- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Problem with DelPhi in chimera (labe boye) (Boaz Shaanan) - correction
by Boaz Shaanan 24 Dec '19

24 Dec '19

In my previous message I meant of course linux Delphi v.6. Sorry. Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Tuesday, December 24, 2019 7:10 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 20 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Problem with DelPhi in chimera (labe boye) (Boaz Shaanan) ---------------------------------------------------------------------- Message: 1 Date: Tue, 24 Dec 2019 17:09:46 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Problem with DelPhi in chimera (labe boye) Message-ID: <a2abfa7a83394a56b27584878c181426(a)bgu.ac.il> Content-Type: text/plain; charset="windows-1255" Hi, The Chimera v.6 that I used was the linux version NOT windows. The answer you got from the Delphi people sounds familiar to me which is why I switched to APBS interface on Chimera (works on both Windows and linux). The .dx file produced by APBS is read and contoured nicely by Chimera. If you need to ionize the structure, there is a Windows PDB2PQR executable as mentioned by Elaine (I understand that you're using Windows). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Tuesday, December 24, 2019 6:34 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 19 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Problem with DelPhi in chimera (Elaine Meng) 2. Re: Chimera-users Digest, Vol 200, Issue 18 (Boaz Shaanan) 3. Re: Problem with DelPhi in chimera (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Dec 2019 12:55:29 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: "sintaspirulina(a)gmail.com" <sintaspirulina(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <B59A5D0E-CA80-4151-9CD6-11B33435CA4A(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 We saw your Chimera bug report. However, the file you attached was not the ?.phi? file (electrostatic potential map) output from DelPhi. It was just the text output from the DelPhi program. If DelPhi runs successfully on your structure, it will create a separate file, with name ending in .phi, that is the electrostatic potential map. If by ?cube? you mean Gaussian cube grid, Chimera does read that format. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> However, this format is handled simply as a map that is not necessarily electrostatic potential, so it would require more steps in Chimera to get the coloring you want. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 23, 2019, at 10:01 AM, sintaspirulina(a)gmail.com wrote: > > OK, > I tried all the three academic versions of DelPhi for windows; and none is working for me. I contacted the DelPhi supporters and SUGGESTED to use CUBE output format which isn't possible in Chimera. In the mean time, the two Chimera versions I installed read 3eeb.phi file from the tutorial. > I will report the problem. > regards, > > Sintayehu M. Shenkutie, Dr. rer. nat. > Assistant Professor of Biochemistry. > Department of Chemistry > Hawassa University > Ethiopia > Mobile: +251902432925 > Email: dr.sintayehu(a)hu.edu.et > Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de > > > > > On Monday, December 23, 2019, 08:30:26 PM GMT+3, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > It should be any DelPhi version that you get from the academic website, which was a link in this page I sent earlier: > > > 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> > > ?specifically this is their academic website <http://compbio.clemson.edu/delphi> > > I don?t remember what version I used several years ago to make 3eebB.phi, but as far as I know the format didn?t change. It is possible it changed and we didn?t know about it, but we would need example(s) of the files. > > If you believe you used the academic version of DelPhi but you get the error opening the phi file, you could try using Chimera menu Help? Report a Bug and attach your phi file so we could take a look at it. However, that does not guarantee it will be possible to fix. > > I hope this helps, > Elaine > > > On Dec 22, 2019, at 4:23 AM, labe boye <sintaspirulina(a)gmail.com> wrote: > > > > Hi > > Thank you for your reply. > > Could you please let me know which version of DelPhi academic version is compatible with Chimera? Which DelPhi version was used to generate the 3eeb.phi file in the tutorial? > > kindest regards, > > > > On Fri, Dec 20, 2019 at 11:16 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > 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(a)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, > > > > > > > > > > > -- > > Sintayehu M. Shenkutie, Dr. rer. nat. > > Assistant Professor of Biochemistry. > > Department of Chemistry > > Hawassa University > > Ethiopia > > Mobile: +251902432925 > > Email: dr.sintayehu(a)hu.edu.et > > Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de > > > > The bamboo that bends is stronger than the oak that resists > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Mon, 23 Dec 2019 21:21:35 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18 Message-ID: <d539fbf953d74b6783b5dc0a632313d3(a)bgu.ac.il> Content-Type: text/plain; charset="windows-1255" 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(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Monday, December 23, 2019 10:48 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 18 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." 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(a)gmail.com) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Dec 2019 12:16:20 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: labe boye <sintaspirulina(a)gmail.com> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <1158BCF0-F94F-4B55-98DA-27166E19CEDC(a)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(a)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, > ------------------------------ Message: 2 Date: Sat, 21 Dec 2019 15:10:00 +0000 (UTC) From: Asmi Mahmood <asmi_mahmood(a)yahoo.com> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu>, "chimera-bugs(a)cgl.ucsf.edu" <chimera-bugs(a)cgl.ucsf.edu> Subject: [Chimera-users] need your assistance Message-ID: <844676351.2239559.1576941000519(a)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

