[chimerax-users] Color docking resulls by rank
Eric Pettersen
pett at cgl.ucsf.edu
Fri Dec 17 17:03:56 PST 2021
Hi Vis,
Since the information available from docking varies from program to program, there are no universal model attributes for the columns shown by ViewDockX, just a model meta-attribute, viewdockx_data, that contains a mapping from column names to values for that model. I've written a Python script that takes that mapping and expands it into model attributes that can then in turn be used by "color byattribute" and other commands to color/select/whatever based on the attribute values. I made a "ChimeraX Recipe" page describing how to use the script and a link to download it. The recipe is here: Make attributes from ViewDockX column information | ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/vdx_attrs/vdx_attrs.html>
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
> On Dec 17, 2021, at 10:42 AM, Visvaldas K. via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear Users and Developers,
>
> I have a ViewdockX question (but I guess it's a more generic one, about coloring models/submodels): is there a trick to color docking results by rank, like rank was some sort of B-factor? Or even by docking energy (score), but that's maybe too much. I could color each "submodel" by hand, but I don't know how to obtain color gradients, say distributed at even distances between blue and red.
>
> Years ago I was able to do similar trick in Chimera, but I completely forgot how I did that :(
>
> Thank you,
>
> Vis
>
>
>
> On Friday, December 17, 2021, 05:24:30 PM GMT, chimerax-users-request at cgl.ucsf.edu <chimerax-users-request at cgl.ucsf.edu> wrote:
>
>
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> Today's Topics:
>
> 1. independent centers of rotation (Elaine Meng)
> 2. Change the directory for data fetched from databases
> (Guillaume Gaullier)
> 3. Re: Change the directory for data fetched from databases
> (Tom Goddard)
> 4. Re: Change the directory for data fetched from databases
> (Guillaume Gaullier)
> 5. Re: Change the directory for data fetched from databases
> (Tristan Croll)
> 6. Re: Change the directory for data fetched from databases
> (Guillaume Gaullier)
> 7. PDB: 7OVR (Veler, Hana (NIH/NCI) [F])
> 8. Re: PDB: 7OVR (Elaine Meng)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 15 Dec 2021 12:51:58 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
> To: Abigail Jackson <ajackson at scripps.edu <mailto:ajackson at scripps.edu>>
> Cc: "chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>" <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: [chimerax-users] independent centers of rotation
> Message-ID: <90DEEA37-1BF5-4F52-AF35-DF81F0B4F273 at cgl.ucsf.edu <mailto:90DEEA37-1BF5-4F52-AF35-DF81F0B4F273 at cgl.ucsf.edu>>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Abigail,
> Ah, you're referring to the "independent centers of rotation" mode in Chimera. By default, the "tile" command in Chimera automatically turns it on.
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/tile.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/tile.html>>
>
> I agree that this mode is very useful, but unfortunately it does not yet exist in ChimeraX. It is listed in the missing features section of the ChimeraX download page.
> <https://www.rbvi.ucsf.edu/chimerax/download.html <https://www.rbvi.ucsf.edu/chimerax/download.html>>
>
> Sorry about that,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Dec 15, 2021, at 12:28 PM, Abigail Jackson via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
> >
> > Hi there,
> > I have a question regarding the tile function in ChimeraX. In the original Chimera, once multiple maps were tiled they would all rotate individually and the grid itself was fixed in space. In ChimeraX, however, once maps are tiled the entire grid rotates as a unit and the individual maps are fixed. Do you know if there is an option to have the maps spin individually instead, like in the original Chimera?
> >
> > Hopefully that description makes sense. Thank you in advance for your help!
> > Best,
> > Abigail Jackson
> > The Scripps Research Institute
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 16 Dec 2021 10:08:26 +0000
> From: Guillaume Gaullier <guillaume.gaullier at icm.uu.se <mailto:guillaume.gaullier at icm.uu.se>>
> To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: [chimerax-users] Change the directory for data fetched from
> databases
> Message-ID: <7B64261E-92A8-45FF-BF14-0B597E14A98B at icm.uu.se <mailto:7B64261E-92A8-45FF-BF14-0B597E14A98B at icm.uu.se>>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands).
>
> The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX).
