From stim52857 at gmail.com  Wed Sep  1 01:29:23 2021
From: stim52857 at gmail.com (tim smith)
Date: Wed, 1 Sep 2021 11:29:23 +0300
Subject: [Chimera-users] Making oligomers from Alphafold predictions
In-Reply-To: <CALOTTMEkFxgtoAKLSV_q_wz8TfsjEO0WfU0qCr52jcvxct07Cg@mail.gmail.com>
References: <CALaho9Y8CCZ0_VAasmsphFA_bK48Ouh3YJmZEtGhknWmxPvUbQ@mail.gmail.com>
 <CALOTTMEkFxgtoAKLSV_q_wz8TfsjEO0WfU0qCr52jcvxct07Cg@mail.gmail.com>
Message-ID: <CALaho9Za_vGzWTYe_L4M3jqjXP4C5f2w4iTv1oComYj+jPzuOw@mail.gmail.com>

Thank you, Elaine and Kevin, for your response.
The Rosetta Symmetry docking is up to 400 amino acids, and mine is 800. I
can't use it as it is. Wondering there is any other server for predicting
symmetry.

Thank you.

Best
Smith

On Tue, Aug 31, 2021 at 7:02 PM Kevin Jude <kjude at stanford.edu> wrote:

>  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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From esserlo at mail.nih.gov  Wed Sep  1 08:36:14 2021
From: esserlo at mail.nih.gov (Esser, Lothar (NIH/NCI) [E])
Date: Wed, 1 Sep 2021 15:36:14 +0000
Subject: [Chimera-users] Ribbon scaling in a script
Message-ID: <PH0PR09MB873265B2873764D14FAA4F3693CD9@PH0PR09MB8732.namprd09.prod.outlook.com>

Hi,
   despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point.
Thanks,

Lothar

Dr. Lothar Esser
National Institutes of Health
37 Convent Dr. Rm2122B
Bethesda, MD 20892

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From meng at cgl.ucsf.edu  Wed Sep  1 09:43:04 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 1 Sep 2021 09:43:04 -0700
Subject: [Chimera-users] Ribbon scaling in a script
In-Reply-To: <PH0PR09MB873265B2873764D14FAA4F3693CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
References: <PH0PR09MB873265B2873764D14FAA4F3693CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
Message-ID: <43E6B4E7-2710-4819-BFD0-D633FEB969ED@cgl.ucsf.edu>

Hi Lothar,
In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling"  (the set of secondary-structure-associated widths etc.).  That name would be saved in your preferences.  Then later you can use the "ribscale" command with that name in your scripts.   Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time.  Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command.

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>

However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

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

> On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
>    despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. 
> Thanks, 
> 
> Lothar



From esserlo at mail.nih.gov  Wed Sep  1 09:54:06 2021
From: esserlo at mail.nih.gov (Esser, Lothar (NIH/NCI) [E])
Date: Wed, 1 Sep 2021 16:54:06 +0000
Subject: [Chimera-users] Ribbon scaling in a script
In-Reply-To: <43E6B4E7-2710-4819-BFD0-D633FEB969ED@cgl.ucsf.edu>
References: <PH0PR09MB873265B2873764D14FAA4F3693CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
 <43E6B4E7-2710-4819-BFD0-D633FEB969ED@cgl.ucsf.edu>
Message-ID: <PH0PR09MB87325E45C2EE1701DAC483F393CD9@PH0PR09MB8732.namprd09.prod.outlook.com>

Hi,

thanks for the fast reply. This surprised me that you cannot just set it. However, I had already created a file with preferred dimensions that I read with ribscale. This works ok.

In the meantime I came across two more things I have a hard time figuring out:

Probably  quite simple but somehow escaped me so far:


  1.  Stick models show split bonds i.e. half of a X-Y bond gets color of X and the other half gets that of Y. However, in some ligand representations, I scale down the carbon atoms for better visibility. This seemed also to change the amount the bond gets carbon color. If one atom is half the size of the other bonded atom, its share of bond that is colored is much (1.5x) larger. I would prefer 1:1 ratio in bond color no matter the size of the atom. How can this be done?
  2.  I could not figure out the parameter that controlls the aromatic circle in say a benzene fragment. The default width seems to be 1 pixel and this is really thin.

Thanks,
Lothar

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, September 1, 2021 12:43 PM
To: Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Ribbon scaling in a script

Hi Lothar,
In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling"  (the set of secondary-structure-associated widths etc.).  That name would be saved in your preferences.  Then later you can use the "ribscale" command with that name in your scripts.   Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time.  Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command.

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>

However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>

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

> On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi,
>    despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point.
> Thanks,
>
> Lothar

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From meng at cgl.ucsf.edu  Wed Sep  1 10:57:39 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 1 Sep 2021 10:57:39 -0700
Subject: [Chimera-users] Ribbon scaling in a script
In-Reply-To: <PH0PR09MB87325E45C2EE1701DAC483F393CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
References: <PH0PR09MB873265B2873764D14FAA4F3693CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
 <43E6B4E7-2710-4819-BFD0-D633FEB969ED@cgl.ucsf.edu>
 <PH0PR09MB87325E45C2EE1701DAC483F393CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
Message-ID: <94229DEA-7B4B-4B63-A8A4-20249968D8F0@cgl.ucsf.edu>

Hi Lothar,
Yes, in Chimera there are several things that are only user-adjustable in graphical interfaces but not commands.  We saw that this could be a frustration for scripting, and so an explicit goal of ChimeraX is to have commands for all of the same settings that are in the GUIs.

OK, back to the questions.  As far as I know, there is no user-interface way of changing either of those behaviors: 

(1) The halfbond color partitioning behavior (sensitivity to VDW radius) might even be a bug.  Perhaps it makes some sense in the context of ball-and-stick display, but certainly not for the stick representation.

(2) There is also no command for adjusting the aromatic circle thickness.

Maybe others can advise on whether it is possible to do what you want by editing code, and if so, how to do it.

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


> On Sep 1, 2021, at 9:54 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> thanks for the fast reply. This surprised me that you cannot just set it. However, I had already created a file with preferred dimensions that I read with ribscale. This works ok. 
> 
> In the meantime I came across two more things I have a hard time figuring out:
> 
> Probably  quite simple but somehow escaped me so far:
> 
> 	? Stick models show split bonds i.e. half of a X-Y bond gets color of X and the other half gets that of Y. However, in some ligand representations, I scale down the carbon atoms for better visibility. This seemed also to change the amount the bond gets carbon color. If one atom is half the size of the other bonded atom, its share of bond that is colored is much (1.5x) larger. I would prefer 1:1 ratio in bond color no matter the size of the atom. How can this be done?
> 	? I could not figure out the parameter that controlls the aromatic circle in say a benzene fragment. The default width seems to be 1 pixel and this is really thin.
> 
> Thanks, 
> Lothar
> 
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Wednesday, September 1, 2021 12:43 PM
> To: Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Ribbon scaling in a script
>  
> Hi Lothar,
> In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling"  (the set of secondary-structure-associated widths etc.).  That name would be saved in your preferences.  Then later you can use the "ribscale" command with that name in your scripts.   Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time.  Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command.
> 
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>
> 
> However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > 
> > Hi, 
> >    despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. 
> > Thanks, 
> > 
> > Lothar



From goddard at sonic.net  Wed Sep  1 10:58:53 2021
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 1 Sep 2021 10:58:53 -0700
Subject: [Chimera-users] Making oligomers from Alphafold predictions
In-Reply-To: <CALaho9Za_vGzWTYe_L4M3jqjXP4C5f2w4iTv1oComYj+jPzuOw@mail.gmail.com>
References: <CALaho9Y8CCZ0_VAasmsphFA_bK48Ouh3YJmZEtGhknWmxPvUbQ@mail.gmail.com>
 <CALOTTMEkFxgtoAKLSV_q_wz8TfsjEO0WfU0qCr52jcvxct07Cg@mail.gmail.com>
 <CALaho9Za_vGzWTYe_L4M3jqjXP4C5f2w4iTv1oComYj+jPzuOw@mail.gmail.com>
Message-ID: <67CE68AF-EDEC-4B9F-8345-DD65201BBA18@sonic.net>

Hi Smith,

Do you know the symmetry of the oligomer you are trying to make?  Is it just a matter of applying positions that you already know?  Or do you need some computational protein-protein docking to figure it out (a vastly harder problem)?  If you know the symmetry you want the Chimera and ChimeraX sym command can place copies of a structure using standard symmetries or a list of position matrices (rotation + translation).

	tom


> On Sep 1, 2021, at 1:29 AM, tim smith via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Thank you, Elaine and Kevin, for your response. 
> The Rosetta Symmetry docking is up to 400 amino acids, and mine is 800. I can't use it as it is. Wondering there is any other server for predicting symmetry. 
> 
> Thank you. 
> 
> Best 
> Smith
> 
> On Tue, Aug 31, 2021 at 7:02 PM Kevin Jude <kjude at stanford.edu <mailto:kjude at stanford.edu>> wrote:
>  Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server
> 
> https://rosie.rosettacommons.org/symmetric_docking <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 <tel:%28650%29%20723-6431>
> On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users <chimera-users at cgl.ucsf.edu <mailto: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 <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

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From esserlo at mail.nih.gov  Wed Sep  1 11:21:49 2021
From: esserlo at mail.nih.gov (Esser, Lothar (NIH/NCI) [E])
Date: Wed, 1 Sep 2021 18:21:49 +0000
Subject: [Chimera-users] Ribbon scaling in a script
In-Reply-To: <94229DEA-7B4B-4B63-A8A4-20249968D8F0@cgl.ucsf.edu>
References: <PH0PR09MB873265B2873764D14FAA4F3693CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
 <43E6B4E7-2710-4819-BFD0-D633FEB969ED@cgl.ucsf.edu>
 <PH0PR09MB87325E45C2EE1701DAC483F393CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
 <94229DEA-7B4B-4B63-A8A4-20249968D8F0@cgl.ucsf.edu>
Message-ID: <PH0PR09MB87325F1D805A2EBB4F4C7EAF93CD9@PH0PR09MB8732.namprd09.prod.outlook.com>

Hi,

okay. The split bond color is not too bad and I don't have to have aromatic rings (although they might help).

Well, did you mean to I should change the source code of chimera ? Editing it may be okay but I seem to remember that the documentation said that compiling it is not easy.

I generated a nice scene (not quite finished but good) and exported it as povray scene:

Parse error at line 1776:
  no element found
Segmentation fault (core dumped)

I tried WebGL and got a crash too (without any additional information).

Is this a problem of my system? CentOS7 7.9.2009.

Thanks,
Lothar
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, September 1, 2021 1:57 PM
To: Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Ribbon scaling in a script

Hi Lothar,
Yes, in Chimera there are several things that are only user-adjustable in graphical interfaces but not commands.  We saw that this could be a frustration for scripting, and so an explicit goal of ChimeraX is to have commands for all of the same settings that are in the GUIs.

OK, back to the questions.  As far as I know, there is no user-interface way of changing either of those behaviors:

(1) The halfbond color partitioning behavior (sensitivity to VDW radius) might even be a bug.  Perhaps it makes some sense in the context of ball-and-stick display, but certainly not for the stick representation.

(2) There is also no command for adjusting the aromatic circle thickness.

Maybe others can advise on whether it is possible to do what you want by editing code, and if so, how to do it.

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


> On Sep 1, 2021, at 9:54 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi,
> thanks for the fast reply. This surprised me that you cannot just set it. However, I had already created a file with preferred dimensions that I read with ribscale. This works ok.
>
> In the meantime I came across two more things I have a hard time figuring out:
>
> Probably  quite simple but somehow escaped me so far:
>
>        ? Stick models show split bonds i.e. half of a X-Y bond gets color of X and the other half gets that of Y. However, in some ligand representations, I scale down the carbon atoms for better visibility. This seemed also to change the amount the bond gets carbon color. If one atom is half the size of the other bonded atom, its share of bond that is colored is much (1.5x) larger. I would prefer 1:1 ratio in bond color no matter the size of the atom. How can this be done?
>        ? I could not figure out the parameter that controlls the aromatic circle in say a benzene fragment. The default width seems to be 1 pixel and this is really thin.
>
> Thanks,
> Lothar
>
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Wednesday, September 1, 2021 12:43 PM
> To: Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Ribbon scaling in a script
>
> Hi Lothar,
> In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling"  (the set of secondary-structure-associated widths etc.).  That name would be saved in your preferences.  Then later you can use the "ribscale" command with that name in your scripts.   Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time.  Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command.
>
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>
>
> However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hi,
> >    despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point.
> > Thanks,
> >
> > Lothar

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From meng at cgl.ucsf.edu  Wed Sep  1 11:40:31 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 1 Sep 2021 11:40:31 -0700
Subject: [Chimera-users] Ribbon scaling in a script
In-Reply-To: <PH0PR09MB87325F1D805A2EBB4F4C7EAF93CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
References: <PH0PR09MB873265B2873764D14FAA4F3693CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
 <43E6B4E7-2710-4819-BFD0-D633FEB969ED@cgl.ucsf.edu>
 <PH0PR09MB87325E45C2EE1701DAC483F393CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
 <94229DEA-7B4B-4B63-A8A4-20249968D8F0@cgl.ucsf.edu>
 <PH0PR09MB87325F1D805A2EBB4F4C7EAF93CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
Message-ID: <70F21567-2912-4A1A-8734-D58EA797F3E4@cgl.ucsf.edu>

Hi Lothar,
If I understand correctly (although it's not my department per se) it is all the associated packages that cause compiling difficulties, whereas generally if somebody can point you to a few lines of python in the Chimera code itself that need to be changed, you don't have to do any compilation.

As for the other problem, no idea: we generally recommend using Help.. Report a Bug which will include your Chimera version and hardware specs, and may also allow you to attach an example session or input file and enter information on any other steps that might be needed to try to reproduce the problem.  Also include your e-mail address to automatically get feedback on the report.