1 0

Re: [Chimera-users] Problem with DelPhi in chimera (labe boye)
by Boaz Shaanan 24 Dec '19

24 Dec '19

Hi, The Chimera v.6 that I used was the linux version NOT windows. The answer you got from the Delphi people sounds familiar to me which is why I switched to APBS interface on Chimera (works on both Windows and linux). The .dx file produced by APBS is read and contoured nicely by Chimera. If you need to ionize the structure, there is a Windows PDB2PQR executable as mentioned by Elaine (I understand that you're using Windows). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Tuesday, December 24, 2019 6:34 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 19 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Problem with DelPhi in chimera (Elaine Meng) 2. Re: Chimera-users Digest, Vol 200, Issue 18 (Boaz Shaanan) 3. Re: Problem with DelPhi in chimera (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Dec 2019 12:55:29 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: "sintaspirulina(a)gmail.com" <sintaspirulina(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <B59A5D0E-CA80-4151-9CD6-11B33435CA4A(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 We saw your Chimera bug report. However, the file you attached was not the ?.phi? file (electrostatic potential map) output from DelPhi. It was just the text output from the DelPhi program. If DelPhi runs successfully on your structure, it will create a separate file, with name ending in .phi, that is the electrostatic potential map. If by ?cube? you mean Gaussian cube grid, Chimera does read that format. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> However, this format is handled simply as a map that is not necessarily electrostatic potential, so it would require more steps in Chimera to get the coloring you want. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 23, 2019, at 10:01 AM, sintaspirulina(a)gmail.com wrote: > > OK, > I tried all the three academic versions of DelPhi for windows; and none is working for me. I contacted the DelPhi supporters and SUGGESTED to use CUBE output format which isn't possible in Chimera. In the mean time, the two Chimera versions I installed read 3eeb.phi file from the tutorial. > I will report the problem. > regards, > > Sintayehu M. Shenkutie, Dr. rer. nat. > Assistant Professor of Biochemistry. > Department of Chemistry > Hawassa University > Ethiopia > Mobile: +251902432925 > Email: dr.sintayehu(a)hu.edu.et > Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de > > > > > On Monday, December 23, 2019, 08:30:26 PM GMT+3, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > It should be any DelPhi version that you get from the academic website, which was a link in this page I sent earlier: > > > 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> > > ?specifically this is their academic website <http://compbio.clemson.edu/delphi> > > I don?t remember what version I used several years ago to make 3eebB.phi, but as far as I know the format didn?t change. It is possible it changed and we didn?t know about it, but we would need example(s) of the files. > > If you believe you used the academic version of DelPhi but you get the error opening the phi file, you could try using Chimera menu Help? Report a Bug and attach your phi file so we could take a look at it. However, that does not guarantee it will be possible to fix. > > I hope this helps, > Elaine > > > On Dec 22, 2019, at 4:23 AM, labe boye <sintaspirulina(a)gmail.com> wrote: > > > > Hi > > Thank you for your reply. > > Could you please let me know which version of DelPhi academic version is compatible with Chimera? Which DelPhi version was used to generate the 3eeb.phi file in the tutorial? > > kindest regards, > > > > On Fri, Dec 20, 2019 at 11:16 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > 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(a)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, > > > > > > > > > > > -- > > Sintayehu M. Shenkutie, Dr. rer. nat. > > Assistant Professor of Biochemistry. > > Department of Chemistry > > Hawassa University > > Ethiopia > > Mobile: +251902432925 > > Email: dr.sintayehu(a)hu.edu.et > > Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de > > > > The bamboo that bends is stronger than the oak that resists > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Mon, 23 Dec 2019 21:21:35 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18 Message-ID: <d539fbf953d74b6783b5dc0a632313d3(a)bgu.ac.il> Content-Type: text/plain; charset="windows-1255" 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(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Monday, December 23, 2019 10:48 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 18 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." 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(a)gmail.com) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Dec 2019 12:16:20 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: labe boye <sintaspirulina(a)gmail.com> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <1158BCF0-F94F-4B55-98DA-27166E19CEDC(a)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(a)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, > ------------------------------ Message: 2 Date: Sat, 21 Dec 2019 15:10:00 +0000 (UTC) From: Asmi Mahmood <asmi_mahmood(a)yahoo.com> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu>, "chimera-bugs(a)cgl.ucsf.edu" <chimera-bugs(a)cgl.ucsf.edu> Subject: [Chimera-users] need your assistance Message-ID: <844676351.2239559.1576941000519(a)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

