From achatz at wzw.tum.de  Fri Aug  6 00:09:44 2021
From: achatz at wzw.tum.de (achatz)
Date: Fri, 06 Aug 2021 09:09:44 +0200
Subject: [Chimera-users] How to recreate point of view
Message-ID: <4be7-610ce000-d-7e84be00@55252969>

Hello,
I have two Chimera sessions which originate from the same pdb. Through rotations and movements the sessions viewpoints diverged over time. Is there a way to synchronize one session with the other so it has the exact same viewing angle?
Thanks
Stefan



From meng at cgl.ucsf.edu  Fri Aug  6 08:33:52 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 6 Aug 2021 08:33:52 -0700
Subject: [Chimera-users] How to recreate point of view
In-Reply-To: <4be7-610ce000-d-7e84be00@55252969>
References: <4be7-610ce000-d-7e84be00@55252969>
Message-ID: <63A7B657-755C-4941-8C49-574C473F895C@cgl.ucsf.edu>

Hi Stefan,
You could try opening one session (the one whose viewpoint you want to use for both), and using "matrixget" to save the transformation matrix to file.  E.g. on my mac I could use:

matrixget ~/Desktop/mymatrixfile

Then close session, open the other session, and use "matrixset" to apply the previously saved transformation:

matrixset ~/Desktop/mymatrixfile

See description of these commands:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.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 Aug 6, 2021, at 12:09 AM, achatz via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I have two Chimera sessions which originate from the same pdb. Through rotations and movements the sessions viewpoints diverged over time. Is there a way to synchronize one session with the other so it has the exact same viewing angle?
> Thanks
> Stefan



From aychen_702 at yahoo.com  Mon Aug  9 07:23:38 2021
From: aychen_702 at yahoo.com (Alice Chen)
Date: Mon, 9 Aug 2021 14:23:38 +0000 (UTC)
Subject: [Chimera-users] Problems with installing on a Windows 10
 expedition Dell laptop
In-Reply-To: <D45EEC8C-6ABA-4EE1-BC39-F6E2BF3D0D4E@sonic.net>
References: <1586612241.2919889.1625765310006.ref@mail.yahoo.com>
 <1586612241.2919889.1625765310006@mail.yahoo.com>
 <21C25191-57F2-4C78-8A59-7CFE92A3D2C8@sonic.net>
 <1247078119.3231004.1626283072068@mail.yahoo.com>
 <D45EEC8C-6ABA-4EE1-BC39-F6E2BF3D0D4E@sonic.net>
Message-ID: <92499663.379731.1628519018606@mail.yahoo.com>

Hi Tom,
Hi, I contacted you a few weeks ago re: an error message I was receiving in trying to install Chimera X onto a Windows 10 PC laptop.?Thank you again for your help with determining that the error message I received had to do with the antivirus software interfering with the install.
In talking with my IT specialist, there's no way for us to disable the antivirus software to get the install to complete. So, do you know if there might another way to get the install to complete? I was able to install an older version of Chimera on that computer, so, is there a possile workaround for Chimera X?
Thanks again-Alice Kitterman
Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com 

    On Wednesday, July 14, 2021, 01:25:16 PM EDT, Tom Goddard <goddard at sonic.net> wrote:  
 
 Using google to search for IPersistFile that appears in the error message says it is probably your antivirus software interfering with the installation and you may need to turn off antivirus while it installs. ?It is not a ChimeraX issue. ?Good luck.
https://www.thewindowsclub.com/ipersistfile-save-failed-error

 Tom


On Jul 14, 2021, at 10:17 AM, Alice Chen via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
Hi Tom,Please see below the email trail. I had my IT specialist try to install ChimeraX again, and the same thing happened: it ran through the install process (watched the progress bar), and at the very end, the error message attached in screen cap format appeared.
I had already had this software program approved to install from our IT head, so, I'm not sure what to do at this point.
Thanks very much-Alice Kitterman
Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com 

    On Thursday, July 8, 2021, 08:35:04 PM EDT, Tom Goddard <goddard at sonic.net> wrote:  
 
 Is there an error message when ChimeraX it fails to install? ?What step is the installer dialog showing before it fails?
 Tom


On Jul 8, 2021, at 10:28 AM, Alice Chen via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
Hello,?I'm on a Dell XPS 9500 laptop running Windows v. 10.0.2.1000. When my IT specialist tried to install it, it would run the install program but at the very end the install would fail. We were able to install the old non-X version of Chimera. Is there something we should/can do to check, settings-wise?
Cheers-Alice Kitterman
Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com_______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


  _______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


  
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From gregc at cgl.ucsf.edu  Mon Aug  9 10:11:44 2021
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 9 Aug 2021 10:11:44 -0700
Subject: [Chimera-users] Problems with installing on a Windows 10
 expedition Dell laptop
In-Reply-To: <92499663.379731.1628519018606@mail.yahoo.com>
References: <1586612241.2919889.1625765310006.ref@mail.yahoo.com>
 <1586612241.2919889.1625765310006@mail.yahoo.com>
 <21C25191-57F2-4C78-8A59-7CFE92A3D2C8@sonic.net>
 <1247078119.3231004.1626283072068@mail.yahoo.com>
 <D45EEC8C-6ABA-4EE1-BC39-F6E2BF3D0D4E@sonic.net>
 <92499663.379731.1628519018606@mail.yahoo.com>
Message-ID: <2848f45e-767e-ceff-7f60-8984349a4a32@cgl.ucsf.edu>

Hi Alice,

Since you are the customer of the antivirus software, you or your IT 
specialist need to submit ChimeraX as a false positive to the antivirus 
vendor.? Then, after that knowledge is incorporated by the antivirus 
software, it should no longer be considered a virus.? You didn't say 
this time if it was the ChimeraX installer, which is cryptographically 
signed, or if it was one of the files ChimeraX installs.? If the latter, 
then that file would be the one that you submit.? And please share which 
file is causing the problem.? I can envision a scenario where the 
antivirus software complains about a third party package in ChimeraX 
that doesn't have the latest security fix, and if that is the case, we 
could update the ChimeraX daily build to work around the issue.? But 
that is normally beyond the scope of antivirus software and would break 
lots of things besides ChimeraX.