>
> Thank you,
>
> Guillaume
>
>
>
>
>
>
>
>
>
> N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ <http://www.uu.se/om-uu/dataskydd-personuppgifter/>
>
> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy <http://www.uu.se/en/about-uu/data-protection-policy>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 16 Dec 2021 14:50:25 -0800
> From: Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>
> To: Guillaume Gaullier <guillaume.gaullier at icm.uu.se <mailto:guillaume.gaullier at icm.uu.se>>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: Re: [chimerax-users] Change the directory for data fetched
> from databases
> Message-ID: <8D292E49-13E7-4DF0-9B94-7EAC424DA7D0 at sonic.net <mailto:8D292E49-13E7-4DF0-9B94-7EAC424DA7D0 at sonic.net>>
> Content-Type: text/plain; charset=utf-8
>
> Hi Guillaume,
>
> There is no setting to change the location where ChimeraX caches fetched files. It is always
>
> ~/Downloads/ChimeraX
>
> On a multi-user workstation is the idea that every person would change the ChimeraX setting to point to a common cache directory? Will people cooperate with that? Each person of course has their own ChimeraX settings. Everyone will also need write access to that directory. There are no site-wide settings in ChimeraX.
>
> You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux)
>
> chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py
>
> making
>
> _cache_dirs = ['/usr/local/chimerax_fetch']
>
> near the top would I think change to use that directory. Of course each time you install a new ChimeraX it would need such a change, and if individual users install their own ChimeraX version it will use ~/Downloads/ChimeraX.
>
> Tom
>
>
> > On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
> >
> > Hello,
> >
> > The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands).
> >
> > The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX).
> >
> > Thank you,
> >
> > Guillaume
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ <http://www.uu.se/om-uu/dataskydd-personuppgifter/>
> >
> > E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy <http://www.uu.se/en/about-uu/data-protection-policy>
> >
> > _______________________________________________
> > ChimeraX-users mailing list
> > ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
> > Manage subscription:
> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
> >
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 17 Dec 2021 08:40:06 +0000
> From: Guillaume Gaullier <guillaume.gaullier at icm.uu.se <mailto:guillaume.gaullier at icm.uu.se>>
> To: Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: Re: [chimerax-users] Change the directory for data fetched
> from databases
> Message-ID: <ED531B0A-5F66-4E86-920E-565966A5D8A3 at icm.uu.se <mailto:ED531B0A-5F66-4E86-920E-565966A5D8A3 at icm.uu.se>>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Tom,
>
> This is the use case I had in mind indeed. Model files are small enough that duplication doesn?t matter, but a shared cache for maps could be convenient. I was simply asking in case there was a supported way to achieve this that I had missed in the documentation, but I can absolutely live with the current default.
>
> Thank you for your answer.
> Cheers,
>
> Guillaume
>
>
> On 16 Dec 2021, at 23:50, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net><mailto:goddard at sonic.net <mailto:goddard at sonic.net>>> wrote:
>
> Hi Guillaume,
>
> There is no setting to change the location where ChimeraX caches fetched files. It is always
>
> ~/Downloads/ChimeraX
>
> On a multi-user workstation is the idea that every person would change the ChimeraX setting to point to a common cache directory? Will people cooperate with that? Each person of course has their own ChimeraX settings. Everyone will also need write access to that directory. There are no site-wide settings in ChimeraX.
>
> You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux)
>
> chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py
>
> making
>
> _cache_dirs = ['/usr/local/chimerax_fetch']
>
> near the top would I think change to use that directory. Of course each time you install a new ChimeraX it would need such a change, and if individual users install their own ChimeraX version it will use ~/Downloads/ChimeraX.
>
> Tom
>
>
> On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu><mailto:chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>> wrote:
>
> Hello,
>
> The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands).
>
> The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX).