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

> On Sep 1, 2021, at 11:21 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> 
> okay. The split bond color is not too bad and I don't have to have aromatic rings (although they might help). 
> 
> Well, did you mean to I should change the source code of chimera ? Editing it may be okay but I seem to remember that the documentation said that compiling it is not easy. 
> 
> I generated a nice scene (not quite finished but good) and exported it as povray scene:
> 
> Parse error at line 1776:
>   no element found
> Segmentation fault (core dumped)
> 
> I tried WebGL and got a crash too (without any additional information). 
> 
> Is this a problem of my system? CentOS7 7.9.2009. 
> 
> Thanks, 
> Lothar
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Wednesday, September 1, 2021 1:57 PM
> To: Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov>
> Cc: Chimera <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Ribbon scaling in a script
>  
> Hi Lothar,
> Yes, in Chimera there are several things that are only user-adjustable in graphical interfaces but not commands.  We saw that this could be a frustration for scripting, and so an explicit goal of ChimeraX is to have commands for all of the same settings that are in the GUIs.
> 
> OK, back to the questions.  As far as I know, there is no user-interface way of changing either of those behaviors: 
> 
> (1) The halfbond color partitioning behavior (sensitivity to VDW radius) might even be a bug.  Perhaps it makes some sense in the context of ball-and-stick display, but certainly not for the stick representation.
> 
> (2) There is also no command for adjusting the aromatic circle thickness.
> 
> Maybe others can advise on whether it is possible to do what you want by editing code, and if so, how to do it.
> 
> Sorry for the issues,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> > On Sep 1, 2021, at 9:54 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > 
> > Hi, 
> > thanks for the fast reply. This surprised me that you cannot just set it. However, I had already created a file with preferred dimensions that I read with ribscale. This works ok. 
> > 
> > In the meantime I came across two more things I have a hard time figuring out:
> > 
> > Probably  quite simple but somehow escaped me so far:
> > 
> >        ? Stick models show split bonds i.e. half of a X-Y bond gets color of X and the other half gets that of Y. However, in some ligand representations, I scale down the carbon atoms for better visibility. This seemed also to change the amount the bond gets carbon color. If one atom is half the size of the other bonded atom, its share of bond that is colored is much (1.5x) larger. I would prefer 1:1 ratio in bond color no matter the size of the atom. How can this be done?
> >        ? I could not figure out the parameter that controlls the aromatic circle in say a benzene fragment. The default width seems to be 1 pixel and this is really thin.
> > 
> > Thanks, 
> > Lothar
> > 
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Wednesday, September 1, 2021 12:43 PM
> > To: Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov>
> > Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> > Subject: Re: [Chimera-users] Ribbon scaling in a script
> >  
> > Hi Lothar,
> > In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling"  (the set of secondary-structure-associated widths etc.).  That name would be saved in your preferences.  Then later you can use the "ribscale" command with that name in your scripts.   Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time.  Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command.
> > 
> > <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>
> > 
> > However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command.
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
> > 
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.                       
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > 
> > > On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > > 
> > > Hi, 
> > >    despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. 
> > > Thanks, 
> > > 
> > > Lothar



From goddard at sonic.net  Wed Sep  1 11:44:11 2021
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 1 Sep 2021 11:44:11 -0700
Subject: [Chimera-users] Making oligomers from Alphafold predictions
In-Reply-To: <CANaMaTM8gXu2OLF07DuQbb9ztDp=MSMbbXLH_nmvDcYxp9T6-g@mail.gmail.com>
References: <CALaho9Y8CCZ0_VAasmsphFA_bK48Ouh3YJmZEtGhknWmxPvUbQ@mail.gmail.com>
 <CALOTTMEkFxgtoAKLSV_q_wz8TfsjEO0WfU0qCr52jcvxct07Cg@mail.gmail.com>
 <CALaho9Za_vGzWTYe_L4M3jqjXP4C5f2w4iTv1oComYj+jPzuOw@mail.gmail.com>
 <67CE68AF-EDEC-4B9F-8345-DD65201BBA18@sonic.net>
 <CANaMaTM8gXu2OLF07DuQbb9ztDp=MSMbbXLH_nmvDcYxp9T6-g@mail.gmail.com>
Message-ID: <D92F8540-4B7D-4741-AA18-38BBF73BD5AD@sonic.net>

Hi Tiru,

If the center of symmetry is at 0,0,0 for your model and it just needs 6 rotated copies placed use Chimera command

	sym #0 group c6

where #0 is the model number of your monomer.  If you do not know the center of symmetry or how the monomers interface with each other (ie their orientation in the hexamer), then that is a protein-protein docking problem and the sym command does not solve that.  For that case you would need to fit in a cryoEM or X-ray map of the hexamer, or align the monomer to a known homologous hexamer, or find some amazing oligomeric structure prediction tool.

	Tom




> On Sep 1, 2021, at 11:24 AM, Tiru Hcu <tiru.hcu09 at gmail.com <mailto:tiru.hcu09 at gmail.com>> wrote:
> 
> Hi Tom, 
> 
> Thank you for your response. My protein symmetry is a hexamer. Please would you mind sharing a little elaborate how to to do in chimera. Thank you. 
> 
> Best regards,
> Tiru
> 
> On Wed, 1 Sep 2021, 21:10 Tom Goddard via Chimera-users, <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>> wrote:
> Hi Smith,
> 
> Do you know the symmetry of the oligomer you are trying to make?  Is it just a matter of applying positions that you already know?  Or do you need some computational protein-protein docking to figure it out (a vastly harder problem)?  If you know the symmetry you want the Chimera and ChimeraX sym command can place copies of a structure using standard symmetries or a list of position matrices (rotation + translation).
> 
> 	tom
> 
> 
>> On Sep 1, 2021, at 1:29 AM, tim smith via Chimera-users <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>> wrote:
>> 
>> Thank you, Elaine and Kevin, for your response. 
>> The Rosetta Symmetry docking is up to 400 amino acids, and mine is 800. I can't use it as it is. Wondering there is any other server for predicting symmetry. 
>> 
>> Thank you. 
>> 
>> Best 
>> Smith
>> 
>> On Tue, Aug 31, 2021 at 7:02 PM Kevin Jude <kjude at stanford.edu <mailto:kjude at stanford.edu>> wrote:
>>  Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server
>> 
>> https://rosie.rosettacommons.org/symmetric_docking <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 <tel:%28650%29%20723-6431>
>> On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users <chimera-users at cgl.ucsf.edu <mailto: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 <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 goddard at sonic.net  Wed Sep  1 11:49:58 2021
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 1 Sep 2021 11:49:58 -0700
Subject: [Chimera-users] Ribbon scaling in a script
In-Reply-To: <70F21567-2912-4A1A-8734-D58EA797F3E4@cgl.ucsf.edu>
References: <PH0PR09MB873265B2873764D14FAA4F3693CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
 <43E6B4E7-2710-4819-BFD0-D633FEB969ED@cgl.ucsf.edu>
 <PH0PR09MB87325E45C2EE1701DAC483F393CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
 <94229DEA-7B4B-4B63-A8A4-20249968D8F0@cgl.ucsf.edu>
 <PH0PR09MB87325F1D805A2EBB4F4C7EAF93CD9@PH0PR09MB8732.namprd09.prod.outlook.com>
 <70F21567-2912-4A1A-8734-D58EA797F3E4@cgl.ucsf.edu>
Message-ID: <0DD6D8A9-6D2B-4BD3-A583-BA25C50772D1@sonic.net>

The halfbond coloring is a feature and is in the Chimera C++ code in MoleculeLensModel.cpp.  It would require recompiling Chimera which is extremely difficult -- might take you a few weeks effort if you are a highly knowledgable software developer.

ChimeraX always splits bonds in half for coloring.

	Tom


> On Sep 1, 2021, at 11:40 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Lothar,
> If I understand correctly (although it's not my department per se) it is all the associated packages that cause compiling difficulties, whereas generally if somebody can point you to a few lines of python in the Chimera code itself that need to be changed, you don't have to do any compilation.
> 
> As for the other problem, no idea: we generally recommend using Help.. Report a Bug which will include your Chimera version and hardware specs, and may also allow you to attach an example session or input file and enter information on any other steps that might be needed to try to reproduce the problem.  Also include your e-mail address to automatically get feedback on the report.
> 
> Thanks/sorry,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Sep 1, 2021, at 11:21 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Hi, 
>> 
>> okay. The split bond color is not too bad and I don't have to have aromatic rings (although they might help). 
>> 
>> Well, did you mean to I should change the source code of chimera ? Editing it may be okay but I seem to remember that the documentation said that compiling it is not easy. 
>> 
>> I generated a nice scene (not quite finished but good) and exported it as povray scene:
>> 
>> Parse error at line 1776:
>>  no element found
>> Segmentation fault (core dumped)
>> 
>> I tried WebGL and got a crash too (without any additional information). 
>> 
>> Is this a problem of my system? CentOS7 7.9.2009. 
>> 
>> Thanks, 
>> Lothar
>> From: Elaine Meng <meng at cgl.ucsf.edu>
>> Sent: Wednesday, September 1, 2021 1:57 PM
>> To: Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov>
>> Cc: Chimera <chimera-users at cgl.ucsf.edu>
>> Subject: Re: [Chimera-users] Ribbon scaling in a script
>> 
>> Hi Lothar,
>> Yes, in Chimera there are several things that are only user-adjustable in graphical interfaces but not commands.  We saw that this could be a frustration for scripting, and so an explicit goal of ChimeraX is to have commands for all of the same settings that are in the GUIs.
>> 
>> OK, back to the questions.  As far as I know, there is no user-interface way of changing either of those behaviors: 
>> 
>> (1) The halfbond color partitioning behavior (sensitivity to VDW radius) might even be a bug.  Perhaps it makes some sense in the context of ball-and-stick display, but certainly not for the stick representation.
>> 
>> (2) There is also no command for adjusting the aromatic circle thickness.
>> 
>> Maybe others can advise on whether it is possible to do what you want by editing code, and if so, how to do it.
>> 
>> Sorry for the issues,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Sep 1, 2021, at 9:54 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hi, 
>>> thanks for the fast reply. This surprised me that you cannot just set it. However, I had already created a file with preferred dimensions that I read with ribscale. This works ok. 
>>> 
>>> In the meantime I came across two more things I have a hard time figuring out:
>>> 
>>> Probably  quite simple but somehow escaped me so far:
>>> 
>>>       ? Stick models show split bonds i.e. half of a X-Y bond gets color of X and the other half gets that of Y. However, in some ligand representations, I scale down the carbon atoms for better visibility. This seemed also to change the amount the bond gets carbon color. If one atom is half the size of the other bonded atom, its share of bond that is colored is much (1.5x) larger. I would prefer 1:1 ratio in bond color no matter the size of the atom. How can this be done?
>>>       ? I could not figure out the parameter that controlls the aromatic circle in say a benzene fragment. The default width seems to be 1 pixel and this is really thin.
>>> 
>>> Thanks, 
>>> Lothar
>>> 
>>> From: Elaine Meng <meng at cgl.ucsf.edu>
>>> Sent: Wednesday, September 1, 2021 12:43 PM
>>> To: Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov>
>>> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
>>> Subject: Re: [Chimera-users] Ribbon scaling in a script
>>> 
>>> Hi Lothar,
>>> In Chimera, you would have to use Ribbon Style Editor to create and name the "scaling"  (the set of secondary-structure-associated widths etc.).  That name would be saved in your preferences.  Then later you can use the "ribscale" command with that name in your scripts.   Sorry, there is no way to just adjust it directly in a command without having to make the scaling ahead of time.  Similarly you need to use the editor dialog to create and name custom styles (cross-sections), which can later be accessed with the "ribstyle" command.
>>> 
>>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>
>>> 
>>> However, in ChimeraX it is done differently; you can specify widths etc. directly in the "cartoon style" command.
>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
>>> 
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>>> On Sep 1, 2021, at 8:36 AM, Esser, Lothar (NIH/NCI) [E] via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>>> 
>>>> Hi, 
>>>>   despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. 
>>>> Thanks, 
>>>> 
>>>> Lothar
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From manikandank at instem.res.in  Thu Sep  2 02:22:08 2021
From: manikandank at instem.res.in (manikandank)
Date: Thu, 02 Sep 2021 14:52:08 +0530
Subject: [Chimera-users] matchmaker for more than one chain
Message-ID: <b49f348d7362f3c4ae8c924c98b8fca5@instem.res.in>

Hi ChimeraX-users, 

I have used recently the mmaker cmd to align two pdb each have multiple
chains as below. 

mmaker #12/L,M,N to #5/S,A,B matrix  blosum-62 showAlignment true 

But the sequence view shows only the alignment of chain L and S.  

1. I would like to have aligned sequences of all chains used in mmaker
alignement. 

2. Is it possible to open the saved RMSD header values in a file later
just to color the pdb? 

3. Do mmaker align entire pdb based on selected chains and Can calculate
RMSD for all residues in the pdb? 

4. I also would like to change the displayed text for the sequence name.
Presently it puts the filename as sequence name. 

    [similar to 'Edit sequence name' in the sequence viewer in chimera] 

Please let me know how this can be done. 

thank you very much 

with kind regards 

Mani.
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From meng at cgl.ucsf.edu  Thu Sep  2 08:37:50 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 2 Sep 2021 08:37:50 -0700
Subject: [Chimera-users] matchmaker for more than one chain
In-Reply-To: <b49f348d7362f3c4ae8c924c98b8fca5@instem.res.in>
References: <b49f348d7362f3c4ae8c924c98b8fca5@instem.res.in>
Message-ID: <262BAF4C-D9FC-4A73-9053-D066213B4926@cgl.ucsf.edu>

Hi Mani,
There is a different e-mail address for ChimeraX questions:  it is chimerax-users at cgl.ucsf.edu CC'd here.

Responses below...

> On Sep 2, 2021, at 2:22 AM, manikandank via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi ChimeraX-users,
> I have used recently the mmaker cmd to align two pdb each have multiple chains as below.
>  
> mmaker #12/L,M,N to #5/S,A,B matrix  blosum-62 showAlignment true
>  
> But the sequence view shows only the alignment of chain L and S. 
> 
> 1. I would like to have aligned sequences of all chains used in mmaker alignement.

Your command above does not use all the chains for fitting, it only chooses the single pair of chains that gives the best sequence-alignment score to superimpose the two models.  The other chains might look superimposed but it is only because they moved along with the ones that were actually used for the fit.   To use all three pairs of chains, you need to also use the "pairing ss" option:

mmaker #12/L,M,N to #5/S,A,B matrix  blosum-62 showAlignment true pair ss

Then you would get three pairwise sequence-alignment windows:  L/S, M/A, and N/B.

matchmaker or mmaker command
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

pairing options
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options>
> 
> 2. Is it possible to open the saved RMSD header values in a file later just to color the pdb?

Yes, but with several steps so it may not be that convenient.  Probably easier just to save and restore the ChimeraX session (which includes the sequence alignment windows). Also remember if you move the structures relative to each other, the RMSD values will change.  However, if you really want to save the RMSD values to file after you showed sequence alignments and header, then you could save them as an attribute file (that could be reopened/applied later):
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>

The attribute name is seq_rmsd as explained here:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers>

> 
> 3. Do mmaker align entire pdb based on selected chains and Can calculate RMSD for all residues in the pdb?

For the first question, 3A: yes, depending on the "pairing" option as explained above.

For the second question, 3B, I'm not sure what you want.  Remember that the main purpose of matchmaker is to superimpose the structures well, and then it happens to also give the RMSD over the positions that it chose to use, which are shown in the pinkish boxes on the sequence alignment.  By default it uses fit iteration and discards loops that don't superimpose well in space. Matchmaker only gives the RMSD over the positions it uses.  You could tell it to use all positions, but that would change the superposition.  If you like the default superposition (that does not use all of the positions), you can use a separate command "rmsd" to measure RMSD over any sets of atoms that you want, without moving the structures or changing the superposition.  Or, if you really want to use all of the positions in the sequence alignment for the fitting, you would have to use matchmaker option "cutoff none" ... but that usually does not give the best superposition.

cutoff option
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#cutoffDistance>

rmsd command (calculate RMSD in current positions, no fitting)
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html>

Matchmaker only gives alpha-carbon RMSD.  The rmsd command can give RMSD for any sets of atoms that you want, alpha-carbons only, or backbone only, or all atoms, as long as you give equal numbers of atoms from the two structures. However, it can be tricky to specify the correct sets of atoms if the residue numbering or residue types are different between the two structures.

So you might want to first use "mmaker" with whichever options give you the best superposition, and then to measure RMSD over all positions in the alignment (which might not be used in the matchmaker fit), use the "rmsd" command afterward.

> 
> 4. I also would like to change the displayed text for the sequence name. Presently it puts the filename as sequence name.
> 
>     [similar to 'Edit sequence name' in the sequence viewer in chimera]

Sorry, there is no way yet to change the displayed sequence name in ChimeraX.
> 
> Please let me know how this can be done. 
> thank you very much
> with kind regards
> Mani.

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


From K.SANDOVAL1 at nuigalway.ie  Fri Sep  3 06:26:55 2021
From: K.SANDOVAL1 at nuigalway.ie (SANDOVAL, KENNETH)
Date: Fri, 3 Sep 2021 13:26:55 +0000
Subject: [Chimera-users] Copy protein orientation
In-Reply-To: <8B85B033-DB06-46A5-8EE0-6669FAAC962D@cgl.ucsf.edu>
References: <AM6PR01MB520789BD50D2637E8063A28DD7F79@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <9631A535-F6E6-4938-B31A-BA187FABB170@ucdavis.edu>
 <8B85B033-DB06-46A5-8EE0-6669FAAC962D@cgl.ucsf.edu>
Message-ID: <AM6PR01MB520727DD4C454CD418D37F60D7CF9@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>

Hello,

Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.

However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.

Thank you,
Kenneth
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, August 10, 2021 6:00 PM
To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Copy protein orientation

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

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From meng at cgl.ucsf.edu  Fri Sep  3 10:52:22 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 3 Sep 2021 10:52:22 -0700
Subject: [Chimera-users] Copy protein orientation
In-Reply-To: <AM6PR01MB520727DD4C454CD418D37F60D7CF9@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
References: <AM6PR01MB520789BD50D2637E8063A28DD7F79@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <9631A535-F6E6-4938-B31A-BA187FABB170@ucdavis.edu>
 <8B85B033-DB06-46A5-8EE0-6669FAAC962D@cgl.ucsf.edu>
 <AM6PR01MB520727DD4C454CD418D37F60D7CF9@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
Message-ID: <92A4521D-7B54-4CE1-9DB0-A590C66FEE00@cgl.ucsf.edu>

Hello Kenneth,
I can't really tell what's going on without having the session file or the atomic coordinates  (PDB file) to look at. 