 ??? HTH,

 ??? Greg

On 8/9/2021 7:23 AM, Alice Chen via Chimera-users wrote:
> Hi Tom,
>
> Hi, I contacted you a few weeks ago re: an error message I was 
> receiving in trying to install Chimera X onto a Windows 10 PC laptop.
> Thank you again for your help with determining that the error message 
> I received had to do with the antivirus software interfering with the 
> install.
>
> In talking with my IT specialist, there's no way for us to disable the 
> antivirus software to get the install to complete. So, do you know if 
> there might another way to get the install to complete? I was able to 
> install an older version of Chimera on that computer, so, is there a 
> possile workaround for Chimera X?
>
> Thanks again-
> Alice Kitterman
>
> Alice Y Chen AY Chen Illustration and Design 
> https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos 
> www.aliceychen.com
>
>
> On Wednesday, July 14, 2021, 01:25:16 PM EDT, Tom Goddard 
> <goddard at sonic.net> wrote:
>
>
> Using google to search for IPersistFile that appears in the error 
> message says it is probably your antivirus software interfering with 
> the installation and you may need to turn off antivirus while it 
> installs. ?It is not a ChimeraX issue. ?Good luck.
>
> https://www.thewindowsclub.com/ipersistfile-save-failed-error 
> <https://www.thewindowsclub.com/ipersistfile-save-failed-error>
>
> Tom
>
>
>> On Jul 14, 2021, at 10:17 AM, Alice Chen via Chimera-users 
>> <chimera-users at cgl.ucsf.edu> wrote:
>>
>> Hi Tom,
>> Please see below the email trail. I had my IT specialist try to 
>> install ChimeraX again, and the same thing happened: it ran through 
>> the install process (watched the progress bar), and at the very end, 
>> the error message attached in screen cap format appeared.
>>
>> I had already had this software program approved to install from our 
>> IT head, so, I'm not sure what to do at this point.
>>
>> Thanks very much-Alice Kitterman
>>
>> Alice Y Chen AY Chen Illustration and Design 
>> https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos 
>> www.aliceychen.com
>>
>>
>> On Thursday, July 8, 2021, 08:35:04 PM EDT, Tom Goddard 
>> <goddard at sonic.net> wrote:
>>
>>
>> Is there an error message when ChimeraX it fails to install? ?What 
>> step is the installer dialog showing before it fails?
>>
>> Tom
>>
>>
>>> On Jul 8, 2021, at 10:28 AM, Alice Chen via Chimera-users 
>>> <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>> wrote:
>>>
>>> Hello,
>>> I'm on a Dell XPS 9500 laptop running Windows v. 10.0.2.1000. When 
>>> my IT specialist tried to install it, it would run the install 
>>> program but at the very end the install would fail. We were able to 
>>> install the old non-X version of Chimera. Is there something we 
>>> should/can do to check, settings-wise?
>>>
>>> Cheers-Alice Kitterman
>>>
>>> Alice Y Chen AY Chen Illustration and Design 
>>> https://www.facebook.com/AYCIAD <https://www.facebook.com/AYCIAD> 
>>> https://vimeo.com/user13507144/videos 
>>> <https://vimeo.com/user13507144/videos> www.aliceychen.com 
>>> <http://www.aliceychen.com/>
>>> _______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu 
>>> <mailto:Chimera-users at cgl.ucsf.edu>
>>> Manage subscription: 
>>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users 
>>> <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: 
>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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From K.SANDOVAL1 at nuigalway.ie  Tue Aug 10 06:47:49 2021
From: K.SANDOVAL1 at nuigalway.ie (SANDOVAL, KENNETH)
Date: Tue, 10 Aug 2021 13:47:49 +0000
Subject: [Chimera-users] Copy protein orientation
Message-ID: <AM6PR01MB520789BD50D2637E8063A28DD7F79@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>

Hello,

I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:

1) Identify orientation of protein A in session 1
2) Copy that orientation
3) Apply that orientation to protein A in session 2
4) Have protein B in session 2 remain aligned to protein A despite the new orientation

Thank you,
Kenneth Sandoval
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From aychen_702 at yahoo.com  Tue Aug 10 07:55:00 2021
From: aychen_702 at yahoo.com (Alice Chen)
Date: Tue, 10 Aug 2021 14:55:00 +0000 (UTC)
Subject: [Chimera-users] Problems with installing on a Windows 10
 expedition Dell laptop
In-Reply-To: <2848f45e-767e-ceff-7f60-8984349a4a32@cgl.ucsf.edu>
References: <1586612241.2919889.1625765310006.ref@mail.yahoo.com>
 <1586612241.2919889.1625765310006@mail.yahoo.com>
 <21C25191-57F2-4C78-8A59-7CFE92A3D2C8@sonic.net>
 <1247078119.3231004.1626283072068@mail.yahoo.com>
 <D45EEC8C-6ABA-4EE1-BC39-F6E2BF3D0D4E@sonic.net>
 <92499663.379731.1628519018606@mail.yahoo.com>
 <2848f45e-767e-ceff-7f60-8984349a4a32@cgl.ucsf.edu>
Message-ID: <594557836.565565.1628607300181@mail.yahoo.com>

Hi Greg,Many thanks for your response. Our IT specialist is out this week, so I will re-connect with her next week to review what you have sent as it is beyond my scope of understanding!
To your questions about where the fail is occurring (the installer vs. one of the files being installed?), I am not sure. The installer seems to run through the entire process (we watch the progress bar go basically to the end), and afterward we get the error message that the install failed. Please see the attached screen cap.
I will for sure follow up as soon as my IT specialist returns.
Thanks so much for being diligent with my issue.
Cheers-Alice Kitterman
Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com 

    On Monday, August 9, 2021, 01:11:51 PM EDT, Greg Couch <gregc at cgl.ucsf.edu> wrote:  
 
  
Hi Alice,
 
Since you are the customer of the antivirus software, you or your IT specialist need to submit ChimeraX as a false positive to the antivirus vendor.? Then, after that knowledge is incorporated by the antivirus software, it should no longer be considered a virus.? You didn't say this time if it was the ChimeraX installer, which is cryptographically signed, or if it was one of the files ChimeraX installs.? If the latter, then that file would be the one that you submit.? And please share which file is causing the problem.? I can envision a scenario where the antivirus software complains about a third party package in ChimeraX that doesn't have the latest security fix, and if that is the case, we could update the ChimeraX daily build to work around the issue.? But that is normally beyond the scope of antivirus software and would break lots of things besides ChimeraX.
 
 
??? HTH,
 
??? Greg
 
 On 8/9/2021 7:23 AM, Alice Chen via Chimera-users wrote:
  
 
  Hi Tom, 
  Hi, I contacted you a few weeks ago re: an error message I was receiving in trying to install Chimera X onto a Windows 10 PC laptop.? Thank you again for your help with determining that the error message I received had to do with the antivirus software interfering with the install. 
  In talking with my IT specialist, there's no way for us to disable the antivirus software to get the install to complete. So, do you know if there might another way to get the install to complete? I was able to install an older version of Chimera on that computer, so, is there a possile workaround for Chimera X? 
  Thanks again- Alice Kitterman 
  Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com  
  
      On Wednesday, July 14, 2021, 01:25:16 PM EDT, Tom Goddard <goddard at sonic.net> wrote:  
  
    Using google to search for IPersistFile that appears in the error message says it is probably your antivirus software interfering with the installation and you may need to turn off antivirus while it installs. ?It is not a ChimeraX issue. ?Good luck. 
  https://www.thewindowsclub.com/ipersistfile-save-failed-error
 
   Tom 
 
 
  On Jul 14, 2021, at 10:17 AM, Alice Chen via Chimera-users <chimera-users at cgl.ucsf.edu> wrote: 
     Hi Tom, Please see below the email trail. I had my IT specialist try to install ChimeraX again, and the same thing happened: it ran through the install process (watched the progress bar), and at the very end, the error message attached in screen cap format appeared. 
  I had already had this software program approved to install from our IT head, so, I'm not sure what to do at this point. 
  Thanks very much-Alice Kitterman 
  Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com  
  
      On Thursday, July 8, 2021, 08:35:04 PM EDT, Tom Goddard <goddard at sonic.net> wrote:  
  
    Is there an error message when ChimeraX it fails to install? ?What step is the installer dialog showing before it fails? 
   Tom 
 
 
  On Jul 8, 2021, at 10:28 AM, Alice Chen via Chimera-users <chimera-users at cgl.ucsf.edu> wrote: 
     Hello,? I'm on a Dell XPS 9500 laptop running Windows v. 10.0.2.1000. When my IT specialist tried to install it, it would run the install program but at the very end the install would fail. We were able to install the old non-X version of Chimera. Is there something we should/can do to check, settings-wise? 
  Cheers-Alice Kitterman 
  Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com   _______________________________________________
 Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
 Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
   
  
        _______________________________________________
 Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
 Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
   
  
        
  _______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
   
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From ddgae at ucdavis.edu  Tue Aug 10 09:34:14 2021
From: ddgae at ucdavis.edu (David Gae)
Date: Tue, 10 Aug 2021 09:34:14 -0700
Subject: [Chimera-users] Copy protein orientation
In-Reply-To: <AM6PR01MB520789BD50D2637E8063A28DD7F79@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
References: <AM6PR01MB520789BD50D2637E8063A28DD7F79@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
Message-ID: <9631A535-F6E6-4938-B31A-BA187FABB170@ucdavis.edu>

Dear Kenneth,

Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files.
Then work on the problem from there on. This seems like a possible direction to try? 