>
> Thank you,
>
> Guillaume
>
>
>
>
>
>
>
>
>
> N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ <http://www.uu.se/om-uu/dataskydd-personuppgifter/>
>
> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy <http://www.uu.se/en/about-uu/data-protection-policy>
>
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu><mailto:ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>>
> Manage subscription:
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>
> ------------------------------
>
> Message: 5
> Date: Fri, 17 Dec 2021 09:11:45 +0000
> From: Tristan Croll <tic20 at cam.ac.uk <mailto:tic20 at cam.ac.uk>>
> To: goddard <goddard at sonic.net <mailto:goddard at sonic.net>>, Guillaume Gaullier
> <guillaume.gaullier at icm.uu.se <mailto:guillaume.gaullier at icm.uu.se>>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: Re: [chimerax-users] Change the directory for data fetched
> from databases
> Message-ID:
> <CWXP265MB3318E17B89A1971E1C5B40F0F5789 at CWXP265MB3318.GBRP265.PROD.OUTLOOK.COM <mailto:CWXP265MB3318E17B89A1971E1C5B40F0F5789 at CWXP265MB3318.GBRP265.PROD.OUTLOOK.COM>>
>
> Content-Type: text/plain; charset="windows-1252"
>
> An alternative approach which doesn't involve modifying ChimeraX (but still requires action in each user account) would be to simply symlink ~/Downloads/ChimeraX to the centralised location.
>
> -- Tristan
> ________________________________
> From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu <mailto:chimerax-users-bounces at cgl.ucsf.edu>> on behalf of Guillaume Gaullier via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Sent: 17 December 2021 08:40
> To: goddard <goddard at sonic.net <mailto:goddard at sonic.net>>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: Re: [chimerax-users] Change the directory for data fetched from databases
>
> Hi Tom,
>
> This is the use case I had in mind indeed. Model files are small enough that duplication doesn?t matter, but a shared cache for maps could be convenient. I was simply asking in case there was a supported way to achieve this that I had missed in the documentation, but I can absolutely live with the current default.
>
> Thank you for your answer.
> Cheers,
>
> Guillaume
>
>
> On 16 Dec 2021, at 23:50, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net><mailto:goddard at sonic.net <mailto:goddard at sonic.net>>> wrote:
>
> Hi Guillaume,
>
> There is no setting to change the location where ChimeraX caches fetched files. It is always
>
> ~/Downloads/ChimeraX
>
> On a multi-user workstation is the idea that every person would change the ChimeraX setting to point to a common cache directory? Will people cooperate with that? Each person of course has their own ChimeraX settings. Everyone will also need write access to that directory. There are no site-wide settings in ChimeraX.
>
> You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux)
>
> chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py
>
> making
>
> _cache_dirs = ['/usr/local/chimerax_fetch']
>
> near the top would I think change to use that directory. Of course each time you install a new ChimeraX it would need such a change, and if individual users install their own ChimeraX version it will use ~/Downloads/ChimeraX.
>
> Tom
>
>
> On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu><mailto:chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>> wrote:
>
> Hello,
>
> The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands).
>
> The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX).
>
> Thank you,
>
> Guillaume
>
>
>
>
>
>
>
>
>
> N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ <http://www.uu.se/om-uu/dataskydd-personuppgifter/>
>
> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy <http://www.uu.se/en/about-uu/data-protection-policy>
>
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu><mailto:ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>>
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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>
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>
> ------------------------------
>
> Message: 6
> Date: Fri, 17 Dec 2021 09:14:32 +0000
> From: Guillaume Gaullier <guillaume.gaullier at icm.uu.se <mailto:guillaume.gaullier at icm.uu.se>>
> To: Tristan Croll <tic20 at CAM.AC.UK <mailto:tic20 at CAM.AC.UK>>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: Re: [chimerax-users] Change the directory for data fetched
> from databases
> Message-ID: <E19B97E0-98D3-4FE4-8EB9-D591BC947449 at icm.uu.se <mailto:E19B97E0-98D3-4FE4-8EB9-D591BC947449 at icm.uu.se>>
> Content-Type: text/plain; charset="utf-8"
>
> Very simple indeed, I should have thought of that first. Thank you Tristan. :-)
>
> Guillaume
>
>
> On 17 Dec 2021, at 10:11, Tristan Croll <tic20 at CAM.AC.UK <mailto:tic20 at CAM.AC.UK><mailto:tic20 at CAM.AC.UK <mailto:tic20 at CAM.AC.UK>>> wrote:
>
> An alternative approach which doesn't involve modifying ChimeraX (but still requires action in each user account) would be to simply symlink ~/Downloads/ChimeraX to the centralised location.