Without that information, my only suggestions are:
(1) make sure you have a reasonably new version of Chimera, say the last production release
(2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command

ksdssp #2

kdssp help:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.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 Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
> 
> However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
> 
> Thank you,
> Kenneth
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Tuesday, August 10, 2021 6:00 PM
> To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Copy protein orientation
>  
> 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
> 
> <Prot_A_aligned.png><Prot_A.png>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From m.jin at msg.ucsf.edu  Fri Sep  3 12:26:20 2021
From: m.jin at msg.ucsf.edu (Jeremy Jin)
Date: Fri, 3 Sep 2021 12:26:20 -0700
Subject: [Chimera-users] Split, Crash out
Message-ID: <C4492DA3-BCFB-4BDE-92D2-5D2DD1AD041C@msg.ucsf.edu>

Hi, 

When I use chimera, I want to split a mode, as long as I split, the software just crashes out.

It works very well before. Also it worked this morning, but after I split the model, fit to my map, it crashed out, then I restart, it showed the same problem. Then I re-installed the program, 2020-12-08 version, it crashed out even when I do split command.

Best Regards!
MJ

MJ, Mingliang Jin
Postdoc of Yifan Cheng?s Lab
Genentech Hall, UCSF Missionbay
Main Email: m.jin at msg.ucsf.edu
Tel: 415-2835-171











From meng at cgl.ucsf.edu  Fri Sep  3 12:52:50 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 3 Sep 2021 12:52:50 -0700
Subject: [Chimera-users] Split, Crash out
In-Reply-To: <C4492DA3-BCFB-4BDE-92D2-5D2DD1AD041C@msg.ucsf.edu>
References: <C4492DA3-BCFB-4BDE-92D2-5D2DD1AD041C@msg.ucsf.edu>
Message-ID: <2540ACF7-18DB-489E-AF9E-C4CFA6C354D0@cgl.ucsf.edu>

Hi MJ,
Sorry about the problems!

Please use Chimera menu: Help... Report a Bug and attach any data (e.g. a session file or PDB file) and any instructions needed to reproduce the crash (e.g. the split command you used).  Otherwise it is hard for us to diagnose/fix.  Certainly it does not always crash whenever split is used. 

 If the data needs to be kept private but you are willing to share with the Chimera(X) dev team, you can send it to just me (meng at cgl.ucsf.edu) or Tom Goddoard instead of attaching it to the bug report.

As an alternative to split, you can open the structure multiple times and delete from each copy the "other" chains so that each copy just has the part that you want.

We are concentrating on ChimeraX development now, and another possible alternative is to use ChimeraX instead Chimera.  It has the same fitting as Chimera, and also a split command, although syntax is a little different.  

ChimeraX split:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html>
ChimeraX fitting:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.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 Sep 3, 2021, at 12:26 PM, Jeremy Jin via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> 
> When I use chimera, I want to split a mode, as long as I split, the software just crashes out.
> 
> It works very well before. Also it worked this morning, but after I split the model, fit to my map, it crashed out, then I restart, it showed the same problem. Then I re-installed the program, 2020-12-08 version, it crashed out even when I do split command.
> 
> Best Regards!
> MJ
> 
> MJ, Mingliang Jin
> Postdoc of Yifan Cheng?s Lab
> Genentech Hall, UCSF Missionbay
> Main Email: m.jin at msg.ucsf.edu
> Tel: 415-2835-171



From goddard at sonic.net  Fri Sep  3 12:53:06 2021
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 3 Sep 2021 12:53:06 -0700
Subject: [Chimera-users] Split, Crash out
In-Reply-To: <C4492DA3-BCFB-4BDE-92D2-5D2DD1AD041C@msg.ucsf.edu>
References: <C4492DA3-BCFB-4BDE-92D2-5D2DD1AD041C@msg.ucsf.edu>
Message-ID: <C91601E8-4C9D-4DCA-967D-5CF6E59D6AA9@sonic.net>

Hi MJ,

Most Chimera crashes are caused by graphics driver bugs.  Updating your graphics driver is the usual fix.  You might try our newer program ChimeraX.  We have only done basic maintenance on Chimera for the past 5 years.  ChimeraX does a better job reporting diagnostics if a crash happens.

	Tom

> On Sep 3, 2021, at 12:26 PM, Jeremy Jin via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> 
> When I use chimera, I want to split a mode, as long as I split, the software just crashes out.
> 
> It works very well before. Also it worked this morning, but after I split the model, fit to my map, it crashed out, then I restart, it showed the same problem. Then I re-installed the program, 2020-12-08 version, it crashed out even when I do split command.
> 
> Best Regards!
> MJ
> 
> MJ, Mingliang Jin
> Postdoc of Yifan Cheng?s Lab
> Genentech Hall, UCSF Missionbay
> Main Email: m.jin at msg.ucsf.edu
> Tel: 415-2835-171
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From K.SANDOVAL1 at nuigalway.ie  Mon Sep  6 02:48:35 2021
From: K.SANDOVAL1 at nuigalway.ie (SANDOVAL, KENNETH)
Date: Mon, 6 Sep 2021 09:48:35 +0000
Subject: [Chimera-users] Copy protein orientation
In-Reply-To: <92A4521D-7B54-4CE1-9DB0-A590C66FEE00@cgl.ucsf.edu>
References: <AM6PR01MB520789BD50D2637E8063A28DD7F79@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <9631A535-F6E6-4938-B31A-BA187FABB170@ucdavis.edu>
 <8B85B033-DB06-46A5-8EE0-6669FAAC962D@cgl.ucsf.edu>
 <AM6PR01MB520727DD4C454CD418D37F60D7CF9@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <92A4521D-7B54-4CE1-9DB0-A590C66FEE00@cgl.ucsf.edu>
Message-ID: <AM6PR01MB5207F42DB3E0AFBA10138AB2D7D29@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>

Hi Elaine,

Thank you for your answer. I attempted to use the ksdssp command, but it doesn't appear to be doing anything. I have attached the two pdb files. I am wanting the structures of the two proteins in F791140.pdb to be like that of the one in A791140.pdb. Do you have advice on how to do this?

Thank you,
Kenneth
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, September 3, 2021 6:52 PM
To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
Cc: Azad, Roksana via Chimera-users <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Copy protein orientation

EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe.
R?OMHPHOST SEACHTRACH: Th?inig an r?omhphost seo as ?it ?igin taobh amuigh de O? Gaillimh. N? clice?il ar naisc agus n? hoscail ceangalt?in mura n-aithn?onn t? seoladh r?omhphoist an tseolt?ra agus mura gcreideann t? go bhfuil an t-?bhar s?bh?ilte.


Hello Kenneth,
I can't really tell what's going on without having the session file or the atomic coordinates  (PDB file) to look at.

Without that information, my only suggestions are:
(1) make sure you have a reasonably new version of Chimera, say the last production release
(2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command

ksdssp #2

kdssp help:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.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 Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hello,
>
> Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
>
> However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
>
> Thank you,
> Kenneth
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Tuesday, August 10, 2021 6:00 PM
> To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Copy protein orientation
>
> 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
>
> <Prot_A_aligned.png><Prot_A.png>_______________________________________________
> 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 meng at cgl.ucsf.edu  Mon Sep  6 08:35:27 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 6 Sep 2021 08:35:27 -0700
Subject: [Chimera-users] Copy protein orientation
In-Reply-To: <AM6PR01MB5207F42DB3E0AFBA10138AB2D7D29@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
References: <AM6PR01MB520789BD50D2637E8063A28DD7F79@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <9631A535-F6E6-4938-B31A-BA187FABB170@ucdavis.edu>
 <8B85B033-DB06-46A5-8EE0-6669FAAC962D@cgl.ucsf.edu>
 <AM6PR01MB520727DD4C454CD418D37F60D7CF9@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <92A4521D-7B54-4CE1-9DB0-A590C66FEE00@cgl.ucsf.edu>
 <AM6PR01MB5207F42DB3E0AFBA10138AB2D7D29@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
Message-ID: <0D1F5899-7A0F-474E-A484-97F64041C8AB@cgl.ucsf.edu>

Hi Kenneth,
The problem with F791140.pdb is that you have two proteins right on top of each other that are chains A and B in the same model.  This ruins the secondary structure calculation (ksdssp) because it is not physically possible for one structure to have all those atoms nearly on top of each other.

Whichever program wrote the file wrote incorrect PDB format.  Although it would still be somewhat incorrect, you can fix the file for purposes of secondary structure calculation by replacing the TER line with ENDMDL (i.e. in your favorite text-editor).

I did that and attached the resulting file.  Then the secondary structure can be calculated automatically and looks reasonable when you open it.

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


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> On Sep 6, 2021, at 2:48 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> Thank you for your answer. I attempted to use the ksdssp command, but it doesn't appear to be doing anything. I have attached the two pdb files. I am wanting the structures of the two proteins in F791140.pdb to be like that of the one in A791140.pdb. Do you have advice on how to do this?
> 
> Thank you,
> Kenneth
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Friday, September 3, 2021 6:52 PM
> To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
> Cc: Azad, Roksana via Chimera-users <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Copy protein orientation
>  
> EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe.
> R?OMHPHOST SEACHTRACH: Th?inig an r?omhphost seo as ?it ?igin taobh amuigh de O? Gaillimh. N? clice?il ar naisc agus n? hoscail ceangalt?in mura n-aithn?onn t? seoladh r?omhphoist an tseolt?ra agus mura gcreideann t? go bhfuil an t-?bhar s?bh?ilte.
> 
> 
> Hello Kenneth,
> I can't really tell what's going on without having the session file or the atomic coordinates  (PDB file) to look at.
> 
> Without that information, my only suggestions are:
> (1) make sure you have a reasonably new version of Chimera, say the last production release
> (2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command
> 
> ksdssp #2
> 
> kdssp help:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.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 Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hello,
> >
> > Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
> >
> > However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
> >
> > Thank you,
> > Kenneth
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Tuesday, August 10, 2021 6:00 PM
> > To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
> > Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> > Subject: Re: [Chimera-users] Copy protein orientation
> >
> > 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
> >
> > <Prot_A_aligned.png><Prot_A.png>_______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> <A791140.pdb><F791140.pdb>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


From K.SANDOVAL1 at nuigalway.ie  Mon Sep  6 08:43:31 2021
From: K.SANDOVAL1 at nuigalway.ie (SANDOVAL, KENNETH)
Date: Mon, 6 Sep 2021 15:43:31 +0000
Subject: [Chimera-users] Copy protein orientation
In-Reply-To: <0D1F5899-7A0F-474E-A484-97F64041C8AB@cgl.ucsf.edu>
References: <AM6PR01MB520789BD50D2637E8063A28DD7F79@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <9631A535-F6E6-4938-B31A-BA187FABB170@ucdavis.edu>
 <8B85B033-DB06-46A5-8EE0-6669FAAC962D@cgl.ucsf.edu>
 <AM6PR01MB520727DD4C454CD418D37F60D7CF9@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <92A4521D-7B54-4CE1-9DB0-A590C66FEE00@cgl.ucsf.edu>
 <AM6PR01MB5207F42DB3E0AFBA10138AB2D7D29@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <0D1F5899-7A0F-474E-A484-97F64041C8AB@cgl.ucsf.edu>
Message-ID: <AM6PR01MB520789997CD5CE226F1C7068D7D29@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>

Hello Elaine,

Thank you very much! I generated that alignment with TM-align so I'm quite surprised that it produced an incorrect PDB format.

https://zhanggroup.org/TM-align/

Anyways I looked at the structure in Chimera and it looks perfect. So I'll be using this in my manuscript now.

Thanks again,
Kenneth
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, September 6, 2021 4:35 PM
To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Copy protein orientation

EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe.
R?OMHPHOST SEACHTRACH: Th?inig an r?omhphost seo as ?it ?igin taobh amuigh de O? Gaillimh. N? clice?il ar naisc agus n? hoscail ceangalt?in mura n-aithn?onn t? seoladh r?omhphoist an tseolt?ra agus mura gcreideann t? go bhfuil an t-?bhar s?bh?ilte.


Hi Kenneth,
The problem with F791140.pdb is that you have two proteins right on top of each other that are chains A and B in the same model.  This ruins the secondary structure calculation (ksdssp) because it is not physically possible for one structure to have all those atoms nearly on top of each other.

Whichever program wrote the file wrote incorrect PDB format.  Although it would still be somewhat incorrect, you can fix the file for purposes of secondary structure calculation by replacing the TER line with ENDMDL (i.e. in your favorite text-editor).

I did that and attached the resulting file.  Then the secondary structure can be calculated automatically and looks reasonable when you open it.

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



> On Sep 6, 2021, at 2:48 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi Elaine,
>
> Thank you for your answer. I attempted to use the ksdssp command, but it doesn't appear to be doing anything. I have attached the two pdb files. I am wanting the structures of the two proteins in F791140.pdb to be like that of the one in A791140.pdb. Do you have advice on how to do this?
>
> Thank you,
> Kenneth
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Friday, September 3, 2021 6:52 PM
> To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
> Cc: Azad, Roksana via Chimera-users <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Copy protein orientation
>
> EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe.
> R?OMHPHOST SEACHTRACH: Th?inig an r?omhphost seo as ?it ?igin taobh amuigh de O? Gaillimh. N? clice?il ar naisc agus n? hoscail ceangalt?in mura n-aithn?onn t? seoladh r?omhphoist an tseolt?ra agus mura gcreideann t? go bhfuil an t-?bhar s?bh?ilte.
>
>
> Hello Kenneth,
> I can't really tell what's going on without having the session file or the atomic coordinates  (PDB file) to look at.
>
> Without that information, my only suggestions are:
> (1) make sure you have a reasonably new version of Chimera, say the last production release
> (2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command
>
> ksdssp #2
>
> kdssp help:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.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 Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hello,
> >
> > Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
> >
> > However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
> >
> > Thank you,
> > Kenneth
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Tuesday, August 10, 2021 6:00 PM
> > To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
> > Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> > Subject: Re: [Chimera-users] Copy protein orientation
> >
> > 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
> >
> > <Prot_A_aligned.png><Prot_A.png>_______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
> <A791140.pdb><F791140.pdb>_______________________________________________
> 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 meng at cgl.ucsf.edu  Mon Sep  6 10:55:39 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 6 Sep 2021 10:55:39 -0700
Subject: [Chimera-users] Copy protein orientation
In-Reply-To: <AM6PR01MB520789997CD5CE226F1C7068D7D29@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
References: <AM6PR01MB520789BD50D2637E8063A28DD7F79@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <9631A535-F6E6-4938-B31A-BA187FABB170@ucdavis.edu>
 <8B85B033-DB06-46A5-8EE0-6669FAAC962D@cgl.ucsf.edu>
 <AM6PR01MB520727DD4C454CD418D37F60D7CF9@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <92A4521D-7B54-4CE1-9DB0-A590C66FEE00@cgl.ucsf.edu>
 <AM6PR01MB5207F42DB3E0AFBA10138AB2D7D29@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
 <0D1F5899-7A0F-474E-A484-97F64041C8AB@cgl.ucsf.edu>
 <AM6PR01MB520789997CD5CE226F1C7068D7D29@AM6PR01MB5207.eurprd01.prod.exchangelabs.com>
Message-ID: <526131D6-79A3-492C-95E7-751A0E171720@cgl.ucsf.edu>

Great, you're welcome!  The file probably looks OK in some other molecular graphics programs.  Diffferent programs make different assumptions when calculating secondary structure.  However, now that you know what's wrong, it's an easy fix for Chimera to text-edit one line.
Best,
Elaine