Sincerely,
David 

> On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
> 
> 1) Identify orientation of protein A in session 1
> 2) Copy that orientation
> 3) Apply that orientation to protein A in session 2
> 4) Have protein B in session 2 remain aligned to protein A despite the new orientation
> 
> Thank you,
> Kenneth Sandoval
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From meng at cgl.ucsf.edu  Tue Aug 10 10:00:27 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 10 Aug 2021 10:00:27 -0700
Subject: [Chimera-users] Copy protein orientation
In-Reply-To: <9631A535-F6E6-4938-B31A-BA187FABB170@ucdavis.edu>
References: <AM6PR01MB520789BD50D2637E8063A28DD7F79@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <9631A535-F6E6-4938-B31A-BA187FABB170@ucdavis.edu>
Message-ID: <8B85B033-DB06-46A5-8EE0-6669FAAC962D@cgl.ucsf.edu>

Hello Kenneth,
Similarly to David I was going to say that the better approach would have been to create only a single session with the aligned proteins and simply hide and show model B to make your two figures.

However, given the situation you have now, maybe:
(1) in session 1, use "matrixget  <file-pathname>" to save file with transformation of protein A. See:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html>

(2) in session 2, use "matrixset  <file-pathname>" to apply the transformation from the file you saved in part 1, assuming protein A has the same model number as in session 1.  However, that will probably ignore protein B, so you may need step 3.

(3) in session 2, if protein A is model #0 and protein B is model #1, use command "matrixcopy #0 #1"
See: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>

I am not completely sure it will work since it depends on how you got the TM-align alignment in there, but it has at least a chance.  Also you may need to adjust the command if you have different model numbers.

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

> On Aug 10, 2021, at 9:34 AM, David Gae via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Kenneth,
> 
> Maybe it be best to put both protein A and B in the same cartisen coordinate system by alignment such as matchmaker program, then save the PDB files.
> Then work on the problem from there on. This seems like a possible direction to try? 
> 
> Sincerely,
> David 
> 
>> On Aug 10, 2021, at 6:47 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Hello,
>> 
>> I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following:
>> 
>> 1) Identify orientation of protein A in session 1
>> 2) Copy that orientation
>> 3) Apply that orientation to protein A in session 2
>> 4) Have protein B in session 2 remain aligned to protein A despite the new orientation
>> 
>> Thank you,
>> Kenneth Sandoval
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From gregc at cgl.ucsf.edu  Tue Aug 10 13:11:48 2021
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Tue, 10 Aug 2021 13:11:48 -0700
Subject: [Chimera-users] Problems with installing on a Windows 10
 expedition Dell laptop
In-Reply-To: <594557836.565565.1628607300181@mail.yahoo.com>
References: <1586612241.2919889.1625765310006.ref@mail.yahoo.com>
 <1586612241.2919889.1625765310006@mail.yahoo.com>
 <21C25191-57F2-4C78-8A59-7CFE92A3D2C8@sonic.net>
 <1247078119.3231004.1626283072068@mail.yahoo.com>
 <D45EEC8C-6ABA-4EE1-BC39-F6E2BF3D0D4E@sonic.net>
 <92499663.379731.1628519018606@mail.yahoo.com>
 <2848f45e-767e-ceff-7f60-8984349a4a32@cgl.ucsf.edu>
 <594557836.565565.1628607300181@mail.yahoo.com>
Message-ID: <5c1f038d-a9a2-06e5-9dfd-8ced116a6b34@cgl.ucsf.edu>

Hi Alice,

Please take a look at 
https://www.thewindowsclub.com/ipersistfile-save-failed-error.? It 
addresses the exact issue you had.? From your screenshot, it looks like 
the failure was when the ChimeraX desktop shortcut was being installed, 
so option (3) from that web page, unchecking the option to create a 
desktop shortcut, might be sufficient to get ChimeraX installed.

 ??? -- Greg

On 8/10/2021 7:55 AM, Alice Chen wrote:
> Hi Greg,
> Many thanks for your response. Our IT specialist is out this week, so 
> I will re-connect with her next week to review what you have sent as 
> it is beyond my scope of understanding!
>
> To your questions about where the fail is occurring (the installer vs. 
> one of the files being installed?), I am not sure. The installer seems 
> to run through the entire process (we watch the progress bar go 
> basically to the end), and afterward we get the error message that the 
> install failed. Please see the attached screen cap.
>
> I will for sure follow up as soon as my IT specialist returns.
>
> Thanks so much for being diligent with my issue.
>
> Cheers-Alice Kitterman
>
> Alice Y Chen AY Chen Illustration and Design 
> https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos 
> www.aliceychen.com
>
>
> On Monday, August 9, 2021, 01:11:51 PM EDT, Greg Couch 
> <gregc at cgl.ucsf.edu> wrote:
>
>
> Hi Alice,
>
> Since you are the customer of the antivirus software, you or your IT 
> specialist need to submit ChimeraX as a false positive to the 
> antivirus vendor.? Then, after that knowledge is incorporated by the 
> antivirus software, it should no longer be considered a virus. You 
> didn't say this time if it was the ChimeraX installer, which is 
> cryptographically signed, or if it was one of the files ChimeraX 
> installs.? If the latter, then that file would be the one that you 
> submit.? And please share which file is causing the problem.? I can 
> envision a scenario where the antivirus software complains about a 
> third party package in ChimeraX that doesn't have the latest security 
> fix, and if that is the case, we could update the ChimeraX daily build 
> to work around the issue. But that is normally beyond the scope of 
> antivirus software and would break lots of things besides ChimeraX.
>
> ??? HTH,
>
> ??? Greg
>
> On 8/9/2021 7:23 AM, Alice Chen via Chimera-users wrote:
> Hi Tom,
>
> Hi, I contacted you a few weeks ago re: an error message I was 
> receiving in trying to install Chimera X onto a Windows 10 PC laptop.
> Thank you again for your help with determining that the error message 
> I received had to do with the antivirus software interfering with the 
> install.
>
> In talking with my IT specialist, there's no way for us to disable the 
> antivirus software to get the install to complete. So, do you know if 
> there might another way to get the install to complete? I was able to 
> install an older version of Chimera on that computer, so, is there a 
> possile workaround for Chimera X?
>
> Thanks again-
> Alice Kitterman
>
> Alice Y Chen AY Chen Illustration and Design 
> https://www.facebook.com/AYCIAD <https://www.facebook.com/AYCIAD> 
> https://vimeo.com/user13507144/videos 
> <https://vimeo.com/user13507144/videos> www.aliceychen.com 
> <http://www.aliceychen.com>
>
>
> On Wednesday, July 14, 2021, 01:25:16 PM EDT, Tom Goddard 
> <goddard at sonic.net> <mailto:goddard at sonic.net> wrote:
>
>
> Using google to search for IPersistFile that appears in the error 
> message says it is probably your antivirus software interfering with 
> the installation and you may need to turn off antivirus while it 
> installs. ?It is not a ChimeraX issue. ?Good luck.
>
> https://www.thewindowsclub.com/ipersistfile-save-failed-error 
> <https://www.thewindowsclub.com/ipersistfile-save-failed-error>
>
> Tom
>
>
>> On Jul 14, 2021, at 10:17 AM, Alice Chen via Chimera-users 
>> <chimera-users at cgl.ucsf.edu> <mailto:chimera-users at cgl.ucsf.edu> wrote:
>>
>> Hi Tom,
>> Please see below the email trail. I had my IT specialist try to 
>> install ChimeraX again, and the same thing happened: it ran through 
>> the install process (watched the progress bar), and at the very end, 
>> the error message attached in screen cap format appeared.
>>
>> I had already had this software program approved to install from our 
>> IT head, so, I'm not sure what to do at this point.
>>
>> Thanks very much-Alice Kitterman
>>
>> Alice Y Chen AY Chen Illustration and Design 
>> https://www.facebook.com/AYCIAD <https://www.facebook.com/AYCIAD> 
>> https://vimeo.com/user13507144/videos 
>> <https://vimeo.com/user13507144/videos> www.aliceychen.com 
>> <http://www.aliceychen.com>
>>
>>
>> On Thursday, July 8, 2021, 08:35:04 PM EDT, Tom Goddard 
>> <goddard at sonic.net> <mailto:goddard at sonic.net> wrote:
>>
>>
>> Is there an error message when ChimeraX it fails to install? ?What 
>> step is the installer dialog showing before it fails?
>>
>> Tom
>>
>>
>>> On Jul 8, 2021, at 10:28 AM, Alice Chen via Chimera-users 
>>> <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>> wrote:
>>>
>>> Hello,
>>> I'm on a Dell XPS 9500 laptop running Windows v. 10.0.2.1000. When 
>>> my IT specialist tried to install it, it would run the install 
>>> program but at the very end the install would fail. We were able to 
>>> install the old non-X version of Chimera. Is there something we 
>>> should/can do to check, settings-wise?
>>>
>>> Cheers-Alice Kitterman
>>>
>>> Alice Y Chen AY Chen Illustration and Design 
>>> https://www.facebook.com/AYCIAD <https://www.facebook.com/AYCIAD> 
>>> https://vimeo.com/user13507144/videos 
>>> <https://vimeo.com/user13507144/videos> www.aliceychen.com 
>>> <http://www.aliceychen.com/>
>>> _______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu 
>>> <mailto:Chimera-users at cgl.ucsf.edu>
>>> Manage subscription: 
>>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users 
>>> <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>>>
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu 
>> <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: 
>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users 
>> <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>
>
> _______________________________________________
> Chimera-users mailing list:Chimera-users at cgl.ucsf.edu  <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users  <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From palusoori at gmail.com  Wed Aug 11 02:58:49 2021
From: palusoori at gmail.com (Seera Suryanarayana)
Date: Wed, 11 Aug 2021 15:28:49 +0530
Subject: [Chimera-users] How to get random velocities?
Message-ID: <CAAr94NNUMbKp31t3aXuD8O+gPV33S++e_8yNp=HgVzk0dsX5EA@mail.gmail.com>

