[Chimera-users] Fit model and density map

Tue Dec 24 13:49:56 PST 2019

Is there any one knows how to fit the density map to this red model?

[cid:71FF4B2F-87EA-443B-B280-CE3ABEA9B11B at its.yale.internal]
On Dec 24, 2019, at 12:26 PM, chimera-users-request at cgl.ucsf.edu<mailto:chimera-users-request at cgl.ucsf.edu> wrote:

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Today's Topics:

  1. Re: Problem with DelPhi in chimera (labe boye) (Boaz Shaanan)
     - correction (Boaz Shaanan)

----------------------------------------------------------------------

Message: 1
Date: Tue, 24 Dec 2019 17:26:14 +0000
From: Boaz Shaanan <bshaanan at bgu.ac.il>
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Problem with DelPhi in chimera (labe
boye) (Boaz Shaanan) - correction
Message-ID: <81ea8ecae3d04575b9c13ac2142612bf at bgu.ac.il>
Content-Type: text/plain; charset="windows-1255"

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 at bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710

________________________________________
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Subject: Chimera-users Digest, Vol 200, Issue 20

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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 at bgu.ac.il>
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Problem with DelPhi in chimera (labe
       boye)
Message-ID: <a2abfa7a83394a56b27584878c181426 at 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 at bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710

________________________________________
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of chimera-users-request at cgl.ucsf.edu <chimera-users-request at cgl.ucsf.edu>
Sent: Tuesday, December 24, 2019 6:34 PM
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Subject: Chimera-users Digest, Vol 200, Issue 19

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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 at cgl.ucsf.edu>
To: "sintaspirulina at gmail.com" <sintaspirulina at gmail.com>
Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Problem with DelPhi in chimera
Message-ID: <B59A5D0E-CA80-4151-9CD6-11B33435CA4A at 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.
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23volume&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=syWyZ7IUR20yv8QyPCDnWM%2BocXEvOGDM8NoPg1Y2Q0I%3D&reserved=0>
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 at 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 at hu.edu.et
Sintayehu.M.Shenkutie at bot3.bio.uni-giessen.de

On Monday, December 23, 2019, 08:30:26 PM GMT+3, Elaine Meng <meng at 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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=qpjwIjue%2BnkBte46u6VICybT3puZdN3LiRCFMoODMwQ%3D&reserved=0>

?specifically this is their academic website <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcompbio.clemson.edu%2Fdelphi&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=tKP9y%2FfkiyRazSZfDWRm18PzmEyT6UYhtoAW8n6fwss%3D&reserved=0>

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 at 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 at 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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=qpjwIjue%2BnkBte46u6VICybT3puZdN3LiRCFMoODMwQ%3D&reserved=0>

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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fsurfprop.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=ddqLEJ%2BfrRaTzDU3FgYmvLAQRKUnxdYjQE2kqLyMpAw%3D&reserved=0>

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 at 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 at hu.edu.et
Sintayehu.M.Shenkutie at bot3.bio.uni-giessen.de

The bamboo that bends is stronger than the oak that resists

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------------------------------

Message: 2
Date: Mon, 23 Dec 2019 21:21:35 +0000
From: Boaz Shaanan <bshaanan at bgu.ac.il>
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18
Message-ID: <d539fbf953d74b6783b5dc0a632313d3 at 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 at bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710

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

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When replying, please edit your Subject line so it is more specific
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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 at gmail.com)

----------------------------------------------------------------------

Message: 1
Date: Fri, 20 Dec 2019 12:16:20 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: labe boye <sintaspirulina at gmail.com>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Problem with DelPhi in chimera
Message-ID: <1158BCF0-F94F-4B55-98DA-27166E19CEDC at 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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=qpjwIjue%2BnkBte46u6VICybT3puZdN3LiRCFMoODMwQ%3D&reserved=0>

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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fsurfprop.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=ddqLEJ%2BfrRaTzDU3FgYmvLAQRKUnxdYjQE2kqLyMpAw%3D&reserved=0>