> On Sep 6, 2021, at 8:43 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello Elaine,
> 
> Thank you very much! I generated that alignment with TM-align so I'm quite surprised that it produced an incorrect PDB format.
> 
> https://zhanggroup.org/TM-align/
> 
> Anyways I looked at the structure in Chimera and it looks perfect. So I'll be using this in my manuscript now.
> 
> Thanks again,
> Kenneth
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Monday, September 6, 2021 4:35 PM
> To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
> Cc: Chimera <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Copy protein orientation
>  
> EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe.
> R?OMHPHOST SEACHTRACH: Th?inig an r?omhphost seo as ?it ?igin taobh amuigh de O? Gaillimh. N? clice?il ar naisc agus n? hoscail ceangalt?in mura n-aithn?onn t? seoladh r?omhphoist an tseolt?ra agus mura gcreideann t? go bhfuil an t-?bhar s?bh?ilte.
> 
> 
> Hi Kenneth,
> The problem with F791140.pdb is that you have two proteins right on top of each other that are chains A and B in the same model.  This ruins the secondary structure calculation (ksdssp) because it is not physically possible for one structure to have all those atoms nearly on top of each other.
> 
> Whichever program wrote the file wrote incorrect PDB format.  Although it would still be somewhat incorrect, you can fix the file for purposes of secondary structure calculation by replacing the TER line with ENDMDL (i.e. in your favorite text-editor).
> 
> I did that and attached the resulting file.  Then the secondary structure can be calculated automatically and looks reasonable when you open it.
> 
> I hope this helps,
> Elaine
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> > On Sep 6, 2021, at 2:48 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > 
> > Hi Elaine,
> > 
> > Thank you for your answer. I attempted to use the ksdssp command, but it doesn't appear to be doing anything. I have attached the two pdb files. I am wanting the structures of the two proteins in F791140.pdb to be like that of the one in A791140.pdb. Do you have advice on how to do this?
> > 
> > Thank you,
> > Kenneth
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Friday, September 3, 2021 6:52 PM
> > To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
> > Cc: Azad, Roksana via Chimera-users <chimera-users at cgl.ucsf.edu>
> > Subject: Re: [Chimera-users] Copy protein orientation
> >  
> > EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe.
> > R?OMHPHOST SEACHTRACH: Th?inig an r?omhphost seo as ?it ?igin taobh amuigh de O? Gaillimh. N? clice?il ar naisc agus n? hoscail ceangalt?in mura n-aithn?onn t? seoladh r?omhphoist an tseolt?ra agus mura gcreideann t? go bhfuil an t-?bhar s?bh?ilte.
> > 
> > 
> > Hello Kenneth,
> > I can't really tell what's going on without having the session file or the atomic coordinates  (PDB file) to look at.
> > 
> > Without that information, my only suggestions are:
> > (1) make sure you have a reasonably new version of Chimera, say the last production release
> > (2) try running secondary structure assignment on that model, e.g. if the funny-looking ribbon model is #2, command
> > 
> > ksdssp #2
> > 
> > kdssp help:
> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.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 Sep 3, 2021, at 6:26 AM, SANDOVAL, KENNETH via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> > >
> > > Hello,
> > >
> > > Thank you for your helpful replies. I apologize for my late response. So following the initial suggestion by David, I have an alignment of protein A with protein B, but with protein B hidden. This is in file prot_A_aligned.png.
> > >
> > > However, I am wanting the ribbons of this file to look like those in the image prot_A.png. This is the chimera view for the .pdb file of protein A before alignment with B using TM-align. That is, I want the parts of the protein which are not alpha-helices or beta-sheets to just be in the licorice form. Is this something I can do in chimera? Or is this something that would be integrated into the actual .pdb file which I would have to manually manipulate? I apologize if this is question has an obvious answer.
> > >
> > > Thank you,
> > > Kenneth
> > > From: Elaine Meng <meng at cgl.ucsf.edu>
> > > Sent: Tuesday, August 10, 2021 6:00 PM
> > > To: SANDOVAL, KENNETH <K.SANDOVAL1 at nuigalway.ie>
> > > Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> > > Subject: Re: [Chimera-users] Copy protein orientation
> > >
> > > 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
> > >
> > > <Prot_A_aligned.png><Prot_A.png>_______________________________________________
> > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> > 
> > <A791140.pdb><F791140.pdb>_______________________________________________
> > 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 goddard at sonic.net  Tue Sep  7 11:07:28 2021
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 7 Sep 2021 11:07:28 -0700
Subject: [Chimera-users] Fwd:  Split, Crash out
References: <1340ED79-A903-480C-8025-D8CC20941A47@msg.ucsf.edu>
Message-ID: <4CEB8199-2016-4666-9F63-252D7F5BC6D2@sonic.net>

MJ reports that rebooting the computer fixed the Chimera crashes.

> Begin forwarded message:
> 
> From: Jeremy Jin
> Subject: Re: [Chimera-users] Split, Crash out
> Date: September 5, 2021 at 10:28:02 PM PDT
> To: Elaine Meng <meng at cgl.ucsf.edu>, Tom Goddard <goddard at sonic.net>
> 
> Hi Elaine adb Tom,
> Sorry to bother, I tried again today, it worked, seems something wrong with my system or reboot several times works. I am also will try ChimeraX! Thanks!
> 
> Best Regards!
> MJ
> 
> MJ, Mingliang Jin
> Postdoc of Yifan Cheng?s Lab
> Genentech Hall, UCSF Missionbay
> Main Email: m.jin at msg.ucsf.edu
> Tel: 415-2835-171
> 
> 
> 
>> On Sep 3, 2021, at 12:53, Tom Goddard <goddard at sonic.net> wrote:
>> 
>> Hi MJ,
>> 
>> Most Chimera crashes are caused by graphics driver bugs.  Updating your graphics driver is the usual fix.  You might try our newer program ChimeraX.  We have only done basic maintenance on Chimera for the past 5 years.  ChimeraX does a better job reporting diagnostics if a crash happens.
>> 
>> 	Tom
>> 
>>> On Sep 3, 2021, at 12:26 PM, Jeremy Jin via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hi, 
>>> 
>>> When I use chimera, I want to split a mode, as long as I split, the software just crashes out.
>>> 
>>> It works very well before. Also it worked this morning, but after I split the model, fit to my map, it crashed out, then I restart, it showed the same problem. Then I re-installed the program, 2020-12-08 version, it crashed out even when I do split command.
>>> 
>>> Best Regards!
>>> MJ
>>> 
>>> MJ, Mingliang Jin
>>> Postdoc of Yifan Cheng?s Lab
>>> Genentech Hall, UCSF Missionbay
>>> Main Email: m.jin at msg.ucsf.edu
>>> Tel: 415-2835-171
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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 yanhezhao1990 at gmail.com  Wed Sep  8 17:40:24 2021
From: yanhezhao1990 at gmail.com (Yanhe Zhao)
Date: Wed, 8 Sep 2021 19:40:24 -0500
Subject: [Chimera-users] local docking
Message-ID: <CAFxHBUFT_XVbqvJPxkixc6huHEaSM+mJa5_cqySp6kpQbWyepQ@mail.gmail.com>

Greeting,

I tried sequential fitting to fit 3 models to my maps. I was wondering that
if I want to fix one model and do local fitting of another models with
limited shift and rotation, what command with options should I use?

Thanks and regards,
Yanhe
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From meng at cgl.ucsf.edu  Wed Sep  8 18:05:09 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 8 Sep 2021 18:05:09 -0700
Subject: [Chimera-users] local docking
In-Reply-To: <CAFxHBUFT_XVbqvJPxkixc6huHEaSM+mJa5_cqySp6kpQbWyepQ@mail.gmail.com>
References: <CAFxHBUFT_XVbqvJPxkixc6huHEaSM+mJa5_cqySp6kpQbWyepQ@mail.gmail.com>
Message-ID: <32506BA4-B581-4AA0-896F-1D27E8FDECE0@cgl.ucsf.edu>

Hi Yanhe,
The "fitmap" command with sequential fitting ("sequence" option) will fit/move all of the specified models.  There is no option to keep one model fixed and move only the other ones. 
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> 
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence>

Also, there is no fitmap option to limit the amount of translation or rotation.  Instead there is only an option to turn off translation completely (shift false) or turn off rotation completely (rotate false).
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#shift>

A longer method might be to first fit one model, then simulate a map from it with "molmap" and then subtract the molmap result from the original map with "vop subtract," and then use a separate "fitmap" command (with "sequence" if you want to sequentially fit the other two).
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>

I hope this helps,
Elaine


> On Sep 8, 2021, at 5:40 PM, Yanhe Zhao via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Greeting,
> 
> I tried sequential fitting to fit 3 models to my maps. I was wondering that if I want to fix one model and do local fitting of another models with limited shift and rotation, what command with options should I use? 
> 
> Thanks and regards,
> Yanhe



From yanhezhao1990 at gmail.com  Wed Sep  8 18:15:00 2021
From: yanhezhao1990 at gmail.com (Yanhe Zhao)
Date: Wed, 8 Sep 2021 20:15:00 -0500
Subject: [Chimera-users] local docking
In-Reply-To: <32506BA4-B581-4AA0-896F-1D27E8FDECE0@cgl.ucsf.edu>
References: <CAFxHBUFT_XVbqvJPxkixc6huHEaSM+mJa5_cqySp6kpQbWyepQ@mail.gmail.com>
 <32506BA4-B581-4AA0-896F-1D27E8FDECE0@cgl.ucsf.edu>
Message-ID: <CAFxHBUHn9rpuD52M4p99bSOgXbiYcMH2fC5Nq9uC2BpmNbHQCw@mail.gmail.com>

Hi Elaine,

Thanks a lot for the reply. I done sequential fitting of 3 models which is
looking good. I will play with the way you mentioned to see whether I can
get it better.

Have good night,
Yanhe

Elaine Meng <meng at cgl.ucsf.edu> ?2021?9?8??? ??8:05???

> Hi Yanhe,
> The "fitmap" command with sequential fitting ("sequence" option) will
> fit/move all of the specified models.  There is no option to keep one model
> fixed and move only the other ones.
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence
> >
>
> Also, there is no fitmap option to limit the amount of translation or
> rotation.  Instead there is only an option to turn off translation
> completely (shift false) or turn off rotation completely (rotate false).
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#shift
> >
>
> A longer method might be to first fit one model, then simulate a map from
> it with "molmap" and then subtract the molmap result from the original map
> with "vop subtract," and then use a separate "fitmap" command (with
> "sequence" if you want to sequentially fit the other two).
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract
> >
>
> I hope this helps,
> Elaine
>
>
> > On Sep 8, 2021, at 5:40 PM, Yanhe Zhao via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Greeting,
> >
> > I tried sequential fitting to fit 3 models to my maps. I was wondering
> that if I want to fix one model and do local fitting of another models with
> limited shift and rotation, what command with options should I use?
> >
> > Thanks and regards,
> > Yanhe
>
>
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From goddard at sonic.net  Wed Sep  8 18:15:42 2021
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 8 Sep 2021 18:15:42 -0700
Subject: [Chimera-users] local docking
In-Reply-To: <32506BA4-B581-4AA0-896F-1D27E8FDECE0@cgl.ucsf.edu>
References: <CAFxHBUFT_XVbqvJPxkixc6huHEaSM+mJa5_cqySp6kpQbWyepQ@mail.gmail.com>
 <32506BA4-B581-4AA0-896F-1D27E8FDECE0@cgl.ucsf.edu>
Message-ID: <9A63FF69-DF06-4F08-8394-A8C5CA6FD0E0@sonic.net>

I think you can fit just one model while subtracting the density of the other models, for example,

	fitmap #1,2,3,4 #5 sequence 1

fits model #1 into map #5 after subtracting off density from models #2,3,4.

	Tom

> On Sep 8, 2021, at 6:05 PM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Yanhe,
> The "fitmap" command with sequential fitting ("sequence" option) will fit/move all of the specified models.  There is no option to keep one model fixed and move only the other ones. 
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> 
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#sequence>
> 
> Also, there is no fitmap option to limit the amount of translation or rotation.  Instead there is only an option to turn off translation completely (shift false) or turn off rotation completely (rotate false).
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#shift>
> 
> A longer method might be to first fit one model, then simulate a map from it with "molmap" and then subtract the molmap result from the original map with "vop subtract," and then use a separate "fitmap" command (with "sequence" if you want to sequentially fit the other two).
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>
> 
> I hope this helps,
> Elaine
> 
> 
>> On Sep 8, 2021, at 5:40 PM, Yanhe Zhao via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Greeting,
>> 
>> I tried sequential fitting to fit 3 models to my maps. I was wondering that if I want to fix one model and do local fitting of another models with limited shift and rotation, what command with options should I use? 
>> 
>> Thanks and regards,
>> Yanhe
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From all_zzw at 163.com  Sat Sep 11 08:13:48 2021
From: all_zzw at 163.com (Zhuangwei Zhang)
Date: Sat, 11 Sep 2021 23:13:48 +0800 (GMT+08:00)
Subject: [Chimera-users] Question about using Chimera
Message-ID: <26045017.5703.17bd56bf8e8.Coremail.all_zzw@163.com>

Hello,
Dear Chimera developers?
I encountered some problems when dealing with complexes of peptide-protein docking?Chimera could not correctly recognize the peptide as a single ligand, but recognized the peptide as model 2 and the receptor protein as model 1.
Like this:
I would appreciate it if you could help me answer this question.
Thank you.
Zhuangwei zhang
Zhejiang Oeacn University

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From meng at cgl.ucsf.edu  Sun Sep 12 10:08:59 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sun, 12 Sep 2021 10:08:59 -0700
Subject: [Chimera-users] Combining two models into one model
In-Reply-To: <26045017.5703.17bd56bf8e8.Coremail.all_zzw@163.com>
References: <26045017.5703.17bd56bf8e8.Coremail.all_zzw@163.com>
Message-ID: <48B444BF-C0FC-4593-A961-DF5F027ACFDD@cgl.ucsf.edu>

Hi Zhuangwei Zhang,
Chimera is not doing any "recognizing," this is just because you have the protein and peptide in two different models because they were opened from two different files.  This output PDB file has them as two models, which is OK for many programs.  However, If you want to write a PDB file where both structures are in one model, you have to first combine them.  

In Chimera you can combine models with the "copy/combine" function in the Model Panel (open Model Panel from Favorites menu, choose the two models on the left, i.e. highlight both rows with the mouse, then click the "copy/combine" button on the right, OR you can use the "combine" command.

copy/combine in Model Panel
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>

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

Then just save the new combined model as a PDB file.

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

> On Sep 11, 2021, at 8:13 AM, Zhuangwei Zhang via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> Dear Chimera developers?
> I encountered some problems when dealing with complexes of peptide-protein docking?Chimera could not correctly recognize the peptide as a single ligand, but recognized the peptide as model 2 and the receptor protein as model 1.
> Like this:<781690BA-E872-401A-96D1-4F34E432BFE8.png>
> I would appreciate it if you could help me answer this question.
> Thank you.
> Zhuangwei zhang
> Zhejiang Oeacn University
> 
> <ligand.pdb><receptor.pdb><complex.pdb>x


From all_zzw at 163.com  Sun Sep 12 18:30:43 2021
From: all_zzw at 163.com (Zhuangwei Zhang)
Date: Mon, 13 Sep 2021 09:30:43 +0800 (GMT+08:00)
Subject: [Chimera-users] Combining two models into one model
In-Reply-To: <48B444BF-C0FC-4593-A961-DF5F027ACFDD@cgl.ucsf.edu>
References: <26045017.5703.17bd56bf8e8.Coremail.all_zzw@163.com>
 <48B444BF-C0FC-4593-A961-DF5F027ACFDD@cgl.ucsf.edu>
Message-ID: <52e38faa.987.17bdcc7220d.Coremail.all_zzw@163.com>

Dear Elaine C. Meng, Ph.D.,
Thank you very much for your suggestion.
Currently, there are not many people using chimera software in China. This is because the professors are using PyMOL, so the students do not have a good understanding of the ease of use of chimera software. I am translating and promoting the basic manual of chimera software. I look forward to more people knowing and using this software in the future.
Thanks again for your help!
Zhuangwei zhang
Zhejiang Oeacn University




On 09/13/2021 01:08?Elaine Meng<meng at cgl.ucsf.edu> wrote?
Hi Zhuangwei Zhang,
Chimera is not doing any "recognizing," this is just because you have the protein and peptide in two different models because they were opened from two different files.  This output PDB file has them as two models, which is OK for many programs.  However, If you want to write a PDB file where both structures are in one model, you have to first combine them.  