1 0

Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18
by Boaz Shaanan 23 Dec '19

23 Dec '19

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(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Monday, December 23, 2019 10:48 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 18 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." 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(a)gmail.com) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Dec 2019 12:16:20 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: labe boye <sintaspirulina(a)gmail.com> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <1158BCF0-F94F-4B55-98DA-27166E19CEDC(a)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(a)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, > ------------------------------ Message: 2 Date: Sat, 21 Dec 2019 15:10:00 +0000 (UTC) From: Asmi Mahmood <asmi_mahmood(a)yahoo.com> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu>, "chimera-bugs(a)cgl.ucsf.edu" <chimera-bugs(a)cgl.ucsf.edu> Subject: [Chimera-users] need your assistance Message-ID: <844676351.2239559.1576941000519(a)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

1 0

Problem with DelPhi in chimera
by labe boye 23 Dec '19

23 Dec '19

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, -- Sintayehu M. Shenkutie, Dr. rer. nat. Assistant Professor of Biochemistry. Department of Chemistry Hawassa University Ethiopia Mobile: +251902432925 Email: dr.sintayehu(a)hu.edu.et Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de *The bamboo that bends is stronger than the oak that resists *

3 5

problems with multifit in chimera
by Nimit Jain 16 Dec '19

16 Dec '19

Hello I have recently been encountering problems with MultiFit within Chimera on both Ubuntu and Windows 10 (trace from reply log below--I get the same error on both operating systems). Even fitting with datasets that was working earlier in the year (~August-September) is not working anymore. My guess is that some changes have happened on the server that hosts Multifit. Could someone please try and reproduce the bug and let me know how I should troubleshoot this? I am trying to fit a single protein structure to an EM map and as I said, this was working earlier this year. I also tried downloading IMP on my Windows machine and using MultiFit from in there. This was running into some separate issues which I will not go into here since they are not directly related to Chimera. Thanks and best Nimit Trace from reply log: Application stderr ----- Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_input.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_all_surfaces.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_anchor_graph.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/run_fitting_fft.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_indexes_from_fitting_solutions.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_auto_proteomics_file.py", line 6, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/align_proteomics_em_atomic_plan.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/usr/local/opal-local/bin/multifitWS.py", line 438, in <module> main() File "/usr/local/opal-local/bin/multifitWS.py", line 46, in main VersionMap[cf["version"]](cf) File "/usr/local/opal-local/bin/multifitWS.py", line 98, in v1_run asymWriteSolution(cf) File "/usr/local/opal-local/bin/multifitWS.py", line 411, in asymWriteSolution raise RuntimeError("Unable to find file combinations.output") RuntimeError: Unable to find file combinations.output -----

3 2

view MD ChimeraX
by Fabian Glaser 16 Dec '19

16 Dec '19

Hi, I installed Molecular Dynamics Viewer in ChimeraX but I am not able to use it, . I use it successfully in Chimera (no X). But in ChimeraX. Can you please help me? Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web http://bku.technion.ac.il/ Tel +972 (0) 4 8293701