Dear chimera users,

Dear VMD users,
I was asked to do simulations five times with the same starting structure
and number of processors. But the velocities should be different. Here my
query is "How do you generate velocities in the gromacs?".

I request you to guide me how to do it.

Thanks in advance
Surya
Graduate student
India.
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From meng at cgl.ucsf.edu  Wed Aug 11 08:02:36 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 11 Aug 2021 08:02:36 -0700
Subject: [Chimera-users] How to get random velocities?
In-Reply-To: <CAAr94NNUMbKp31t3aXuD8O+gPV33S++e_8yNp=HgVzk0dsX5EA@mail.gmail.com>
References: <CAAr94NNUMbKp31t3aXuD8O+gPV33S++e_8yNp=HgVzk0dsX5EA@mail.gmail.com>
Message-ID: <D5D024B3-D86F-4D67-8112-EC3AA45106DE@cgl.ucsf.edu>

Hi Surya,
This e-mail address is for Chimera questions... we are not experts in other programs.

For Gromacs, see its own documentation, help archive, etc.
<https://manual.gromacs.org/current/user-guide/mdp-options.html>

I can only say that molecular dynamics (MD) means that the atoms are moving, so they have velocities.  There are several methods for assigning and adjusting the velocities in MD.  

In the Gromacs MD documentation try searching for "velocity generation" and "velocity" to see all those parameters.
<https://manual.gromacs.org/current/user-guide/mdp-options.html>

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


> On Aug 11, 2021, at 2:58 AM, Seera Suryanarayana via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear chimera users,
> 
> Dear VMD users,
> I was asked to do simulations five times with the same starting structure and number of processors. But the velocities should be different. Here my query is "How do you generate velocities in the gromacs?".
> 
> I request you to guide me how to do it.
> 
> Thanks in advance
> Surya
> Graduate student
> India.



From meng at cgl.ucsf.edu  Wed Aug 11 08:06:04 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 11 Aug 2021 08:06:04 -0700
Subject: [Chimera-users] How to get random velocities?
In-Reply-To: <D5D024B3-D86F-4D67-8112-EC3AA45106DE@cgl.ucsf.edu>
References: <CAAr94NNUMbKp31t3aXuD8O+gPV33S++e_8yNp=HgVzk0dsX5EA@mail.gmail.com>
 <D5D024B3-D86F-4D67-8112-EC3AA45106DE@cgl.ucsf.edu>
Message-ID: <AFD465BB-EEC9-4543-8258-823C4B387994@cgl.ucsf.edu>



> On Aug 11, 2021, at 8:02 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Surya,
> This e-mail address is for Chimera questions... we are not experts in other programs.
> 
> For Gromacs, see its own documentation, help archive, etc.
> <https://manual.gromacs.org/current/user-guide/mdp-options.html>

Sorry, I put the wrong link there.  Instead it should be the following (but you could just use Google to find it, like I did):
<https://www.gromacs.org/Support>

> 
> I can only say that molecular dynamics (MD) means that the atoms are moving, so they have velocities.  There are several methods for assigning and adjusting the velocities in MD.  
> 
> In the Gromacs MD documentation try searching for "velocity generation" and "velocity" to see all those parameters.
> <https://manual.gromacs.org/current/user-guide/mdp-options.html>
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Aug 11, 2021, at 2:58 AM, Seera Suryanarayana via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Dear chimera users,
>> 
>> Dear VMD users,
>> I was asked to do simulations five times with the same starting structure and number of processors. But the velocities should be different. Here my query is "How do you generate velocities in the gromacs?".
>> 
>> I request you to guide me how to do it.
>> 
>> Thanks in advance
>> Surya
>> Graduate student
>> India.
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From tigerwang26 at yahoo.com  Sun Aug 15 16:47:39 2021
From: tigerwang26 at yahoo.com (tiger wang)
Date: Sun, 15 Aug 2021 23:47:39 +0000 (UTC)
Subject: [Chimera-users] Fc dimer fall apart after fusion with a GS linker
References: <620261718.484638.1629071259698.ref@mail.yahoo.com>
Message-ID: <620261718.484638.1629071259698@mail.yahoo.com>

Dear Ms/Mr helper:
I encounted an issue when I try to fuse one (G4S)x linker to one of the Fc "C" terminal using "join bond". Once selected the "C" atom on Fc C terminal and "N" atom on (G4S)x N terminal and hit "apply" button, the Fc dimer fall apart but the (G4S)x linker was connected to the C terminal of Fc. How to avoid the Fc dimer from falling apart??
Thanks very much for your help
Sincerely?
TW
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From meng at cgl.ucsf.edu  Mon Aug 16 07:58:35 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 16 Aug 2021 07:58:35 -0700
Subject: [Chimera-users] Fc dimer fall apart after fusion with a GS
	linker
In-Reply-To: <620261718.484638.1629071259698@mail.yahoo.com>
References: <620261718.484638.1629071259698.ref@mail.yahoo.com>
 <620261718.484638.1629071259698@mail.yahoo.com>
Message-ID: <ECD9087A-756B-4D57-B7EC-C375AE47B460@cgl.ucsf.edu>