In Chimera you can combine models with the "copy/combine" function in the Model Panel (open Model Panel from Favorites menu, choose the two models on the left, i.e. highlight both rows with the mouse, then click the "copy/combine" button on the right, OR you can use the "combine" command.

copy/combine in Model Panel
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>

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

Then just save the new combined model as a PDB file.

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

On Sep 11, 2021, at 8:13 AM, Zhuangwei Zhang via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:

Hello,
Dear Chimera developers?
I encountered some problems when dealing with complexes of peptide-protein docking?Chimera could not correctly recognize the peptide as a single ligand, but recognized the peptide as model 2 and the receptor protein as model 1.
Like this:<781690BA-E872-401A-96D1-4F34E432BFE8.png>
I would appreciate it if you could help me answer this question.
Thank you.
Zhuangwei zhang
Zhejiang Oeacn University

<ligand.pdb><receptor.pdb><complex.pdb>x
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From prathvi at iitk.ac.in  Thu Sep 16 00:21:36 2021
From: prathvi at iitk.ac.in (Prathvi Singh)
Date: Thu, 16 Sep 2021 12:51:36 +0530
Subject: [Chimera-users] How to sequentially open PDB files using a "for
 loop" in the UCSF chimera's command line?
Message-ID: <CAD3Hi5Y_vmQn0btKKHAnOqdPD+Gtp_bOWMUMbJes75LCXW8B_g@mail.gmail.com>

Greetings,

Is it possible to use a "for loop" in the UCSF chimera's command line to
open a PDB file, perform an action (say delete an atom), save the PDB file
& close it, open the next PDB file, perform the same operation, save it &
close it and so on.

Thanks,
Prathvi
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From meng at cgl.ucsf.edu  Thu Sep 16 09:09:33 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 16 Sep 2021 09:09:33 -0700
Subject: [Chimera-users] How to sequentially open PDB files using a "for
 loop" in the UCSF chimera's command line?
In-Reply-To: <CAD3Hi5Y_vmQn0btKKHAnOqdPD+Gtp_bOWMUMbJes75LCXW8B_g@mail.gmail.com>
References: <CAD3Hi5Y_vmQn0btKKHAnOqdPD+Gtp_bOWMUMbJes75LCXW8B_g@mail.gmail.com>
Message-ID: <AEE4655A-5396-4A49-A777-A9F69684B8B1@cgl.ucsf.edu>

Hi Prathvi,
There is no "for loop" to process multiple PDB files using the Chimera command line.  Instead you would have to use Python as described here:
<https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

However, you can do it in ChimeraX:  when opening a ChimeraX command file, you can use the ChimeraX command "open" with the "forEachFile" option to run it on multiple input files, e.g.

open myscript.cxc foreach  ~/mypdbfolder/*.pdb

<https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files>
<https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile>

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

> On Sep 16, 2021, at 12:21 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Greetings,
> Is it possible to use a "for loop" in the UCSF chimera's command line to open a PDB file, perform an action (say delete an atom), save the PDB file & close it, open the next PDB file, perform the same operation, save it & close it and so on.
> Thanks,
> Prathvi



From meng at cgl.ucsf.edu  Thu Sep 16 09:10:02 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 16 Sep 2021 09:10:02 -0700
Subject: [Chimera-users] Combining two models into one model
In-Reply-To: <52e38faa.987.17bdcc7220d.Coremail.all_zzw@163.com>
References: <26045017.5703.17bd56bf8e8.Coremail.all_zzw@163.com>
 <48B444BF-C0FC-4593-A961-DF5F027ACFDD@cgl.ucsf.edu>
 <52e38faa.987.17bdcc7220d.Coremail.all_zzw@163.com>
Message-ID: <62EE7D74-FD45-46F6-9406-D5D3E75C0229@cgl.ucsf.edu>

Thanks for helping people use Chimera!

I encourage you to take a look at ChimeraX, our newer program.  If we make new tools and developments, they will be in ChimeraX (not Chimera), and it already has many improvements relative to Chimera.  It also has many of the most popular features of Chimera, and I also think it is easier to use.  

<https://www.rbvi.ucsf.edu/chimerax/index.html>
<https://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html>
<https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html>

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

> On Sep 12, 2021, at 6:30 PM, Zhuangwei Zhang via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Elaine C. Meng, Ph.D.,
> Thank you very much for your suggestion.
> Currently, there are not many people using chimera software in China. This is because the professors are using PyMOL, so the students do not have a good understanding of the ease of use of chimera software. I am translating and promoting the basic manual of chimera software. I look forward to more people knowing and using this software in the future.
> Thanks again for your help!
> Zhuangwei zhang
> Zhejiang Oeacn University
> 
> 
> On 09/13/2021 01:08?Elaine Meng<meng at cgl.ucsf.edu> wrote? 
> Hi Zhuangwei Zhang,
> Chimera is not doing any "recognizing," this is just because you have the protein and peptide in two different models because they were opened from two different files.  This output PDB file has them as two models, which is OK for many programs.  However, If you want to write a PDB file where both structures are in one model, you have to first combine them.  
> 
> In Chimera you can combine models with the "copy/combine" function in the Model Panel (open Model Panel from Favorites menu, choose the two models on the left, i.e. highlight both rows with the mouse, then click the "copy/combine" button on the right, OR you can use the "combine" command.
> 
> copy/combine in Model Panel
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>
> 
> combine command:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
> 
> Then just save the new combined model as a PDB file.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Sep 11, 2021, at 8:13 AM, Zhuangwei Zhang via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> Dear Chimera developers?
> I encountered some problems when dealing with complexes of peptide-protein docking?Chimera could not correctly recognize the peptide as a single ligand, but recognized the peptide as model 2 and the receptor protein as model 1.
> Like this:<781690BA-E872-401A-96D1-4F34E432BFE8.png>
> I would appreciate it if you could help me answer this question.
> Thank you.
> Zhuangwei zhang
> Zhejiang Oeacn University
> 
> <ligand.pdb><receptor.pdb><complex.pdb>x
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From joshloecker at icloud.com  Thu Sep 16 09:21:46 2021
From: joshloecker at icloud.com (joshloecker at icloud.com)
Date: Thu, 16 Sep 2021 16:21:46 +0000
Subject: [Chimera-users] Setting Default Colors
Message-ID: <DM6PR16MB29397CC32A32CA648349A4D3A5DC9@DM6PR16MB2939.namprd16.prod.outlook.com>

Hello,
I have recently started using Chimera and I am having a problem setting a default color when starting a session (if this is possible). When I open a model, it opens in a tan color, which I like because it is easy to pick out other molecules, such as SO4, etc. However, when closing the session and opening the same model, it opens in a variety of other colors, such as bright red, pink, purple, orange, etc. that are distracting to what I am trying to do.

I have found the section in Preferences > New Molecules to not use a new color for each model, but then if I load multiple models I cannot distinguish between them. I was wondering if it was possible to set a default color to open models in, or if I have to quit Chimera each time I open a single model in order to get the easy-to-see tan color?

--
Thank you,
Josh Loecker
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From meng at cgl.ucsf.edu  Thu Sep 16 10:53:42 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 16 Sep 2021 10:53:42 -0700
Subject: [Chimera-users] Setting Default Colors
In-Reply-To: <DM6PR16MB29397CC32A32CA648349A4D3A5DC9@DM6PR16MB2939.namprd16.prod.outlook.com>
References: <DM6PR16MB29397CC32A32CA648349A4D3A5DC9@DM6PR16MB2939.namprd16.prod.outlook.com>
Message-ID: <DACD715E-EC1B-4006-9AC5-38800965A425@cgl.ucsf.edu>

Hi Josh,
When I "close session" or "close all" models and open a new atomic model, it always starts over with the first color (tan). I don't know why you would get a different behavior... are you using a very old version of Chimera?

In the New Molecules preferences that you mentioned, you can set default model color.  I.e. set the "use new color for each model" to false, then right below it, change the "otherwise, use color" setting.   Click the square color well to open the color chooser, where you can designate tan or some other color. This will make all (atomic) models that same color, however, so you wouldn't be able to tell them apart. 

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules>

There isn't an option to set multiple default colors for the different model numbers, if that's what you meant.

Besides the preferences, you can always change the color after opening, e.g. if the model is #0, command

modelcolor tan #0

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

Color names:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortables.html#allcolors>

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

> On Sep 16, 2021, at 9:21 AM, joshloecker--- via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I have recently started using Chimera and I am having a problem setting a default color when starting a session (if this is possible). When I open a model, it opens in a tan color, which I like because it is easy to pick out other molecules, such as SO4, etc. However, when closing the session and opening the same model, it opens in a variety of other colors, such as bright red, pink, purple, orange, etc. that are distracting to what I am trying to do.
> 
> I have found the section in Preferences > New Molecules to not use a new color for each model, but then if I load multiple models I cannot distinguish between them. I was wondering if it was possible to set a default color to open models in, or if I have to quit Chimera each time I open a single model in order to get the easy-to-see tan color? 
> -- 
> Thank you,
> Josh Loecker



From joshloecker at icloud.com  Thu Sep 16 10:59:43 2021
From: joshloecker at icloud.com (joshloecker at icloud.com)
Date: Thu, 16 Sep 2021 17:59:43 +0000
Subject: [Chimera-users] Setting Default Colors
In-Reply-To: <DACD715E-EC1B-4006-9AC5-38800965A425@cgl.ucsf.edu>
References: <DM6PR16MB29397CC32A32CA648349A4D3A5DC9@DM6PR16MB2939.namprd16.prod.outlook.com>
 <DACD715E-EC1B-4006-9AC5-38800965A425@cgl.ucsf.edu>
Message-ID: <DM6PR16MB29393A8195ED287A09F7F319A5DC9@DM6PR16MB2939.namprd16.prod.outlook.com>

I am currently using Chimera 1.15 for Mac. I will try uninstalling and re-installing to see if this fixes the issue. Thank you for letting me know, though, that opening the first model should open with the tan color

--
Thank you,
Josh Loecker

From: Elaine Meng <meng at cgl.ucsf.edu>
Date: Thursday, September 16, 2021 at 12:53 PM
To: joshloecker at icloud.com <joshloecker at icloud.com>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Setting Default Colors
Hi Josh,
When I "close session" or "close all" models and open a new atomic model, it always starts over with the first color (tan). I don't know why you would get a different behavior... are you using a very old version of Chimera?

In the New Molecules preferences that you mentioned, you can set default model color.  I.e. set the "use new color for each model" to false, then right below it, change the "otherwise, use color" setting.   Click the square color well to open the color chooser, where you can designate tan or some other color. This will make all (atomic) models that same color, however, so you wouldn't be able to tell them apart.

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules>

There isn't an option to set multiple default colors for the different model numbers, if that's what you meant.

Besides the preferences, you can always change the color after opening, e.g. if the model is #0, command

modelcolor tan #0

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

Color names:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortables.html#allcolors>

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

> On Sep 16, 2021, at 9:21 AM, joshloecker--- via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hello,
> I have recently started using Chimera and I am having a problem setting a default color when starting a session (if this is possible). When I open a model, it opens in a tan color, which I like because it is easy to pick out other molecules, such as SO4, etc. However, when closing the session and opening the same model, it opens in a variety of other colors, such as bright red, pink, purple, orange, etc. that are distracting to what I am trying to do.
>
> I have found the section in Preferences > New Molecules to not use a new color for each model, but then if I load multiple models I cannot distinguish between them. I was wondering if it was possible to set a default color to open models in, or if I have to quit Chimera each time I open a single model in order to get the easy-to-see tan color?
> --
> Thank you,
> Josh Loecker
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From prathvi at iitk.ac.in  Sat Sep 18 07:13:33 2021
From: prathvi at iitk.ac.in (Prathvi Singh)
Date: Sat, 18 Sep 2021 19:43:33 +0530
Subject: [Chimera-users] How to sequentially open PDB files using a "for
 loop" in the UCSF chimera's command line?
In-Reply-To: <AEE4655A-5396-4A49-A777-A9F69684B8B1@cgl.ucsf.edu>
References: <CAD3Hi5Y_vmQn0btKKHAnOqdPD+Gtp_bOWMUMbJes75LCXW8B_g@mail.gmail.com>
 <AEE4655A-5396-4A49-A777-A9F69684B8B1@cgl.ucsf.edu>
Message-ID: <CAD3Hi5Y9-x_ivXzvNBwHXY1ZLHpmQAXSS6KW4UG9An2CsU63LA@mail.gmail.com>

Thanks a lot!

On Thu, Sep 16, 2021 at 9:39 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Prathvi,
> There is no "for loop" to process multiple PDB files using the Chimera
> command line.  Instead you would have to use Python as described here:
> <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
>
> However, you can do it in ChimeraX:  when opening a ChimeraX command file,
> you can use the ChimeraX command "open" with the "forEachFile" option to
> run it on multiple input files, e.g.
>
> open myscript.cxc foreach  ~/mypdbfolder/*.pdb
>
> <
> https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files
> >
> <
> https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Sep 16, 2021, at 12:21 AM, Prathvi Singh via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Greetings,
> > Is it possible to use a "for loop" in the UCSF chimera's command line to
> open a PDB file, perform an action (say delete an atom), save the PDB file
> & close it, open the next PDB file, perform the same operation, save it &
> close it and so on.
> > Thanks,
> > Prathvi
>
>

-- 
Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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From yuweizhu at hit.edu.cn  Wed Sep 22 01:35:33 2021
From: yuweizhu at hit.edu.cn (=?UTF-8?B?5pyx546J5aiB?=)
Date: Wed, 22 Sep 2021 16:35:33 +0800 (GMT+08:00)
Subject: [Chimera-users] question about label chain?
Message-ID: <353c3fc2.2e97.17c0ca550f5.Coremail.yuweizhu@hit.edu.cn>

Dear developer?




  Could you kindly tell me how to label each chains. I need it to make a movie.




  Thank you very much.




  Best wishes!
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From meng at cgl.ucsf.edu  Wed Sep 22 08:28:15 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 22 Sep 2021 08:28:15 -0700
Subject: [Chimera-users] question about label chain?
In-Reply-To: <353c3fc2.2e97.17c0ca550f5.Coremail.yuweizhu@hit.edu.cn>
References: <353c3fc2.2e97.17c0ca550f5.Coremail.yuweizhu@hit.edu.cn>
Message-ID: <D061A1B6-3FF4-43B2-A5A9-112F6FB7D0A8@cgl.ucsf.edu>

Dear user,
For making nice labels that can be any sizes and colors for figures and movies, we usually recommend 2D Labels (graphical interface) or for scripting, the 2dlabels command.  These 2D labels just stay in the place that you put them and do not automatically move with the structure.

2D Labels GUI:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html>

2dlabels command:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html>

See also movie example command files:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples>

Here's a nice example open-access publication with two movies that have 2D labels and arrows:
<https://www.nature.com/articles/s41467-021-24651-2>

However, if you meant labels that automatically move with the structure, then you have to use custom atom ("3D") labeling.   There isn't really a label chain, instead you have to choose which atoms to label and then show the chain info in the atom label.  For example you could select one atom, then open Selection Inspector (by clicking the green magnifying glass on the bottom right corner of the window), then just enter in the "label" field whatever you want the label to say.  Or, you could use menu: Actions... Label... other... and again enter what you want the label to say. 

Those "3D labels" are all the same size as each other, controlled in the Preferences (category: Labels) and you'd need to use "color" to change their colors.

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

> On Sep 22, 2021, at 1:35 AM, ??? via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear developer?
>   Could you kindly tell me how to label each chains. I need it to make a movie.
>   Thank you very much.
>   Best wishes!



