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@cgl.ucsf.edu <chimerax-users-request@cgl.ucsf.edu> wrote: Send ChimeraX-users mailing list submissions to chimerax-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request@cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." 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@cgl.ucsf.edu> To: Abigail Jackson <ajackson@scripps.edu> Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] independent centers of rotation Message-ID: <90DEEA37-1BF5-4F52-AF35-DF81F0B4F273@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> 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> 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@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@icm.uu.se> To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Change the directory for data fetched from databases Message-ID: <7B64261E-92A8-45FF-BF14-0B597E14A98B@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/ 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 ------------------------------ Message: 3 Date: Thu, 16 Dec 2021 14:50:25 -0800 From: Tom Goddard <goddard@sonic.net> To: Guillaume Gaullier <guillaume.gaullier@icm.uu.se> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Change the directory for data fetched from databases Message-ID: <8D292E49-13E7-4DF0-9B94-7EAC424DA7D0@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@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: 4 Date: Fri, 17 Dec 2021 08:40:06 +0000 From: Guillaume Gaullier <guillaume.gaullier@icm.uu.se> To: Tom Goddard <goddard@sonic.net> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Change the directory for data fetched from databases Message-ID: <ED531B0A-5F66-4E86-920E-565966A5D8A3@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@sonic.net<mailto:goddard@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@cgl.ucsf.edu<mailto:chimerax-users@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/ 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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@cgl.ucsf.edu <chimerax-users-request@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@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> To: Abigail Jackson <ajackson@scripps.edu <mailto:ajackson@scripps.edu>> Cc: "chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: [chimerax-users] independent centers of rotation Message-ID: <90DEEA37-1BF5-4F52-AF35-DF81F0B4F273@cgl.ucsf.edu <mailto:90DEEA37-1BF5-4F52-AF35-DF81F0B4F273@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@cgl.ucsf.edu <mailto:chimerax-users@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@icm.uu.se <mailto:guillaume.gaullier@icm.uu.se>> To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: [chimerax-users] Change the directory for data fetched from databases Message-ID: <7B64261E-92A8-45FF-BF14-0B597E14A98B@icm.uu.se <mailto:7B64261E-92A8-45FF-BF14-0B597E14A98B@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@sonic.net <mailto:goddard@sonic.net>> To: Guillaume Gaullier <guillaume.gaullier@icm.uu.se <mailto:guillaume.gaullier@icm.uu.se>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Change the directory for data fetched from databases Message-ID: <8D292E49-13E7-4DF0-9B94-7EAC424DA7D0@sonic.net <mailto:8D292E49-13E7-4DF0-9B94-7EAC424DA7D0@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@cgl.ucsf.edu <mailto:chimerax-users@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>
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------------------------------
Message: 4 Date: Fri, 17 Dec 2021 08:40:06 +0000 From: Guillaume Gaullier <guillaume.gaullier@icm.uu.se <mailto:guillaume.gaullier@icm.uu.se>> To: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Change the directory for data fetched from databases Message-ID: <ED531B0A-5F66-4E86-920E-565966A5D8A3@icm.uu.se <mailto:ED531B0A-5F66-4E86-920E-565966A5D8A3@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@sonic.net <mailto:goddard@sonic.net><mailto:goddard@sonic.net <mailto:goddard@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@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu><mailto:chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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>
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participants (2)
-
Eric Pettersen -
Visvaldas K.