Hi TW,
My only guess is that these parts are originally in two different models and you are using the Join Models panel in Build Structure to form "C-N peptide bond."  In that case, make sure you are setting the "Move atoms on [...] side" option so that it moves the linker part, not the Fc part.  You said the linker is the part with "N" selected, so try:

Move atoms on [selected N atom] side

See the help:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>

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

> On Aug 15, 2021, at 4:47 PM, tiger wang via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Ms/Mr helper:
> I encounted an issue when I try to fuse one (G4S)x linker to one of the Fc "C" terminal using "join bond". Once selected the "C" atom on Fc C terminal and "N" atom on (G4S)x N terminal and hit "apply" button, the Fc dimer fall apart but the (G4S)x linker was connected to the C terminal of Fc. How to avoid the Fc dimer from falling apart? 
> Thanks very much for your help
> Sincerely 
> TW



From Josh.Moon at kzoo.edu  Tue Aug 17 10:10:45 2021
From: Josh.Moon at kzoo.edu (Josh Moon)
Date: Tue, 17 Aug 2021 17:10:45 +0000
Subject: [Chimera-users] Hollow Sticks When Exporting as STLs?
Message-ID: <CH0PR12MB5234ECBC0DE4971F0596AEE982FE9@CH0PR12MB5234.namprd12.prod.outlook.com>

Hello,

I hope to make this question as direct and simple as I can!

When I export a scene of a molecule displayed as a ball-and-stick as a STL, I find that many of my "stick" portions are hollow.  This creates thin, weak walls for 3D printing.  I've included a screenshot of an intended plane cut from Meshmixer so that you can see the internal structure.

What am I doing incorrectly?  Is there something I can do in Chimera to export a solid object with no "hollow tubes."  Fixing this with 3d programs can be time consuming.

Sincere thanks,
Josh
-----------------------------------------
Josh Moon, Ph.D. (he/him/his)
Educational Technology Specialist
Kalamazoo College
(269) 337-7415

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From goddard at sonic.net  Tue Aug 17 11:49:47 2021
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 17 Aug 2021 11:49:47 -0700
Subject: [Chimera-users] Hollow Sticks When Exporting as STLs?
In-Reply-To: <CH0PR12MB5234ECBC0DE4971F0596AEE982FE9@CH0PR12MB5234.namprd12.prod.outlook.com>
References: <CH0PR12MB5234ECBC0DE4971F0596AEE982FE9@CH0PR12MB5234.namprd12.prod.outlook.com>
Message-ID: <DF4A1D51-38E9-4D60-BAC5-4F6D3BD33F40@sonic.net>

Hi Josh,

  You are right that Chimera makes bonds as cylinders with no end caps and 3D printer software sometimes has trouble with that.  If the cylinders had end caps then they would probably be treated as solid for 3D printing but this slows down rendering by adding end caps that cannot be seen, so Chimera does not do that.  Even with end caps, the atom sphere intersects the bond cylinder and in the past I have seen 3D printers make the overlap between the two hollow (using old uPrint printer).  What the 3D printer software really wants is a single closed mesh.  That is computationally very difficult to produce in molecular visualization software so I don't know any that do it.  Instead post processing software needs to fix the mesh problems.  I don't know what the current best methods are to do that -- it was very difficult to achieve several years ago when I used to make 3D prints.

  Here is a nice web page on Chimera 3D printing

	https://openwetware.org/wiki/UCSF_Chimera_for_3D_Printing <https://openwetware.org/wiki/UCSF_Chimera_for_3D_Printing>

  The NIH Print Exchange are experts at making printable models using Chimera -- you might use their pipeline or read about or ask how they do it.

  I see some old 2013 info when I google for chimera 3d print ball and stick.

  I think ultimately this is a hard problem to solve and you have to find the right software that can make good closed meshes, or good toolpath software that can deal with meshes that have holes.

	Tom


> On Aug 17, 2021, at 10:10 AM, Josh Moon via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
>  
> I hope to make this question as direct and simple as I can!
>  
> When I export a scene of a molecule displayed as a ball-and-stick as a STL, I find that many of my ?stick? portions are hollow.  This creates thin, weak walls for 3D printing.  I?ve included a screenshot of an intended plane cut from Meshmixer so that you can see the internal structure.
>  
> What am I doing incorrectly?  Is there something I can do in Chimera to export a solid object with no ?hollow tubes.?  Fixing this with 3d programs can be time consuming.
>  
> Sincere thanks,
> Josh
> -----------------------------------------
> Josh Moon, Ph.D. (he/him/his)
> Educational Technology Specialist
> Kalamazoo College
> (269) 337-7415
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From deyp7084 at gmail.com  Mon Aug 23 10:51:04 2021
From: deyp7084 at gmail.com (Pritam Dey)
Date: Mon, 23 Aug 2021 23:21:04 +0530
Subject: [Chimera-users] Chimera not responding
Message-ID: <CAGqEWP+PbMbEtCjK952ytfOUVbWkhYdAa0Z7pQQo2V0GQ9mJRw@mail.gmail.com>

Cannot execute 'gzip': no automatic decompression of .Z files

Return code: -1073741819
Press return or enter to to exit
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From gregc at cgl.ucsf.edu  Mon Aug 23 11:08:48 2021
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Mon, 23 Aug 2021 11:08:48 -0700
Subject: [Chimera-users] Chimera not responding
In-Reply-To: <CAGqEWP+PbMbEtCjK952ytfOUVbWkhYdAa0Z7pQQo2V0GQ9mJRw@mail.gmail.com>
References: <CAGqEWP+PbMbEtCjK952ytfOUVbWkhYdAa0Z7pQQo2V0GQ9mJRw@mail.gmail.com>
Message-ID: <bf8aec27-6003-8d50-6555-b028dc78540b@cgl.ucsf.edu>

So it appears you are trying to run Chimera on Microsoft Windows.? The 
warning about gzip is normal and should be ignored. The most likely 
cause of your error is that your graphics driver is out of date.? So 
please update your graphics driver and try again.? If it still doesn't 
work, then please use our online bug submission form, 
https://www.cgl.ucsf.edu/cgi-bin/chimera_bug_report_2.py, and attach the 
output from the dxdiag program (type dxdiag into the Windows search bar 
by the Start button, click on the dxdiag program it finds, then click on 
"Save All Information..." to save all of the information, and attach 
that file.)

 ??? Good luck,

 ??? Greg

On 8/23/2021 10:51 AM, Pritam Dey via Chimera-users wrote:
> Cannot execute 'gzip': no automatic decompression of .Z files
>
> Return code: -1073741819
> Press return or enter to to exit
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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From dysong at g.harvard.edu  Wed Aug 25 12:49:26 2021
From: dysong at g.harvard.edu (Song, David)
Date: Wed, 25 Aug 2021 15:49:26 -0400
Subject: [Chimera-users] 3D Visualization
Message-ID: <CAMXkz9A7wBq8dH8e7FhPa4+zOYtb8sHM2KN8ViOoCJ7CdAgo5w@mail.gmail.com>

Hi,

My name is Dave Song, and I am a graduate student interested in visualizing
protein structures in 3D. I was wondering if you had any recommendations in
regards to computer hardware requirements for maximum performance while
using Chimera/ChimeraX. Additionally, do you have any suggestions on
monitors and 3D glasses that work well with Chimera?