From mr_yuzhou at yahoo.com  Wed Sep 22 09:05:02 2021
From: mr_yuzhou at yahoo.com (Yu Zhou)
Date: Wed, 22 Sep 2021 16:05:02 +0000 (UTC)
Subject: [Chimera-users] Visualize chain break in Chimera
References: <797071059.242839.1632326703294.ref@mail.yahoo.com>
Message-ID: <797071059.242839.1632326703294@mail.yahoo.com>

Dear all,
I am going through a Rosetta protein-protein docking tutorial using Chimera as the structure viewer. There is a chain break in the structure used for this tutorial (3gbn), which is caused by a severed connection between residue 127 and 128. Such chain break needs to be identified and fixed in a structural model before it could be used for Rosetta simulation.?
This chain break can be easily identified in Pymol as it is displayed as a dotted line. However, I cannot see this chain break in Chimera (and ChimeraX) as the segment is rendered as a beta-sheet.?
Is there a way to visualize such chain break in Chimera?
Thanks,
Yu Zhou


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From meng at cgl.ucsf.edu  Wed Sep 22 10:43:00 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 22 Sep 2021 10:43:00 -0700
Subject: [Chimera-users] Visualize chain break in Chimera
In-Reply-To: <797071059.242839.1632326703294@mail.yahoo.com>
References: <797071059.242839.1632326703294.ref@mail.yahoo.com>
 <797071059.242839.1632326703294@mail.yahoo.com>
Message-ID: <5C1802DF-7163-44EB-8AEC-4477961D4490@cgl.ucsf.edu>

Dear Yu Zou,
The PDB file does not explicitly say there is a chain break (there is no TER line) and there are no missing backbone atoms, so Chimera assumes that the consecutive residues in the same chain are bonded as normal.  In other structures where there are missing residues, Chimera does show the dotted line (e.g. PDB structure 1maz).

However, the bond between 127 and 128 is abnormally long (2.1 Angstroms).  Probably Pymol detects the abnormally long bond and automatically makes it a chain break.

I could tell that by hiding the ribbons (command: ~ribbon) and showing atoms (command: display) in Chimera, and then putting the cursor over the bond to show the pop-up with the bond length.  You can remove the bond, e.g. command:

~bond :127 at c:128 at n

However, it still won't show the dotted line automatically because none of the atoms are missing.  You could draw a dotted line by measuring the distance and then hiding the distance label, command:

distance :127 at c:128 at n

... and then menu: Tools... Structure Analysis... Distance, and use settings in that dialog to hide label, change color of dotted line, etc.  See attached image.

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




> On Sep 22, 2021, at 9:05 AM, Yu Zhou via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear all,
> 
> I am going through a Rosetta protein-protein docking tutorial using Chimera as the structure viewer. There is a chain break in the structure used for this tutorial (3gbn), which is caused by a severed connection between residue 127 and 128. Such chain break needs to be identified and fixed in a structural model before it could be used for Rosetta simulation. 
> 
> This chain break can be easily identified in Pymol as it is displayed as a dotted line. However, I cannot see this chain break in Chimera (and ChimeraX) as the segment is rendered as a beta-sheet. 
> 
> Is there a way to visualize such chain break in Chimera?
> 
> Thanks,
> 
> Yu Zhou
> 
> 
> 
> <Pymol_chain break.jpg><Chimera_no chain break.jpg><3gbn_Ab.pdb>_______________________________________________
> 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 mr_yuzhou at yahoo.com  Wed Sep 22 11:09:58 2021
From: mr_yuzhou at yahoo.com (Yu Zhou)
Date: Wed, 22 Sep 2021 18:09:58 +0000 (UTC)
Subject: [Chimera-users] Visualize chain break in Chimera
In-Reply-To: <5C1802DF-7163-44EB-8AEC-4477961D4490@cgl.ucsf.edu>
References: <797071059.242839.1632326703294.ref@mail.yahoo.com>
 <797071059.242839.1632326703294@mail.yahoo.com>
 <5C1802DF-7163-44EB-8AEC-4477961D4490@cgl.ucsf.edu>
Message-ID: <1617667164.284792.1632334198260@mail.yahoo.com>

 Elaine

Thank you for your help.
Yu

    On Wednesday, September 22, 2021, 12:43:02 PM CDT, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 
 Dear Yu Zou,The PDB file does not explicitly say there is a chain break (there is no TER line) and there are no missing backbone atoms, so Chimera assumes that the consecutive residues in the same chain are bonded as normal. ?In other structures where there are missing residues, Chimera does show the dotted line (e.g. PDB structure 1maz).
However, the bond between 127 and 128 is abnormally long (2.1 Angstroms). ?Probably Pymol detects the abnormally long bond and automatically makes it a chain break.
I could tell that by hiding the ribbons (command: ~ribbon) and showing atoms (command: display) in Chimera, and then putting the cursor over the bond to show the pop-up with the bond length. ?You can remove the bond, e.g. command:
~bond :127 at c:128 at n
However, it still won't show the dotted line automatically because none of the atoms are missing. ?You could draw a dotted line by measuring the distance and then hiding the distance label, command:
distance?:127 at c:128 at n
... and then menu: Tools... Structure Analysis... Distance, and use settings in that dialog to hide label, change color of dotted line, etc. ?See attached image.
I hope this helps,Elaine
-----
Elaine C. Meng, Ph.D.? ? ? ? ? ? ? ? ? ? ? ?
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco





On Sep 22, 2021, at 9:05 AM, Yu Zhou via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:

Dear all,

I am going through a Rosetta protein-protein docking tutorial using Chimera as the structure viewer. There is a chain break in the structure used for this?tutorial (3gbn), which is caused by a severed connection between residue 127 and 128. Such chain break needs to be identified and fixed in a?structural model before it could be used for Rosetta simulation.?

This chain break can be easily identified in Pymol as it is displayed as a dotted line. However, I cannot see this chain break in Chimera (and ChimeraX)?as the segment is rendered as a beta-sheet.?

Is there a way to visualize such chain break in Chimera?

Thanks,

Yu Zhou



<Pymol_chain break.jpg><Chimera_no chain break.jpg><3gbn_Ab.pdb>_______________________________________________
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 nostrov at bu.edu  Wed Sep 22 13:56:06 2021
From: nostrov at bu.edu (Nicole Ostrovsky)
Date: Wed, 22 Sep 2021 16:56:06 -0400
Subject: [Chimera-users] Connecting ends of a peptide
Message-ID: <CAMiWtun7kEnS6pHEOTFLkgK+rFFTJqLLM0ywEJ49CEAnHfbSxw@mail.gmail.com>

Hello,

I am trying to connect two sides of a peptide together to make it cyclic.
Is there a way to do this that doesn't involve adding in another amino
acid? I have been adding a glycine by individual atom using the modify
structure tool but I'm wondering if I can do it a different way.

Best,
Nicole Ostrovsky
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From meng at cgl.ucsf.edu  Wed Sep 22 14:14:57 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 22 Sep 2021 14:14:57 -0700
Subject: [Chimera-users] Connecting ends of a peptide
In-Reply-To: <CAMiWtun7kEnS6pHEOTFLkgK+rFFTJqLLM0ywEJ49CEAnHfbSxw@mail.gmail.com>
References: <CAMiWtun7kEnS6pHEOTFLkgK+rFFTJqLLM0ywEJ49CEAnHfbSxw@mail.gmail.com>
Message-ID: <4235E0AF-BCB7-477C-B0CF-CA6DC56DBFE8@cgl.ucsf.edu>

Hi Nicole,
You could just add a bond (after deleting any other atoms as needed to make a "vacancy" on the two atoms to be bonded).  E.g. see attached picture from opening 1gcn, hiding ribbon, showing atoms, deleting one of the C-terminal carboxylate oxygens, and then adding a bond.

open 1gcn
~ribbon
display
delete :29 at oxt
bond :1 at n:29 at c

Of course this could make a really bad structure with a ridiculous long bond, and minimization has only very limited ability to "rescue" such a thing.  But maybe you were planning to do molecular dynamics or other modeling that might be able to work from that starting point.  Or you could try rotating some of the backbone torsions before forming the bond to make it less ridiculous.

See "modifying structures" page and links therein
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.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 Sep 22, 2021, at 1:56 PM, Nicole Ostrovsky via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> I am trying to connect two sides of a peptide together to make it cyclic. Is there a way to do this that doesn't involve adding in another amino acid? I have been adding a glycine by individual atom using the modify structure tool but I'm wondering if I can do it a different way.
> 
> Best,
> Nicole Ostrovsky



From meng at cgl.ucsf.edu  Wed Sep 22 14:17:52 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 22 Sep 2021 14:17:52 -0700
Subject: [Chimera-users] Connecting ends of a peptide
In-Reply-To: <4235E0AF-BCB7-477C-B0CF-CA6DC56DBFE8@cgl.ucsf.edu>
References: <CAMiWtun7kEnS6pHEOTFLkgK+rFFTJqLLM0ywEJ49CEAnHfbSxw@mail.gmail.com>
 <4235E0AF-BCB7-477C-B0CF-CA6DC56DBFE8@cgl.ucsf.edu>
Message-ID: <8326F444-98E6-4048-9E5D-FF5E43406ADA@cgl.ucsf.edu>

Oops, here is the picture I forgot to attach (not that it's terribly useful anyway)!




> On Sep 22, 2021, at 2:14 PM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Nicole,
> You could just add a bond (after deleting any other atoms as needed to make a "vacancy" on the two atoms to be bonded).  E.g. see attached picture from opening 1gcn, hiding ribbon, showing atoms, deleting one of the C-terminal carboxylate oxygens, and then adding a bond.
> 
> open 1gcn
> ~ribbon
> display
> delete :29 at oxt
> bond :1 at n:29 at c
> 
> Of course this could make a really bad structure with a ridiculous long bond, and minimization has only very limited ability to "rescue" such a thing.  But maybe you were planning to do molecular dynamics or other modeling that might be able to work from that starting point.  Or you could try rotating some of the backbone torsions before forming the bond to make it less ridiculous.
> 
> See "modifying structures" page and links therein
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.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 Sep 22, 2021, at 1:56 PM, Nicole Ostrovsky via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Hello,
>> 
>> I am trying to connect two sides of a peptide together to make it cyclic. Is there a way to do this that doesn't involve adding in another amino acid? I have been adding a glycine by individual atom using the modify structure tool but I'm wondering if I can do it a different way.
>> 
>> Best,
>> Nicole Ostrovsky
> 
> 
> _______________________________________________
> 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 olibclarke at gmail.com  Thu Sep 23 16:23:48 2021
From: olibclarke at gmail.com (Oliver Clarke)
Date: Thu, 23 Sep 2021 19:23:48 -0400
Subject: [Chimera-users] Running 3D-FSC script causes freeze
Message-ID: <31BFD5EA-217B-4569-BD85-B3FFA3DF9EE8@gmail.com>

Hi,

Running the chimera command file included with the example data for 3D-FSC (https://github.com/LyumkisLab/3DFSC/tree/master/Example/Results_T40-3DFSC/Chimera <https://github.com/LyumkisLab/3DFSC/tree/master/Example/Results_T40-3DFSC/Chimera>) causes the latest daily build of Chimera to freeze - it executes lineplot.py, but then just locks up and does not respond. This happens whether I run it as `chimera 3DFSCPlot_Chimera.cmd` or load the command file after opening the GUI. Am I doing something wrong, or has something changed in Chimera that has broken this script?

Cheers
Oli
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From goddard at sonic.net  Thu Sep 23 18:10:55 2021
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 23 Sep 2021 18:10:55 -0700
Subject: [Chimera-users] Running 3D-FSC script causes freeze
In-Reply-To: <31BFD5EA-217B-4569-BD85-B3FFA3DF9EE8@gmail.com>
References: <31BFD5EA-217B-4569-BD85-B3FFA3DF9EE8@gmail.com>
Message-ID: <2D519DF0-B931-4737-8F11-144BB8AC40A4@sonic.net>

Hi Oliver,

  I find that that example code also hangs in Chimera 1.15 most of the time.  The problem seems to be with matplotlib showing the plot window.  If the plot window shows then it does not hang.  If the plot window does not show then it hangs.  Which happens seems to depend on some timing issue.  When I click on the Recent Files button for script 3DFSCPlot_Chimera.cmd (which I previously tried to open by command) then it seemed to always work.  Sometimes it works 3 times in a row with the command, then hangs for the next 3 tries.

  I did my test on macOS Big Sur (11.5.7).  Maybe the problem depends on your operating system.  I would not be surprised if this is a macOS-only Tk bug.  It appears to be a problem with the Tk window toolkit showing the matplotlib window.  The poor support for the archaic Tk toolkit used by Chimera is a major reason why we developed ChimeraX based on the Qt window toolkit.

  At any rate, I don't have any suggestion for fixing this.  We only debug and fix critical bugs in Chimera, all funding has for many years been for ChimeraX development only.

	Tom

> On Sep 23, 2021, at 4:23 PM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> 
> Running the chimera command file included with the example data for 3D-FSC (https://github.com/LyumkisLab/3DFSC/tree/master/Example/Results_T40-3DFSC/Chimera <https://github.com/LyumkisLab/3DFSC/tree/master/Example/Results_T40-3DFSC/Chimera>) causes the latest daily build of Chimera to freeze - it executes lineplot.py, but then just locks up and does not respond. This happens whether I run it as `chimera 3DFSCPlot_Chimera.cmd` or load the command file after opening the GUI. Am I doing something wrong, or has something changed in Chimera that has broken this script?
> 
> Cheers
> Oli
> _______________________________________________
> 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 leiqian at temple.edu  Sat Sep 25 10:17:47 2021
From: leiqian at temple.edu (Lei Qian)
Date: Sat, 25 Sep 2021 17:17:47 +0000
Subject: [Chimera-users] question on protein structure change after
 matchmaker (position-change) operation
Message-ID: <CY4PR11MB1448880358D4A79529372111D2A59@CY4PR11MB1448.namprd11.prod.outlook.com>

Dear users,
After aligning protein A to protein B using matchmaker, I found the protein A structure slightly changed compared with its original structure (RMSD: 0.001).
Could I ask how I can keep protein A structure unchanged after matchmaker (position-change) operation?
Thanks!
Lei
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From meng at cgl.ucsf.edu  Sun Sep 26 09:11:58 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sun, 26 Sep 2021 09:11:58 -0700
Subject: [Chimera-users] question on protein structure change after
 matchmaker (position-change) operation
In-Reply-To: <CY4PR11MB1448880358D4A79529372111D2A59@CY4PR11MB1448.namprd11.prod.outlook.com>
References: <CY4PR11MB1448880358D4A79529372111D2A59@CY4PR11MB1448.namprd11.prod.outlook.com>
Message-ID: <BD63F822-C716-463B-9B04-7E02DD231972@cgl.ucsf.edu>

Hi Lei,
Matchmaker itself does not change the structure. However, if you save a PDB file after moving any atomic structure (by any method), because of rounding you may get tiny differences comparing the structures before and after.  PDB file format only has 3 digits after the decimal in X,Y,Z coordinates.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 25, 2021, at 10:17 AM, Lei Qian via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear users,
> After aligning protein A to protein B using matchmaker, I found the protein A structure slightly changed compared with its original structure (RMSD: 0.001).
> Could I ask how I can keep protein A structure unchanged after matchmaker (position-change) operation?
> Thanks!
> Lei



From leiqian at temple.edu  Mon Sep 27 10:06:59 2021
From: leiqian at temple.edu (Lei Qian)
Date: Mon, 27 Sep 2021 17:06:59 +0000
Subject: [Chimera-users] question on protein structure change after
 matchmaker (position-change) operation
In-Reply-To: <BD63F822-C716-463B-9B04-7E02DD231972@cgl.ucsf.edu>
References: <CY4PR11MB1448880358D4A79529372111D2A59@CY4PR11MB1448.namprd11.prod.outlook.com>
 <BD63F822-C716-463B-9B04-7E02DD231972@cgl.ucsf.edu>
Message-ID: <CY4PR11MB14483BC60F9E96D4D904A82BD2A79@CY4PR11MB1448.namprd11.prod.outlook.com>

Hi Elaine,
Thank you very much for your explanation!
Best,
Lei
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, September 27, 2021 12:11 AM
To: Lei Qian <leiqian at temple.edu>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] question on protein structure change after matchmaker (position-change) operation

Hi Lei,
Matchmaker itself does not change the structure. However, if you save a PDB file after moving any atomic structure (by any method), because of rounding you may get tiny differences comparing the structures before and after.  PDB file format only has 3 digits after the decimal in X,Y,Z coordinates.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 25, 2021, at 10:17 AM, Lei Qian via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Dear users,
> After aligning protein A to protein B using matchmaker, I found the protein A structure slightly changed compared with its original structure (RMSD: 0.001).
> Could I ask how I can keep protein A structure unchanged after matchmaker (position-change) operation?
> Thanks!
> Lei

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From jtrickett at uri.edu  Mon Sep 27 14:08:48 2021
From: jtrickett at uri.edu (Justin Trickett)
Date: Mon, 27 Sep 2021 17:08:48 -0400
Subject: [Chimera-users] Crashes during Dock Prep
Message-ID: <CAKWqZKZMn05V8bpXbdL6Kt_Uwq_PddW2NqTM3G+jwGPGxahBhw@mail.gmail.com>

Hello,

I am prepping 43 structures for docking using the "Dock Prep" feature in
Chimera 1.15, and it crashes every time it gets to "Retrieving rotamers
from Dunbrack library."