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 at 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 at yahoo.com>
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>,
       "chimera-bugs at cgl.ucsf.edu" <chimera-bugs at cgl.ucsf.edu>
Subject: [Chimera-users] need your assistance
Message-ID: <844676351.2239559.1576941000519 at 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
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------------------------------

Message: 3
Date: Sun, 22 Dec 2019 15:23:32 +0300
From: labe boye <sintaspirulina at gmail.com>
To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Problem with DelPhi in chimera
Message-ID:
       <CAHh6TEAF+C8-MyVcNMQ3+Qr4n8=wZVHuwWWDxGnmrkbPaWCugA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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 at 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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=qpjwIjue%2BnkBte46u6VICybT3puZdN3LiRCFMoODMwQ%3D&reserved=0>

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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fsurfprop.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937326851&sdata=ddqLEJ%2BfrRaTzDU3FgYmvLAQRKUnxdYjQE2kqLyMpAw%3D&reserved=0>

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 at 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 at hu.edu.et
Sintayehu.M.Shenkutie at bot3.bio.uni-giessen.de

*The bamboo that bends is stronger than the oak that resists *
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------------------------------

Message: 4
Date: Mon, 23 Dec 2019 09:30:25 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: labe boye <sintaspirulina at gmail.com>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Problem with DelPhi in chimera
Message-ID: <2ED6BCEC-E45E-4B5C-9125-6ADB02A92976 at cgl.ucsf.edu>
Content-Type: text/plain;       charset=utf-8

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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=6PfdtvdluGZuwFA4AvBfP53ZhTo%2Fo2RN1soGqoEyIGI%3D&reserved=0>

?specifically this is their academic website <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcompbio.clemson.edu%2Fdelphi&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=9oormq8%2FyWPrmwE%2BEaNCEg4cTHpb6zoLTqltE6wlQ0I%3D&reserved=0>

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 at 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 at 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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=6PfdtvdluGZuwFA4AvBfP53ZhTo%2Fo2RN1soGqoEyIGI%3D&reserved=0>

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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fsurfprop.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=wiqS8CjW0OYUrFbgk9t7HdyrFOl5axU9MuSTmVQXE78%3D&reserved=0>

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 at 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 at hu.edu.et
Sintayehu.M.Shenkutie at bot3.bio.uni-giessen.de

The bamboo that bends is stronger than the oak that resists
_______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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------------------------------

Message: 5
Date: Mon, 23 Dec 2019 09:46:23 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Asmi Mahmood <asmi_mahmood at yahoo.com>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] dock prep for many ligands
Message-ID: <0FCC2DA1-6FEB-41E6-9752-690E79154619 at cgl.ucsf.edu>
Content-Type: text/plain;       charset=utf-8

Hi Asmi Tariq,
This is not a bug, so please do not send mail to the bugs address.

There is no such PDF or video, sorry.   However, I do know that lots of people use Chimera to prep many ligands.  Here are some tips:

(1) You didn?t say what docking program you are using. Different programs take different input formats.  Chimera would be used to prepare ligands and write them in mol2 format.  If your docking program doesn?t take mol2, then Chimera is less useful for you.

(2) My guess is that it wouldn?t be practical/feasible to read one giant SDF file with all those ligands for prepping.  If using Chimera, it would probably work better if you had individual files for the individual ligands instead, e.g. lig00001.sdf, lig00002.sdf, etc.  Also the SDF needs to be 3D coordinates.  if you have SDFs with 2D chemical diagrams, Chimera will NOT be able to prep them into reasonable 3D molecules.

(3) then you would have to manually figure out which command(s) to use to prep a single ligand.  Probably you would need to use ?open? (open ligand file), ?addh?, ?addcharge? and ?write? (output mol2 file).  There is usually some trial and error for you to figure out what command options you want.  See the individual command help pages here:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fframecommand.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=JKhd4qYPJLCCxVvrJ8id5UjC8PPz9fejd7Hu28lmodQ%3D&reserved=0>

(4) After you have figured out which commands you want to use, then you would write a script to loop through your many ligands as discussed here in the programmer?s guide.
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FProgrammersGuide%2FbasicPrimer.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=K12oyqTkWYpyb%2B%2FSlXZhLGR6Ps5WGwzEREU3yZCe%2BQ4%3D&reserved=0>

P.S. I changed the subject line to something useful.