>
> -- Tristan
> ________________________________
> From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu <mailto:chimerax-users-bounces at cgl.ucsf.edu><mailto:chimerax-users-bounces at cgl.ucsf.edu <mailto:chimerax-users-bounces at cgl.ucsf.edu>>> on behalf of Guillaume Gaullier via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu><mailto:chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>>
> Sent: 17 December 2021 08:40
> To: goddard <goddard at sonic.net <mailto:goddard at sonic.net><mailto:goddard at sonic.net <mailto:goddard at sonic.net>>>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu><mailto:chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>>
> Subject: Re: [chimerax-users] Change the directory for data fetched from databases
>
> Hi Tom,
>
> This is the use case I had in mind indeed. Model files are small enough that duplication doesn?t matter, but a shared cache for maps could be convenient. I was simply asking in case there was a supported way to achieve this that I had missed in the documentation, but I can absolutely live with the current default.
>
> Thank you for your answer.
> Cheers,
>
> Guillaume
>
>
> On 16 Dec 2021, at 23:50, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net><mailto:goddard at sonic.net <mailto:goddard at sonic.net>>> wrote:
>
> Hi Guillaume,
>
> There is no setting to change the location where ChimeraX caches fetched files. It is always
>
> ~/Downloads/ChimeraX
>
> On a multi-user workstation is the idea that every person would change the ChimeraX setting to point to a common cache directory? Will people cooperate with that? Each person of course has their own ChimeraX settings. Everyone will also need write access to that directory. There are no site-wide settings in ChimeraX.
>
> You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux)
>
> chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py
>
> making
>
> _cache_dirs = ['/usr/local/chimerax_fetch']
>
> near the top would I think change to use that directory. Of course each time you install a new ChimeraX it would need such a change, and if individual users install their own ChimeraX version it will use ~/Downloads/ChimeraX.
>
> Tom
>
>
> On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu><mailto:chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>> wrote:
>
> Hello,
>
> The documentation for the open command says "Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory)". Is there a way to change this directory? I couldn?t find one in the settings window, but maybe a command could do that? (in that case I would simply need to add this command to the startup commands).
>
> The use case I have in mind is to share the ChimeraX cache between all accounts on a multi-user workstation (so, relocate the cache at some place like /data/ChimeraX).
>
> Thank you,
>
> Guillaume
>
>
>
>
>
>
>
>
>
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> ------------------------------
>
> Message: 7
> Date: Fri, 17 Dec 2021 17:18:57 +0000
> From: "Veler, Hana (NIH/NCI) [F]" <hana.veler at nih.gov <mailto:hana.veler at nih.gov>>
> To: "chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>" <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: [chimerax-users] PDB: 7OVR
> Message-ID: <387A4521-19AF-4D23-8BA8-6DB6DD300F3B at contoso.com <mailto:387A4521-19AF-4D23-8BA8-6DB6DD300F3B at contoso.com>>
> Content-Type: text/plain; charset="utf-8"
>
> To whom it may concern,
>
> The command ?show sel atoms? does not work in the 7OVR structure and I was wondering how can I fix this? I wanted to show certain residues as atoms in the structure. When I open other structures, e.g. 5FMM, the command works perfectly fine.
>
> Would you know what could be the cause?
>
> Thanks,
> Hana
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>
> ------------------------------
>
> Message: 8
> Date: Fri, 17 Dec 2021 09:23:32 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
> To: "Veler, Hana (NIH/NCI) [F]" <hana.veler at nih.gov <mailto:hana.veler at nih.gov>>
> Cc: "chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>" <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: Re: [chimerax-users] PDB: 7OVR
> Message-ID: <8FE6FF2D-AAF7-46A6-8997-FD73E7910BE8 at cgl.ucsf.edu <mailto:8FE6FF2D-AAF7-46A6-8997-FD73E7910BE8 at cgl.ucsf.edu>>
> Content-Type: text/plain; charset=utf-8
>
> Hello Hana,
> I can't tell what you have selected, so it is impossible to say. Remember, the "sel" in the command means the current selection. Do you have any atoms selected?
>
> Also, when I open structure 7ovr in ChimeraX, all of the atoms are shown already.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Dec 17, 2021, at 9:18 AM, Veler, Hana (NIH/NCI) [F] via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
> >
> > To whom it may concern,
> >
> > The command ?show sel atoms? does not work in the 7OVR structure and I was wondering how can I fix this? I wanted to show certain residues as atoms in the structure. When I open other structures, e.g. 5FMM, the command works perfectly fine.
> >
> > Would you know what could be the cause?
> >
> > Thanks,
> > Hana
>
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
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>
> End of ChimeraX-users Digest, Vol 60, Issue 7
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