Am I doing something wrong?

Many thanks,
Justin
-- 
Justin Trickett
Graduate Student
College of Pharmacy, University of Rhode Island
(603) 505-1061
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From meng at cgl.ucsf.edu  Mon Sep 27 14:25:51 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 27 Sep 2021 14:25:51 -0700
Subject: [Chimera-users] Crashes during Dock Prep
In-Reply-To: <CAKWqZKZMn05V8bpXbdL6Kt_Uwq_PddW2NqTM3G+jwGPGxahBhw@mail.gmail.com>
References: <CAKWqZKZMn05V8bpXbdL6Kt_Uwq_PddW2NqTM3G+jwGPGxahBhw@mail.gmail.com>
Message-ID: <5D79D21C-FEAD-468A-8694-F93E78D70A3F@cgl.ucsf.edu>

Hi Justin,
This isn't enough information to tell what is happening.  Please use menu: Help... Report a Bug, and in that bug-report form include your e-mail address if you want feedback, describe all  the steps needed to get the crash, and attach any data file needed to reproduce the crash  (e.g. one of your input structures, if that is enough to do it).  The bug-reporting form will also automatically tell us what platform you are on and what version of Chimera you were using.  Then we might be able to tell if you did anything wrong, or if it's a bug, to try to fix it, or figure out if it's something weird about your input structures.
Thanks
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 27, 2021, at 2:08 PM, Justin Trickett via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I am prepping 43 structures for docking using the "Dock Prep" feature in Chimera 1.15, and it crashes every time it gets to "Retrieving rotamers from Dunbrack library."
> 
> Am I doing something wrong?
> Many thanks,
> Justin



From arley.paez at estudante.ufla.br  Wed Sep 29 07:35:16 2021
From: arley.paez at estudante.ufla.br (ARLEY REY PAEZ)
Date: Wed, 29 Sep 2021 11:35:16 -0300
Subject: [Chimera-users] questions
Message-ID: <CAAgwpEmOp5vzzontHiLTtNPp-Z+rNBn3v7esB7ViL+LGiWyuxA@mail.gmail.com>

Best regard,
My name is Arley, I am a postgraduate student at the federal university of
Lavras, Brazil.
I write this message because I have doubts about how to calculate the RMSD
between two ligands after docking and redocking. My question is if Chimera
works well to perform that calculation, since when for example I have two
structures (ligands) that are, visually well superimposed and I calculate
the value of RMSD with the use of the rmsd # 0 # 1 command, their value is
high when compared With a structure that is not visually superimposed, why
does that happen? Is it that chimera is not useful to carry out this task?
I appreciate you can help me with that concern.

Att;

Arley

-- 
Este e-mail foi enviado por um estudante da Universidade Federal de Lavras 
(UFLA). Caso esta mensagem possua algum conte?do n?o apropriado, favor 
desconsider?-la.
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From meng at cgl.ucsf.edu  Wed Sep 29 08:47:43 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 29 Sep 2021 08:47:43 -0700
Subject: [Chimera-users] using rmsd to compare ligand positions
In-Reply-To: <CAAgwpEmOp5vzzontHiLTtNPp-Z+rNBn3v7esB7ViL+LGiWyuxA@mail.gmail.com>
References: <CAAgwpEmOp5vzzontHiLTtNPp-Z+rNBn3v7esB7ViL+LGiWyuxA@mail.gmail.com>
Message-ID: <0160C97A-8EF3-4DFF-906F-DADF73DEF74F@cgl.ucsf.edu>

Hi Arley,
The issue is how the atoms of the two copies are paired.  If the atoms to be matched with one another do not have the same atom names in #0 and #1, then simply saying "rmsd #0 #1" will give a higher value than expected.  To control the order in which they are paired, you may need to list the atoms individually in the command. Here is what it says in the help page for "rmsd":
=-=
If atom order is not specified, for example,

rmsd #1:fad #0:fad 
rmsd #2:246,295 #0:195,221

...the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number.
=-=
see: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>

To list the atoms individually in the command would look something like this, pretending my ligand residues are named XXX and YYY :

rmsd #0:XXX at C1,C4,C3,C2,N  #1:YYY at C1,C2,C3,C4,N3

... would pair C1 of XXX with C1 of YYY, C4 with C2, C3 with C3, C2 with C4, and N with N3 to calculate the RMSD.

Or, as also mentioned in the help page, you can select the atoms with the mouse (Shift-Ctrl-click) one by one in the same order first from #0 and then from #1 and then use command

rmsd sel

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




> On Sep 29, 2021, at 7:35 AM, ARLEY REY PAEZ via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Best regard,
> My name is Arley, I am a postgraduate student at the federal university of Lavras, Brazil.
> I write this message because I have doubts about how to calculate the RMSD between two ligands after docking and redocking. My question is if Chimera works well to perform that calculation, since when for example I have two structures (ligands) that are, visually well superimposed and I calculate the value of RMSD with the use of the rmsd # 0 # 1 command, their value is high when compared With a structure that is not visually superimposed, why does that happen? Is it that chimera is not useful to carry out this task?
> I appreciate you can help me with that concern.
> 
> Att; 
> 
> Arley 



From mr_yuzhou at yahoo.com  Wed Sep 29 08:59:30 2021
From: mr_yuzhou at yahoo.com (Yu Zhou)
Date: Wed, 29 Sep 2021 15:59:30 +0000 (UTC)
Subject: [Chimera-users] Select model based on its position and orientation
References: <1065983227.209658.1632931170840.ref@mail.yahoo.com>
Message-ID: <1065983227.209658.1632931170840@mail.yahoo.com>

Dear all,
I tried global docking of two proteins and ended up with hundreds of possible poses. Is it possible to automatically select the poses based on the position and orientation of one partner, for example, the ones in which the ligand protein is close to the transmembrane region of the receptor protein and oriented with its N-terminus on the extracellular side?
Thanks
Yu Zhou
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From arley.paez at estudante.ufla.br  Wed Sep 29 10:32:50 2021
From: arley.paez at estudante.ufla.br (ARLEY REY PAEZ)
Date: Wed, 29 Sep 2021 14:32:50 -0300
Subject: [Chimera-users] using rmsd to compare ligand positions
In-Reply-To: <0160C97A-8EF3-4DFF-906F-DADF73DEF74F@cgl.ucsf.edu>
References: <CAAgwpEmOp5vzzontHiLTtNPp-Z+rNBn3v7esB7ViL+LGiWyuxA@mail.gmail.com>
 <0160C97A-8EF3-4DFF-906F-DADF73DEF74F@cgl.ucsf.edu>
Message-ID: <CAAgwpEkt+5c02GMKWYyhkEePiXfzHjbJsyuinJcH-OsJ=H5fpg@mail.gmail.com>

Ok, thanks very

Em qua., 29 de set. de 2021 ?s 12:47, Elaine Meng <meng at cgl.ucsf.edu>
escreveu:

> Hi Arley,
> The issue is how the atoms of the two copies are paired.  If the atoms to
> be matched with one another do not have the same atom names in #0 and #1,
> then simply saying "rmsd #0 #1" will give a higher value than expected.  To
> control the order in which they are paired, you may need to list the atoms
> individually in the command. Here is what it says in the help page for
> "rmsd":
> =-=
> If atom order is not specified, for example,
>
> rmsd #1:fad #0:fad
> rmsd #2:246,295 #0:195,221
>
> ...the atoms within a residue are ordered first by name, and where these
> are identical, by alternate location identifier, and where these are also
> identical, by serial number.
> =-=
> see: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
>
> To list the atoms individually in the command would look something like
> this, pretending my ligand residues are named XXX and YYY :
>
> rmsd #0:XXX at C1,C4,C3,C2,N  #1:YYY at C1,C2,C3,C4,N3
>
> ... would pair C1 of XXX with C1 of YYY, C4 with C2, C3 with C3, C2 with
> C4, and N with N3 to calculate the RMSD.
>
> Or, as also mentioned in the help page, you can select the atoms with the
> mouse (Shift-Ctrl-click) one by one in the same order first from #0 and
> then from #1 and then use command
>
> rmsd sel
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> > On Sep 29, 2021, at 7:35 AM, ARLEY REY PAEZ via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Best regard,
> > My name is Arley, I am a postgraduate student at the federal university
> of Lavras, Brazil.
> > I write this message because I have doubts about how to calculate the
> RMSD between two ligands after docking and redocking. My question is if
> Chimera works well to perform that calculation, since when for example I
> have two structures (ligands) that are, visually well superimposed and I
> calculate the value of RMSD with the use of the rmsd # 0 # 1 command, their
> value is high when compared With a structure that is not visually
> superimposed, why does that happen? Is it that chimera is not useful to
> carry out this task?
> > I appreciate you can help me with that concern.
> >
> > Att;
> >
> > Arley
>
>

-- 
Este e-mail foi enviado por um estudante da Universidade Federal de Lavras 
(UFLA). Caso esta mensagem possua algum conte?do n?o apropriado, favor 
desconsider?-la.
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From meng at cgl.ucsf.edu  Wed Sep 29 11:02:08 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 29 Sep 2021 11:02:08 -0700
Subject: [Chimera-users] Select model based on its position and
 orientation
In-Reply-To: <1065983227.209658.1632931170840@mail.yahoo.com>
References: <1065983227.209658.1632931170840.ref@mail.yahoo.com>
 <1065983227.209658.1632931170840@mail.yahoo.com>
Message-ID: <D56B2CBA-A837-450E-AFFD-26D9F7CDE88B@cgl.ucsf.edu>

Dear Yu Zhou,
I wouldn't call it "automatic"  ... you would have to figure out (by trial and error) some measurements that would distinguish the interesting ones from the others.  It would probably be some combination of distance zones, or distance zone plus angle measurement.  

E.g. some specific atoms of protein A must be within distance X of some specific atoms of protein B, and the crossing angle of an axis defined from some atoms of A with the axis defined from some atoms of B must be smaller than Y.  See command-line distance zone specification and commands "define" (define axis) and "angle" (measure angle between axes).

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

Once you figure out commands that distinguish the classes of solutions, then you would need to script going through the docking solutions and keeping or discarding them.   If for all the dockings one protein stays in the same place and only the other one moves, you might be able to do it interactively by entering the commands in the Chimera command line.  Otherwise, you would need to script with Python to loop through the different A-B positions, see:
<https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

For example, in the case where one protein (say #0) is always in the same place but #1.1, #1.2, #1.3 (etc.) are the dockings of the other protein, then this would select the dockings that have residue 123 more than 8 angstroms from residue 10 in #0. 

select #1:123 & #0:10 za<8

If that was reason enough for you to discard the solutions, you could increase selection to whole models (e.g. all atoms of #1.3) and delete those docked positions, e.g.

sel up
delete sel

You might need to use "sel up" more than once depending on what's in your docked models #1.1, #1.2, ...  For angle measurements you wouldn't select in the same command, you'd have to use the "angle" command to measure and then decide (interactively or in the script) whether to discard the solution based on the result.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 29, 2021, at 8:59 AM, Yu Zhou via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear all,
> 
> I tried global docking of two proteins and ended up with hundreds of possible poses. Is it possible to automatically select the poses based on the position and orientation of one partner, for example, the ones in which the ligand protein is close to the transmembrane region of the receptor protein and oriented with its N-terminus on the extracellular side?
> 
> Thanks
> 
> Yu Zhou
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users



From mr_yuzhou at yahoo.com  Wed Sep 29 16:58:50 2021
From: mr_yuzhou at yahoo.com (Yu Zhou)
Date: Wed, 29 Sep 2021 23:58:50 +0000 (UTC)
Subject: [Chimera-users] Select model based on its position and
 orientation
In-Reply-To: <D56B2CBA-A837-450E-AFFD-26D9F7CDE88B@cgl.ucsf.edu>
References: <1065983227.209658.1632931170840.ref@mail.yahoo.com>
 <1065983227.209658.1632931170840@mail.yahoo.com>
 <D56B2CBA-A837-450E-AFFD-26D9F7CDE88B@cgl.ucsf.edu>
Message-ID: <1519808632.350295.1632959931008@mail.yahoo.com>

 Elaine,
Thank you so much for your help.
The "sel up" does the trick.
Yu?
    On Wednesday, September 29, 2021, 01:02:11 PM CDT, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 
 Dear Yu Zhou,
I wouldn't call it "automatic"? ... you would have to figure out (by trial and error) some measurements that would distinguish the interesting ones from the others.? It would probably be some combination of distance zones, or distance zone plus angle measurement.? 

E.g. some specific atoms of protein A must be within distance X of some specific atoms of protein B, and the crossing angle of an axis defined from some atoms of A with the axis defined from some atoms of B must be smaller than Y.? See command-line distance zone specification and commands "define" (define axis) and "angle" (measure angle between axes).

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

Once you figure out commands that distinguish the classes of solutions, then you would need to script going through the docking solutions and keeping or discarding them.? If for all the dockings one protein stays in the same place and only the other one moves, you might be able to do it interactively by entering the commands in the Chimera command line.? Otherwise, you would need to script with Python to loop through the different A-B positions, see:
<https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

For example, in the case where one protein (say #0) is always in the same place but #1.1, #1.2, #1.3 (etc.) are the dockings of the other protein, then this would select the dockings that have residue 123 more than 8 angstroms from residue 10 in #0. 

select #1:123 & #0:10 za<8

If that was reason enough for you to discard the solutions, you could increase selection to whole models (e.g. all atoms of #1.3) and delete those docked positions, e.g.

sel up
delete sel

You might need to use "sel up" more than once depending on what's in your docked models #1.1, #1.2, ...? For angle measurements you wouldn't select in the same command, you'd have to use the "angle" command to measure and then decide (interactively or in the script) whether to discard the solution based on the result.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.? ? ? ? ? ? ? ? ? ? ? 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 29, 2021, at 8:59 AM, Yu Zhou via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear all,
> 
> I tried global docking of two proteins and ended up with hundreds of possible poses. Is it possible to automatically select the poses based on the position and orientation of one partner, for example, the ones in which the ligand protein is close to the transmembrane region of the receptor protein and oriented with its N-terminus on the extracellular side?
> 
> Thanks
> 
> Yu Zhou
> _______________________________________________
> 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 alessandro.strofaldi at bristol.ac.uk  Thu Sep 30 07:06:37 2021
From: alessandro.strofaldi at bristol.ac.uk (Alessandro Strofaldi)
Date: Thu, 30 Sep 2021 14:06:37 +0000
Subject: [Chimera-users] Surface exposed residue in a protein assembly
Message-ID: <AM6PR06MB5192F9AB0A8A3CB24CB664C3D7AA9@AM6PR06MB5192.eurprd06.prod.outlook.com>


Dear Chimera developers,

I?m working on a protein complex and I?d like to analyse the SASA and hydrophobicity on the surface.
I have worked with Chimera before so I know how to do those basic tasks for a monomeric protein; however, since I have five monomers interacting together I was wondering how to calculate the SASA (and later showing the hydrophobic residues of the surface) excluding the monomer-monomer interfacial regions.
I would also need those values tabulated to show hydrophobicity vs primary sequence but still excluding the monomer-monomer interfaces!
It seems like there is no basic tool to do that (or am I missing something?); is there any procedure I could apply?
Unfortunately I can?t code in Python so I?m looking for a solution that involves using the GUI.