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 21, 2019, at 7:10 AM, Asmi Mahmood <asmi_mahmood at yahoo.com> wrote:

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

------------------------------

Message: 6
Date: Mon, 23 Dec 2019 18:01:05 +0000 (UTC)
From: "sintaspirulina at gmail.com" <sintaspirulina at gmail.com>
To: Chimera BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Problem with DelPhi in chimera
Message-ID: <211204532.2918376.1577124065204 at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

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 UniversityEthiopiaMobile: +251902432925Email:?dr.sintayehu at hu.edu.et?Sintayehu.M.Shenkutie at bot3.bio.uni-giessen.de

   On Monday, December 23, 2019, 08:30:26 PM GMT+3, Elaine Meng <meng at 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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=6PfdtvdluGZuwFA4AvBfP53ZhTo%2Fo2RN1soGqoEyIGI%3D&reserved=0>

?specifically this is their academic website <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcompbio.clemson.edu%2Fdelphi&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=9oormq8%2FyWPrmwE%2BEaNCEg4cTHpb6zoLTqltE6wlQ0I%3D&reserved=0>

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 at 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 at 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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23esp&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=6PfdtvdluGZuwFA4AvBfP53ZhTo%2Fo2RN1soGqoEyIGI%3D&reserved=0>

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:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ftutorials%2Fsurfprop.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=wiqS8CjW0OYUrFbgk9t7HdyrFOl5axU9MuSTmVQXE78%3D&reserved=0>

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 at 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 at hu.edu.et
Sintayehu.M.Shenkutie at bot3.bio.uni-giessen.de

The bamboo that bends is stronger than the oak that resists
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Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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Subject: Digest Footer

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End of Chimera-users Digest, Vol 200, Issue 18
**********************************************

------------------------------

Message: 3
Date: Tue, 24 Dec 2019 08:34:24 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: "sintaspirulina at gmail.com" <sintaspirulina at gmail.com>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Problem with DelPhi in chimera
Message-ID: <BAD49C83-D9B7-42E1-A3E9-D0FB56CCDF31 at cgl.ucsf.edu>
Content-Type: text/plain;       charset=utf-8

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:

<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fapbs%2Fpdb2pqr.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=bhoWIm6xgKZsdvry4egru%2Bya615sl7%2F6beN3eQQUtJQ%3D&reserved=0>
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fapbs%2Fapbs.html&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=7aLdzRR9SaPhO%2BYkqfYAXyDgs3LRisizCfwlmRxyI6o%3D&reserved=0>

?or you can use their web server directly, outside of Chimera:
<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fnbcr-222.ucsd.edu%2Fpdb2pqr_2.1.1%2F&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937336845&sdata=I8cxonBe0RMWeMJxJRrG5h4WJTWxRuZeZ7n8G44Zlh4%3D&reserved=0>
<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fimsva91-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttps%253a%252f%252fapbs%252dpdb2pqr.readthedocs.io%252fen%252flatest%252fdownloads.html%2523web%252dservers%26umid%3DA9632B4F-9A75-C205-9750-7484A8300BF7%26auth%3D701951cf8dfb7cd99762e0f5be252082d875f1cf-082163e1d1ed2b88e4dc6a972a0664a6fa5833bb&data=02%7C01%7Cwangbiao.guo%40yale.edu%7Cb2b73b6e75974030162708d78896e1f2%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637128053937346840&sdata=wImbdgtvdlSuN1w1Hi9rZfveu%2FAE%2FLpg5FN9VDjP86A%3D&reserved=0>

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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End of Chimera-users Digest, Vol 200, Issue 21
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