Thank you for your time, and I look forward to hearing from you.

Best,
Dave
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From goddard at sonic.net  Wed Aug 25 14:10:57 2021
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 25 Aug 2021 14:10:57 -0700
Subject: [Chimera-users] 3D Visualization
In-Reply-To: <CAMXkz9A7wBq8dH8e7FhPa4+zOYtb8sHM2KN8ViOoCJ7CdAgo5w@mail.gmail.com>
References: <CAMXkz9A7wBq8dH8e7FhPa4+zOYtb8sHM2KN8ViOoCJ7CdAgo5w@mail.gmail.com>
Message-ID: <E08449CE-9D80-4645-9417-DA089BB0559B@sonic.net>

Hi Dave,

I would recommend ChimeraX, not Chimera for large protein structures (more than 100,000 atoms).  Chimera has extremely slow handling of mmCIF files used by the PDB for all structures over 100,000 atoms, can take minutes to load, while ChimeraX loads in seconds.

Computer recommendations would be the same for Chimera or ChimeraX.  Fast graphics (video gamer cards) helps, an SSD drive for fast data read helps, 16 Gbytes fine for most data, unless you work with exceptionally large (million atom) structures then 32 Gb or more is useful.

Previous discussions of ChimeraX hardware found by Google

https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-September/001504.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-September/001504.html>
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-October/001585.html
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-July/000271.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-July/000271.html>
...

3D glasses other than virtual reality are all but dead.  ChimeraX works well with VR.  Chimera does not support VR.

A high resolution monitor (e.g. 4K) is nice for looking at large structures if you don't like seeing all the screen pixels.

	Tom


> On Aug 25, 2021, at 12:49 PM, Song, David via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> 
> My name is Dave Song, and I am a graduate student interested in visualizing protein structures in 3D. I was wondering if you had any recommendations in regards to computer hardware requirements for maximum performance while using Chimera/ChimeraX. Additionally, do you have any suggestions on monitors and 3D glasses that work well with Chimera? 
> 
> Thank you for your time, and I look forward to hearing from you.
> 
> Best,
> Dave
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From Athena.Andreosso at qimrberghofer.edu.au  Wed Aug 25 17:03:19 2021
From: Athena.Andreosso at qimrberghofer.edu.au (Athena Andreosso)
Date: Thu, 26 Aug 2021 00:03:19 +0000
Subject: [Chimera-users] ITasser model looks different once PDB opened in
	UCSF Chimera
Message-ID: <e532f9e0400340b99a54aafadd08fb11@qimrberghofer.edu.au>

Hi,

I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page - it had less beta strands.  When I clicked on model 2 it was better but there's still a visible discrepancy.

Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ?

Any help is appreciated.

Cheers

Athena Andreosso, D.Phil.  | Research Officer
Mucosal Immunology
QIMR Berghofer Medical Research Institute
e AthenaAndreosso at qimrberghofer.edu.au<mailto:AthenaAndreosso at qimrberghofer.edu.au>  |  www.qimr.edu.au<http://www.qimr.edu.au/>
300 Herston Road, Herston QLD 4006



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From meng at cgl.ucsf.edu  Wed Aug 25 17:36:43 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 25 Aug 2021 17:36:43 -0700
Subject: [Chimera-users] ITasser model looks different once PDB opened
 in UCSF Chimera
In-Reply-To: <e532f9e0400340b99a54aafadd08fb11@qimrberghofer.edu.au>
References: <e532f9e0400340b99a54aafadd08fb11@qimrberghofer.edu.au>
Message-ID: <D0C8C772-CCFF-4AFA-A386-E6D69A0095EE@cgl.ucsf.edu>

Hi Athena,
You are not doing anything wrong.

Although the atomic coordinates are identical, it is simply that different programs have different methods for deciding what is helix and strand.  When you get an experimental PDB file from the databank, the file contains information on where these were assigned, and then Chimera uses that.  However, when the PDB file does not contain such information, Chimera runs its own calculation to figure out what is strand and helix.  Again, the model atomic positions are not affected at all.  It is only how the ribbon is drawn.

Presumably the iTasser website uses some different method to figure out what is strand and helix, but the iTasser output download file only contains the atomic coordinates, not this extra information.

You can try re-running the calculation in Chimera with the "ksdssp" command using different (nondefault) parameter settings, or you can manually reassign secondary structure to specific ranges of residue numbers to control how the ribbon is drawn.

ksdssp command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

manual reassignment examples are given in previous posts, e.g.
<https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013106.html>
... and in this tutorial
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.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 Aug 25, 2021, at 5:03 PM, Athena Andreosso via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,  
> I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page ? it had less beta strands.  When I clicked on model 2 it was better but there?s still a visible discrepancy. 
>  
> Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ?
>  
> Any help is appreciated.  
> Cheers
> Athena Andreosso, D.Phil.  | Research Officer 
> Mucosal Immunology  
> QIMR Berghofer Medical Research Institute
> e AthenaAndreosso at qimrberghofer.edu.au  |  www.qimr.edu.au
> 300 Herston Road, Herston QLD 4006



From Athena.Andreosso at qimrberghofer.edu.au  Wed Aug 25 17:48:12 2021
From: Athena.Andreosso at qimrberghofer.edu.au (Athena Andreosso)
Date: Thu, 26 Aug 2021 00:48:12 +0000
Subject: [Chimera-users] ITasser model looks different once PDB opened
 in UCSF Chimera
In-Reply-To: <D0C8C772-CCFF-4AFA-A386-E6D69A0095EE@cgl.ucsf.edu>
References: <e532f9e0400340b99a54aafadd08fb11@qimrberghofer.edu.au>
 <D0C8C772-CCFF-4AFA-A386-E6D69A0095EE@cgl.ucsf.edu>
Message-ID: <62d86fd6970b46aaa40d47eac52f031e@qimrberghofer.edu.au>

Hi Elaine, 

Thank you for your swift reply. 

Well so I know ITASSER uses other known protein structures and superimposes them on unknown proteins to obtain models - would this information not be included in the PDB file? If not - is it possible to tell Chimera to superimpose a known protein on my model ?

Kind regards

Athena Andreosso, D.Phil.??| Research Officer 
Mucosal Immunology??
QIMR Berghofer Medical Research Institute
e AthenaAndreosso at qimrberghofer.edu.au??|??www.qimr.edu.au
300 Herston Road, Herston QLD 4006




-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Thursday, 26 August 2021 10:37 AM
To: Athena Andreosso <Athena.Andreosso at qimrberghofer.edu.au>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] ITasser model looks different once PDB opened in UCSF Chimera

Hi Athena,
You are not doing anything wrong.

Although the atomic coordinates are identical, it is simply that different programs have different methods for deciding what is helix and strand.  When you get an experimental PDB file from the databank, the file contains information on where these were assigned, and then Chimera uses that.  However, when the PDB file does not contain such information, Chimera runs its own calculation to figure out what is strand and helix.  Again, the model atomic positions are not affected at all.  It is only how the ribbon is drawn.

Presumably the iTasser website uses some different method to figure out what is strand and helix, but the iTasser output download file only contains the atomic coordinates, not this extra information.