Thank you,
Best regards,
Alessandro Strofaldi, PhD
University of Bristol
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From meng at cgl.ucsf.edu  Thu Sep 30 09:22:25 2021
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 30 Sep 2021 09:22:25 -0700
Subject: [Chimera-users] Surface exposed residue in a protein assembly
In-Reply-To: <AM6PR06MB5192F9AB0A8A3CB24CB664C3D7AA9@AM6PR06MB5192.eurprd06.prod.outlook.com>
References: <AM6PR06MB5192F9AB0A8A3CB24CB664C3D7AA9@AM6PR06MB5192.eurprd06.prod.outlook.com>
Message-ID: <8F772C65-10C9-45F3-8FBB-8ED7ADEDDFE4@cgl.ucsf.edu>

Hi Alessandro,
If the assembly is opened from a single file, by default Chimera puts a molecular surface around all of the subunits together as one "blob" (does not make an individual surface for each subunit) so it should be the same as what you do for monomers.  I.e. buried residues including the ones in the interfaces should have zero or small surface area.

The hydrophobicity assigned by Chimera is a simple lookup table based only on the residue type.  See "kdHydrophobicity" in this table.
<https://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>

I'm not completely sure what outputs you need, but maybe something like the following steps, which might be the same as you are doing already for monomers:

(1) show the molecular surface so that surface area values are calculated (residue attribute areaSAS for solvent-accessible, or areaSES for solvent-excluded).  See diagram explaining these types of surfaces:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

(2) select residues with area greater than some cutoff value, whatever you think is enough to make the residue a "surface" residue.  E.g. command

select :/areaSAS>50

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/select.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors>

... or for GUI approach showing the histogram of values in the structure, menu: Select... by Attribute Value.., set to Attributes of "residues", name "areaSAS" or "areaSES" as you prefer, then use the vertical bars to set value range of selection.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select>

(3) write list of selected residues only, and their surface areas, and their hydrophobicity values. Menu:  Tools... Depiction... Render by Attribute, and then in the menu of that tool, File... Save Attribute.  You could save residue areaSAS or areaSES, and then another file with residue kdHydrophobicity.  In the saving dialog, turn on the option "Restrict save to current selection, if any"
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

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

> On Sep 30, 2021, at 7:06 AM, Alessandro Strofaldi via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Dear Chimera developers, 
> I?m working on a protein complex and I?d like to analyse the SASA and hydrophobicity on the surface.
> I have worked with Chimera before so I know how to do those basic tasks for a monomeric protein; however, since I have five monomers interacting together I was wondering how to calculate the SASA (and later showing the hydrophobic residues of the surface) excluding the monomer-monomer interfacial regions.
> I would also need those values tabulated to show hydrophobicity vs primary sequence but still excluding the monomer-monomer interfaces!
> It seems like there is no basic tool to do that (or am I missing something?); is there any procedure I could apply?
> Unfortunately I can?t code in Python so I?m looking for a solution that involves using the GUI.
> Thank you,
> Best regards,
> Alessandro Strofaldi, PhD
> University of Bristol



From zongli.li at gmail.com  Thu Sep 30 10:56:39 2021
From: zongli.li at gmail.com (Zongli Li)
Date: Thu, 30 Sep 2021 13:56:39 -0400
Subject: [Chimera-users] Error to run chimera remotely on a GPU computer
	from Mac computer
Message-ID: <CAPWpDO0t1V1fbhXxy=+v41v90CC7WdPf=vXbjUwOAFEFout-Qw@mail.gmail.com>

Dear listers,

I ssh with "-Y"  from my Mac desktop to a GPU computer and process my data
there. Quite often I need to look at the 3D volumes with chimera. This had
been working nicely for long time. But all suddenly it stopped working and
game the error 3:

X Error of failed request:  GLXBadCurrentWindow

  Major opcode of failed request:  149 (GLX)

  Minor opcode of failed request:  5 (X_GLXMakeCurrent)

  Serial number of failed request:  1400

  Current serial number in output stream:  1400



Did anyone encounter the same error? Any suggestions or tips to overcome
this problem would be appreciated.


Thanks,


Zongli
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From mdelacr at gmail.com  Thu Sep 30 12:49:32 2021
From: mdelacr at gmail.com (M. Jason de la Cruz)
Date: Thu, 30 Sep 2021 15:49:32 -0400
Subject: [Chimera-users] [3dem] Error to run chimera remotely on a GPU
	computer from Mac computer
In-Reply-To: <CAPWpDO0t1V1fbhXxy=+v41v90CC7WdPf=vXbjUwOAFEFout-Qw@mail.gmail.com>
References: <CAPWpDO0t1V1fbhXxy=+v41v90CC7WdPf=vXbjUwOAFEFout-Qw@mail.gmail.com>
Message-ID: <CAF5e_RyKMif268-ckUQ_HmQW=zxDk_tzn2SeUfMQ-L5+UnY2uQ@mail.gmail.com>

Hi Zongli,


As Colin mentioned, this error is likely due to GLX indirect rendering and
XQuartz on the Mac client.  We had this problem a few months ago when Mac
users updated their operating system to macOS Catalina (version 10.15.7) or
later, and/or upgraded to the most recent version of XQuartz (version 2.8.1
at the time), and suddenly had trouble displaying remotely-rendered
graphics on their local terminal.


The following instructions are what I sent to my colleagues on this issue
back then (May 2021), hopefully they are still valid now:



1.  In a terminal on your Mac, enter the following command:



defaults write org.xquartz.X11 enable_iglx -bool true



2.  If you don?t have the most recent XQuartz on your system, go to
https://www.xquartz.org/ and download version 2.8.1 (you may also be able
to update it when prompted by your system).  If you downloaded the package,
mount the disk image and install the package to your computer.  Then log
out and log back in again.



3.  On your Mac, open a terminal and connect to the remote Linux system
using the ssh command such as below:



ssh -X [user]@[remote-computer] or ssh -Y [user]@[remote-computer]



4.  Source SBGrid if necessary, then try to open an image using 3dmod or
e2display.py.  Alternatively, you can enter the commands glxinfo or glxgears to
test and make sure you have no errors.



Hope that helps!



Best,

--Jason




On Thu, Sep 30, 2021 at 3:15 PM Colin Gauvin <colin at gauvin.id> wrote:

It sounds like you need to enable indirect GLX (iGLX) on the client machine.

If you are using XQuartz, iGLX is disabled by default.


--

Best Regards,


Colin Gauvin

colin at gauvin.id

Lawrence Laboratory, Montana State University

(401) 263-0343

On Thu, Sep 30, 2021 at 1:57 PM Zongli Li <zongli.li at gmail.com> wrote:

> Dear listers,
>
> I ssh with "-Y"  from my Mac desktop to a GPU computer and process my data
> there. Quite often I need to look at the 3D volumes with chimera. This had
> been working nicely for long time. But all suddenly it stopped working and
> game the error 3:
>
> X Error of failed request:  GLXBadCurrentWindow
>
>   Major opcode of failed request:  149 (GLX)
>
>   Minor opcode of failed request:  5 (X_GLXMakeCurrent)
>
>   Serial number of failed request:  1400
>
>   Current serial number in output stream:  1400
>
>
>
> Did anyone encounter the same error? Any suggestions or tips to overcome
> this problem would be appreciated.
>
>
> Thanks,
>
>
> Zongli
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
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From goddard at sonic.net  Thu Sep 30 19:17:54 2021
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 30 Sep 2021 19:17:54 -0700
Subject: [Chimera-users] [3dem] Error to run chimera remotely on a GPU
 computer from Mac computer
In-Reply-To: <CAF5e_RyKMif268-ckUQ_HmQW=zxDk_tzn2SeUfMQ-L5+UnY2uQ@mail.gmail.com>
References: <CAPWpDO0t1V1fbhXxy=+v41v90CC7WdPf=vXbjUwOAFEFout-Qw@mail.gmail.com>
 <CAF5e_RyKMif268-ckUQ_HmQW=zxDk_tzn2SeUfMQ-L5+UnY2uQ@mail.gmail.com>
Message-ID: <2E063203-4141-42B1-818A-D7B15A501A15@sonic.net>

Hi Jason,

  Thanks for those tips.  We usually tell ChimeraX and Chimera users to give up any hope of OpenGL remote display with X windows as this rarely works unless the graphics drivers on the two machines are identical.  This has nothing to do with the specific apps, no OpenGL apps work.  This kind of remote display worked pretty reliably 20 years ago in the days of SGI but seems barely supported now.  Glad to hear that it can sometimes work for those who need to use this low performance 3D rendering method.  We recommend moving your data to the visualization machine for the best visualization experience.

	Tom


> On Sep 30, 2021, at 12:49 PM, M. Jason de la Cruz via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Zongli,
> 
> As Colin mentioned, this error is likely due to GLX indirect rendering and XQuartz on the Mac client.  We had this problem a few months ago when Mac users updated their operating system to macOS Catalina (version 10.15.7) or later, and/or upgraded to the most recent version of XQuartz (version 2.8.1 at the time), and suddenly had trouble displaying remotely-rendered graphics on their local terminal.
> 
> The following instructions are what I sent to my colleagues on this issue back then (May 2021), hopefully they are still valid now:
>  
> 1.  In a terminal on your Mac, enter the following command:
>  
> defaults write org.xquartz.X11 enable_iglx -bool true
>  
> 2.  If you don?t have the most recent XQuartz on your system, go to https://www.xquartz.org <https://www.xquartz.org/>/ and download version 2.8.1 (you may also be able to update it when prompted by your system).  If you downloaded the package, mount the disk image and install the package to your computer.  Then log out and log back in again.
>  
> 3.  On your Mac, open a terminal and connect to the remote Linux system using the ssh command such as below:
>  
> ssh -X [user]@[remote-computer] or ssh -Y [user]@[remote-computer]
>  
> 4.  Source SBGrid if necessary, then try to open an image using 3dmod or e2display.py.  Alternatively, you can enter the commands glxinfo or glxgears to test and make sure you have no errors.
>  
> Hope that helps!
>  
> Best,
> --Jason
> 
> 
> 
> On Thu, Sep 30, 2021 at 3:15 PM Colin Gauvin <colin at gauvin.id <mailto:colin at gauvin.id>> wrote:
> It sounds like you need to enable indirect GLX (iGLX) on the client machine.
> If you are using XQuartz, iGLX is disabled by default.
> 
> --
> Best Regards,
> 
> Colin Gauvin
> colin at gauvin.id <mailto:colin at gauvin.id>
> Lawrence Laboratory, Montana State University
> (401) 263-0343
> 
> On Thu, Sep 30, 2021 at 1:57 PM Zongli Li <zongli.li at gmail.com <mailto:zongli.li at gmail.com>> wrote:
> Dear listers,
> 
> I ssh with "-Y"  from my Mac desktop to a GPU computer and process my data there. Quite often I need to look at the 3D volumes with chimera. This had been working nicely for long time. But all suddenly it stopped working and game the error 3:
> 
> X Error of failed request:  GLXBadCurrentWindow
>   Major opcode of failed request:  149 (GLX)
>   Minor opcode of failed request:  5 (X_GLXMakeCurrent)
>   Serial number of failed request:  1400
>   Current serial number in output stream:  1400
> 
> 
> Did anyone encounter the same error? Any suggestions or tips to overcome this problem would be appreciated. 
> 
> Thanks,
> 
> Zongli
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem <https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem>
> _______________________________________________
> 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 Zongli_Li at hms.harvard.edu  Thu Sep 30 19:44:19 2021
From: Zongli_Li at hms.harvard.edu (Li, Zongli)
Date: Fri, 1 Oct 2021 02:44:19 +0000
Subject: [Chimera-users] [3dem] Error to run chimera remotely on a GPU
 computer from Mac computer
In-Reply-To: <2E063203-4141-42B1-818A-D7B15A501A15@sonic.net>
References: <CAPWpDO0t1V1fbhXxy=+v41v90CC7WdPf=vXbjUwOAFEFout-Qw@mail.gmail.com>
 <CAF5e_RyKMif268-ckUQ_HmQW=zxDk_tzn2SeUfMQ-L5+UnY2uQ@mail.gmail.com>
 <2E063203-4141-42B1-818A-D7B15A501A15@sonic.net>
Message-ID: <MW4PR07MB87166D8CDCFD7DCC8058F6F3C1AB9@MW4PR07MB8716.namprd07.prod.outlook.com>

Hi Tom,

Thank you for the information.

Best,

Zongli
________________________________
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Tom Goddard via Chimera-users <chimera-users at cgl.ucsf.edu>
Sent: Thursday, September 30, 2021 10:17 PM
To: M. Jason de la Cruz <mdelacr at gmail.com>
Cc: Zongli Li <zongli.li at gmail.com>; 3dem <3dem at ncmir.ucsd.edu>; chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] [3dem] Error to run chimera remotely on a GPU computer from Mac computer

Hi Jason,

  Thanks for those tips.  We usually tell ChimeraX and Chimera users to give up any hope of OpenGL remote display with X windows as this rarely works unless the graphics drivers on the two machines are identical.  This has nothing to do with the specific apps, no OpenGL apps work.  This kind of remote display worked pretty reliably 20 years ago in the days of SGI but seems barely supported now.  Glad to hear that it can sometimes work for those who need to use this low performance 3D rendering method.  We recommend moving your data to the visualization machine for the best visualization experience.

Tom


On Sep 30, 2021, at 12:49 PM, M. Jason de la Cruz via Chimera-users <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>> wrote:

Hi Zongli,

As Colin mentioned, this error is likely due to GLX indirect rendering and XQuartz on the Mac client.  We had this problem a few months ago when Mac users updated their operating system to macOS Catalina (version 10.15.7) or later, and/or upgraded to the most recent version of XQuartz (version 2.8.1 at the time), and suddenly had trouble displaying remotely-rendered graphics on their local terminal.

The following instructions are what I sent to my colleagues on this issue back then (May 2021), hopefully they are still valid now:



1.  In a terminal on your Mac, enter the following command:



defaults write org.xquartz.X11 enable_iglx -bool true



2.  If you don?t have the most recent XQuartz on your system, go to https://www.xquartz.org<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.xquartz.org_&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=uQMJAWlPEv596kvCdV_ot7YTGNux4AXH5-WfTfSNGmY&m=bDNBV_qd4jNX6kYE6M4YlGm_Xg3SG1_qAxuOrc7-FSg&s=GSwXOAkF0cvLrs9vXOtvN_udfrIFEFlnC2Q0rtap9S0&e=>/ and download version 2.8.1 (you may also be able to update it when prompted by your system).  If you downloaded the package, mount the disk image and install the package to your computer.  Then log out and log back in again.



3.  On your Mac, open a terminal and connect to the remote Linux system using the ssh command such as below:



ssh -X [user]@[remote-computer] or ssh -Y [user]@[remote-computer]



4.  Source SBGrid if necessary, then try to open an image using 3dmod or e2display.py.  Alternatively, you can enter the commands glxinfo or glxgears to test and make sure you have no errors.



Hope that helps!



Best,
--Jason



On Thu, Sep 30, 2021 at 3:15 PM Colin Gauvin <colin at gauvin.id<mailto:colin at gauvin.id>> wrote:
It sounds like you need to enable indirect GLX (iGLX) on the client machine.
If you are using XQuartz, iGLX is disabled by default.

--
Best Regards,

Colin Gauvin
colin at gauvin.id<mailto:colin at gauvin.id>
Lawrence Laboratory, Montana State University
(401) 263-0343

On Thu, Sep 30, 2021 at 1:57 PM Zongli Li <zongli.li at gmail.com<mailto:zongli.li at gmail.com>> wrote:
Dear listers,

I ssh with "-Y"  from my Mac desktop to a GPU computer and process my data there. Quite often I need to look at the 3D volumes with chimera. This had been working nicely for long time. But all suddenly it stopped working and game the error 3:

X Error of failed request:  GLXBadCurrentWindow
  Major opcode of failed request:  149 (GLX)
  Minor opcode of failed request:  5 (X_GLXMakeCurrent)
  Serial number of failed request:  1400
  Current serial number in output stream:  1400


Did anyone encounter the same error? Any suggestions or tips to overcome this problem would be appreciated.

Thanks,

Zongli
_______________________________________________
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