 1158BCF0-F94F-4B55-98DA-27166E19CEDC@cgl.ucsf.edu Content-Type: text/plain; charset=us-ascii

Hi, Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry.

The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp

If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it.

Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html

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 20, 2019, at 10:33 AM, labe boye sintaspirulina@gmail.com wrote:

Hi, I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error Error reading file default.phi, format delphi Record size > file size What is the solution? regards,

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Message: 2 Date: Sat, 21 Dec 2019 15:10:00 +0000 (UTC) From: Asmi Mahmood asmi_mahmood@yahoo.com To: "chimera-users@cgl.ucsf.edu" chimera-users@cgl.ucsf.edu, "chimera-bugs@cgl.ucsf.edu" chimera-bugs@cgl.ucsf.edu Subject: [Chimera-users] need your assistance Message-ID: 844676351.2239559.1576941000519@mail.yahoo.com Content-Type: text/plain; charset="utf-8"

Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video.

Regards Waiting for a quick response Asma Tariq