You can try re-running the calculation in Chimera with the "ksdssp" command using different (nondefault) parameter settings, or you can manually reassign secondary structure to specific ranges of residue numbers to control how the ribbon is drawn.

ksdssp command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

manual reassignment examples are given in previous posts, e.g.
<https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013106.html>
... and in this tutorial
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.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 Aug 25, 2021, at 5:03 PM, Athena Andreosso via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi,
> I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page ? it had less beta strands.  When I clicked on model 2 it was better but there?s still a visible discrepancy.
>
> Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ?
>
> Any help is appreciated.
> Cheers
> Athena Andreosso, D.Phil.  | Research Officer Mucosal Immunology QIMR 
> Berghofer Medical Research Institute e 
> AthenaAndreosso at qimrberghofer.edu.au  |  www.qimr.edu.au
> 300 Herston Road, Herston QLD 4006

[EXTERNAL EMAIL] This message originates from an external email address, please exercise caution when clicking any links or opening attachments. If you believe the sender is impersonating someone at QIMR Berghofer, please forward this message to phishing at qimrberghofer.edu.au.


From meng at cgl.ucsf.edu  Wed Aug 25 17:59:09 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 25 Aug 2021 17:59:09 -0700
Subject: [Chimera-users] ITasser model looks different once PDB opened
 in UCSF Chimera
In-Reply-To: <62d86fd6970b46aaa40d47eac52f031e@qimrberghofer.edu.au>
References: <e532f9e0400340b99a54aafadd08fb11@qimrberghofer.edu.au>
 <D0C8C772-CCFF-4AFA-A386-E6D69A0095EE@cgl.ucsf.edu>
 <62d86fd6970b46aaa40d47eac52f031e@qimrberghofer.edu.au>
Message-ID: <1728E129-1A07-479A-AC7A-60D8B93DF8BB@cgl.ucsf.edu>

Hi Athena,
As long as the format of the PDB file is correct, Chimera is not hiding any structures that are in it: it is just showing whatever proteins are included in the file.  I don't know what the iTasser website does or whether it allows you to download any of the additional stuff that is displaying, or if it tells you which structures were used as the templates for modeling.  As far as I know, you would have to open those other structures separately in Chimera and then superimpose them, e.g. using Matchmaker (if you want to use Chimera, that is).

Discussion of ways to superimpose structures in Chimera:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

Elaine

> On Aug 25, 2021, at 5:48 PM, Athena Andreosso via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine, 
> 
> Thank you for your swift reply. 
> 
> Well so I know ITASSER uses other known protein structures and superimposes them on unknown proteins to obtain models - would this information not be included in the PDB file? If not - is it possible to tell Chimera to superimpose a known protein on my model ?
> 
> Kind regards
> 
> Athena Andreosso, D.Phil.  | Research Officer 
> Mucosal Immunology  
> QIMR Berghofer Medical Research Institute
> e AthenaAndreosso at qimrberghofer.edu.au  |  www.qimr.edu.au
> 300 Herston Road, Herston QLD 4006
> 
> 
> 
> 
> -----Original Message-----
> From: Elaine Meng <meng at cgl.ucsf.edu> 
> Sent: Thursday, 26 August 2021 10:37 AM
> To: Athena Andreosso <Athena.Andreosso at qimrberghofer.edu.au>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] ITasser model looks different once PDB opened in UCSF Chimera
> 
> Hi Athena,
> You are not doing anything wrong.
> 
> Although the atomic coordinates are identical, it is simply that different programs have different methods for deciding what is helix and strand.  When you get an experimental PDB file from the databank, the file contains information on where these were assigned, and then Chimera uses that.  However, when the PDB file does not contain such information, Chimera runs its own calculation to figure out what is strand and helix.  Again, the model atomic positions are not affected at all.  It is only how the ribbon is drawn.
> 
> Presumably the iTasser website uses some different method to figure out what is strand and helix, but the iTasser output download file only contains the atomic coordinates, not this extra information.
> 
> You can try re-running the calculation in Chimera with the "ksdssp" command using different (nondefault) parameter settings, or you can manually reassign secondary structure to specific ranges of residue numbers to control how the ribbon is drawn.
> 
> ksdssp command:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
> 
> manual reassignment examples are given in previous posts, e.g.
> <https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013106.html>
> ... and in this tutorial
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.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 Aug 25, 2021, at 5:03 PM, Athena Andreosso via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Hi,
>> I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page ? it had less beta strands.  When I clicked on model 2 it was better but there?s still a visible discrepancy.
>> 
>> Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ?
>> 
>> Any help is appreciated.
>> Cheers
>> Athena Andreosso, D.Phil.  | Research Officer Mucosal Immunology QIMR 
>> Berghofer Medical Research Institute e 
>> AthenaAndreosso at qimrberghofer.edu.au  |  www.qimr.edu.au
>> 300 Herston Road, Herston QLD 4006
> 
> [EXTERNAL EMAIL] This message originates from an external email address, please exercise caution when clicking any links or opening attachments. If you believe the sender is impersonating someone at QIMR Berghofer, please forward this message to phishing at qimrberghofer.edu.au.
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From Athena.Andreosso at qimrberghofer.edu.au  Wed Aug 25 18:04:15 2021
From: Athena.Andreosso at qimrberghofer.edu.au (Athena Andreosso)
Date: Thu, 26 Aug 2021 01:04:15 +0000
Subject: [Chimera-users] ITasser model looks different once PDB opened
 in UCSF Chimera
In-Reply-To: <1728E129-1A07-479A-AC7A-60D8B93DF8BB@cgl.ucsf.edu>
References: <e532f9e0400340b99a54aafadd08fb11@qimrberghofer.edu.au>
 <D0C8C772-CCFF-4AFA-A386-E6D69A0095EE@cgl.ucsf.edu>
 <62d86fd6970b46aaa40d47eac52f031e@qimrberghofer.edu.au>
 <1728E129-1A07-479A-AC7A-60D8B93DF8BB@cgl.ucsf.edu>
Message-ID: <8ad8c767f86a4c20b84aae1fdad7aa3d@qimrberghofer.edu.au>

Amazing. Thanks Elaine!

Athena Andreosso, D.Phil.??| Research Officer 
Mucosal Immunology??
QIMR Berghofer Medical Research Institute
e AthenaAndreosso at qimrberghofer.edu.au??|??www.qimr.edu.au
300 Herston Road, Herston QLD 4006




-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Thursday, 26 August 2021 10:59 AM
To: Athena Andreosso <Athena.Andreosso at qimrberghofer.edu.au>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] ITasser model looks different once PDB opened in UCSF Chimera

Hi Athena,
As long as the format of the PDB file is correct, Chimera is not hiding any structures that are in it: it is just showing whatever proteins are included in the file.  I don't know what the iTasser website does or whether it allows you to download any of the additional stuff that is displaying, or if it tells you which structures were used as the templates for modeling.  As far as I know, you would have to open those other structures separately in Chimera and then superimpose them, e.g. using Matchmaker (if you want to use Chimera, that is).