2 1

Regarding the UNDO issue raised by Luca
by Boaz Shaanan 13 Dec '19

13 Dec '19

Hi, Is not possible to install an automatic 'save session' at intervals determined by the user just as done in an MS word session? This at least may rescue the last operations. Following my own Chimera 'disasters' of this kind, I actually save session quite frequently when it becomes heavily loaded, particularly prior to a major new operation. My 2p. Happy and warm Thanksgiving. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Wednesday, November 27, 2019 11:07 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 199, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. secondary structure restraints and crosslink restraints (Fr?nze M?ller) 2. Undo option? (Luca Pellegrini) 3. Re: Undo option? (Elaine Meng) 4. Re: secondary structure restraints and crosslink restraints (Elaine Meng) 5. Re: Auto-associate define attribute/render by attribute (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Nov 2019 13:50:32 +0100 From: Fr?nze M?ller <fraenze.mueller(a)biologie.uni-freiburg.de> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] secondary structure restraints and crosslink restraints Message-ID: <cde7ad0e-503b-b0cc-5466-006d64019f5a(a)biologie.uni-freiburg.de> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear Chimera developers, I would like to perform homology modelling using Modeller in Chimera. At the moment I am using just distance restraints formatted like in the Chimera documentation (res1 res2 dist stdev). This file only contains crosslinking data. Is there a way to also include secondary structure restraints, that can serve as additional information during homology modelling? Or can I provide some were another file including this information separate from the crosslink information? Best wishes and Thanks for your help, -- *Fr?nze M?ller* Postdoctoral Researcher *Biochemistry and Functional Proteomics, Warscheid Lab* University of Freiburg|Sch?nzlestr. 1|79104 Freiburg|Germany Phone +49 761 203 2681

2 1

Export of small molecule in ball-and-stick form to VRML
by Bickel, Aaron 13 Dec '19

13 Dec '19

Hi, I have successfully used Chimera many times to export 3D-printable STL files from small and large molecules. However, when I try to export a ball-and-stick small molecule scene to a file type with color information to print in color (such as X3D, OBJ, or VRML) the resulting file only has the sticks shown and none of the balls. This seems to be replicated across any molecule that I try to export. In general my process is to import a PDB file, visualize as ball and stick through the Actions menu, and then use the Model Panel Attributes menu to adjust the thickness of the balls and sticks to ensure a strong physical structure. Is there an additional step I am missing to export as VRML/X3D/OBJ? Thank you, Aaron

2 1

Volume Eraser
by Guo, Wangbiao 12 Dec '19

12 Dec '19

Dear all: I use the chimera (chimera-alpha-mac64) and input the room temperature FIB data (.mrc file), which is a huge algae cell (see below). I want to delete some map area, and used the Volume Eraser. But it can not delete but increase map. Is there any one knows how to fix it? I attached my screen record. Seven Guo [cid:1931c4b2-7958-40eb-88a9-6640c394c5b8@namprd08.prod.outlook.com] > On Dec 11, 2019, at 1:25 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: ViewDock not showing results (Don Gabo) > 2. Conference Announcement: Molecular Modeling Workshop, Feb > 17-19, 2020 in Erlangen, Germany (Harald Lanig) > 3. selection of specific bonds (Damien Larivi?re) > 4. Re: selection of specific bonds (Elaine Meng) > 5. Re: selection of specific bonds (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Dec 2019 13:10:30 -0600 > From: Don Gabo <gabrielsrbio(a)gmail.com> > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] ViewDock not showing results > Message-ID: > <CAPSp8=gVkkMUrUac_7EQsV0B4P45dAPGg9DekyS1wQ2Z4hqOgw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Tried it but you have to save the whole structure, docking included, > otherwise you will get only the receptor or the ligand. > > El lun., 9 de diciembre de 2019 11:32, Elaine Meng <meng(a)cgl.ucsf.edu> > escribi?: > >> Hi Reshma, >> ViewDock is for viewing results that you already calculated using another >> program. It does not make these results for you. >> >> As an example, see tutorials for the DOCK6.9 docking program (not part of >> Chimera): >> <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdock.compb…> >> >> If you did get output file(s) from running a separate docking program >> (DOCK, Glide, Autodock Vina, etc.) but then ViewDock would not show them, >> then we would need an example of that output. >> >> I changed the subject line to be more descriptive. >> Best, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >>> On Dec 8, 2019, at 2:19 AM, Reshma Sri Punya <project.mpharma(a)yahoo.com> >> wrote: >>> >>> Hello good afternoon UCSF chimera is installed in my laptop but not >> showing docking results when I use the view dock options it was not showing >> any results it's not I tired several times please tell me the solutions to >> the problem >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: >> https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… >> >

3 2

selection of specific bonds
by Damien Larivière 12 Dec '19

12 Dec '19

Dear All, My question is naive but I have difficulties to figure out how to do it with Chimera. I would like to select specifically the group of two atoms (C and O) formed in a carbonyl bond C=O for all, say, GLU residues of a protein. Is there a way, via a command line, to do it? Thanks for your help on this. Damien

3 3