Discussion of ways to superimpose structures in Chimera:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

Elaine

> On Aug 25, 2021, at 5:48 PM, Athena Andreosso via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> Thank you for your swift reply. 
> 
> Well so I know ITASSER uses other known protein structures and superimposes them on unknown proteins to obtain models - would this information not be included in the PDB file? If not - is it possible to tell Chimera to superimpose a known protein on my model ?
> 
> Kind regards
> 
> Athena Andreosso, D.Phil.  | Research Officer Mucosal Immunology QIMR 
> Berghofer Medical Research Institute e 
> AthenaAndreosso at qimrberghofer.edu.au  |  www.qimr.edu.au
> 300 Herston Road, Herston QLD 4006
> 
> 
> 
> 
> -----Original Message-----
> From: Elaine Meng <meng at cgl.ucsf.edu> 
> Sent: Thursday, 26 August 2021 10:37 AM
> To: Athena Andreosso <Athena.Andreosso at qimrberghofer.edu.au>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] ITasser model looks different once PDB opened in UCSF Chimera
> 
> Hi Athena,
> You are not doing anything wrong.
> 
> Although the atomic coordinates are identical, it is simply that different programs have different methods for deciding what is helix and strand.  When you get an experimental PDB file from the databank, the file contains information on where these were assigned, and then Chimera uses that.  However, when the PDB file does not contain such information, Chimera runs its own calculation to figure out what is strand and helix.  Again, the model atomic positions are not affected at all.  It is only how the ribbon is drawn.
> 
> Presumably the iTasser website uses some different method to figure out what is strand and helix, but the iTasser output download file only contains the atomic coordinates, not this extra information.
> 
> You can try re-running the calculation in Chimera with the "ksdssp" command using different (nondefault) parameter settings, or you can manually reassign secondary structure to specific ranges of residue numbers to control how the ribbon is drawn.
> 
> ksdssp command:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
> 
> manual reassignment examples are given in previous posts, e.g.
> <https://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013106.html>
> ... and in this tutorial
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.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 Aug 25, 2021, at 5:03 PM, Athena Andreosso via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Hi,
>> I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page ? it had less beta strands.  When I clicked on model 2 it was better but there?s still a visible discrepancy.
>> 
>> Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ?
>> 
>> Any help is appreciated.
>> Cheers
>> Athena Andreosso, D.Phil.  | Research Officer Mucosal Immunology QIMR 
>> Berghofer Medical Research Institute e 
>> AthenaAndreosso at qimrberghofer.edu.au  |  www.qimr.edu.au
>> 300 Herston Road, Herston QLD 4006
> 
> [EXTERNAL EMAIL] This message originates from an external email address, please exercise caution when clicking any links or opening attachments. If you believe the sender is impersonating someone at QIMR Berghofer, please forward this message to phishing at qimrberghofer.edu.au.
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From jeni_zen2004 at yahoo.co.in  Mon Aug 30 11:48:21 2021
From: jeni_zen2004 at yahoo.co.in (jeni_zen2004 at yahoo.co.in)
Date: Mon, 30 Aug 2021 18:48:21 +0000 (UTC)
Subject: [Chimera-users] Capture click event
References: <1658000416.531638.1630349301380.ref@mail.yahoo.com>
Message-ID: <1658000416.531638.1630349301380@mail.yahoo.com>

Hi,
Is there a way to capture the Chimera click event or a way to work around?I'm trying to do something from python code like., when a user clicks on a residue, it pops up a tooltip or shows the centroid.
Thanks,Catherine
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From pett at cgl.ucsf.edu  Mon Aug 30 14:04:15 2021
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 30 Aug 2021 14:04:15 -0700
Subject: [Chimera-users] Capture click event
In-Reply-To: <1658000416.531638.1630349301380@mail.yahoo.com>
References: <1658000416.531638.1630349301380.ref@mail.yahoo.com>
 <1658000416.531638.1630349301380@mail.yahoo.com>
Message-ID: <D2A1A338-2F34-4381-8C7C-9F75D1F5F5AF@cgl.ucsf.edu>

Hi Catherine,
	You can use chimera.mousemodes.addFunction(name, callables) to define a possible mouse button function and chimera.mousemodes.setButtonFunction(button, modifiers, function) to assign the defined function to a particular mouse button.
	For addFunction(), "name" is just some descriptive text (e.g. "show centroid") and "callables" are a list of either 3 or 5 Python functions (that each take two args: viewer, event) for when the mouse button is pressed, the mouse is moved (with the button down), or the mouse is released, and for the 5-function version, also double-click pressed, double-click released.  Any of those functions can be None if you don't have any need to respond to them.
	For setButtonFunction(), button is "1" (left), "2" (middle), or "3" (right) [strings, not integers].  "modifiers" is a tuple of "Ctrl", "Shift", or nothing.  "function" is the same as the "name" arg for addFunction().
	If you want an example of their use, the gui.py file in the Ilabel module uses these functions.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Aug 30, 2021, at 11:48 AM, jeni_zen2004--- via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> 
> Is there a way to capture the Chimera click event or a way to work around?
> I'm trying to do something from python code like., when a user clicks on a residue, it pops up a tooltip or shows the centroid.
> 
> Thanks,
> Catherine
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From stim52857 at gmail.com  Tue Aug 31 04:28:02 2021
From: stim52857 at gmail.com (tim smith)
Date: Tue, 31 Aug 2021 14:28:02 +0300
Subject: [Chimera-users] Making oligomers from Alphafold predictions
Message-ID: <CALaho9Y8CCZ0_VAasmsphFA_bK48Ouh3YJmZEtGhknWmxPvUbQ@mail.gmail.com>

Hi All,
Apologies for the nonrelated question!!

Wondering if there are any tools (can make in chimera/chimerax/Pymol) that
predict or build protein oligomers based on alphfold structure.   Please
let me know. I will be grateful for your kind responses. Thank you

Best
Smith
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From meng at cgl.ucsf.edu  Tue Aug 31 08:18:16 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 31 Aug 2021 08:18:16 -0700
Subject: [Chimera-users] Making oligomers from Alphafold predictions
In-Reply-To: <CALaho9Y8CCZ0_VAasmsphFA_bK48Ouh3YJmZEtGhknWmxPvUbQ@mail.gmail.com>
References: <CALaho9Y8CCZ0_VAasmsphFA_bK48Ouh3YJmZEtGhknWmxPvUbQ@mail.gmail.com>
Message-ID: <72E10879-11ED-45FE-B25E-6CC7AB665464@cgl.ucsf.edu>

Hi Smith,
The latest ChimeraX daily builds (not the production release) include getting AlphaFold-predicted structures from the freely available AlphaFold Database.

However, these are single-chain predictions only.  There is an option to superimpose the single-chain predictions on an experimentally determined structure of a multimer so that the result looks like a multimer, but that is not truly the same as predicting the multimer.

AlphaFold Database:
<https://alphafold.ebi.ac.uk/>

ChimeraX AlphaFold tool and command:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.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 Aug 31, 2021, at 4:28 AM, tim smith via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi All,
> Apologies for the nonrelated question!!
> 
> Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure.   Please let me know. I will be grateful for your kind responses. Thank you 
> 
> Best
> Smith



From kjude at stanford.edu  Tue Aug 31 09:01:54 2021
From: kjude at stanford.edu (Kevin Jude)
Date: Tue, 31 Aug 2021 09:01:54 -0700
Subject: [Chimera-users] Making oligomers from Alphafold predictions
In-Reply-To: <CALaho9Y8CCZ0_VAasmsphFA_bK48Ouh3YJmZEtGhknWmxPvUbQ@mail.gmail.com>
References: <CALaho9Y8CCZ0_VAasmsphFA_bK48Ouh3YJmZEtGhknWmxPvUbQ@mail.gmail.com>
Message-ID: <CALOTTMEkFxgtoAKLSV_q_wz8TfsjEO0WfU0qCr52jcvxct07Cg@mail.gmail.com>

 Hi Smith, you can use Rosetta Symmetric Docking. It's available on the
ROSIE server

https://rosie.rosettacommons.org/symmetric_docking

--
Kevin Jude, PhD (he/him/his)
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431

On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users <
chimera-users at cgl.ucsf.edu> wrote:

> Hi All,
> Apologies for the nonrelated question!!
>
> Wondering if there are any tools (can make in chimera/chimerax/Pymol) that
> predict or build protein oligomers based on alphfold structure.   Please
> let me know. I will be grateful for your kind responses. Thank you
>
> Best
> Smith
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
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