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<div dir="ltr" data-setdir="false">Dear Users and Developers,</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">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. <br><br>Years ago I was able to do similar trick in Chimera, but I completely forgot how I did that :(</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Thank you,</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Vis<br></div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false"><br></div><div><br></div>
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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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<div><div dir="ltr">Send ChimeraX-users mailing list submissions to<br></div><div dir="ltr"> <a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a><br></div><div dir="ltr"><br></div><div dir="ltr">To subscribe or unsubscribe via the World Wide Web, visit<br></div><div dir="ltr"> <a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" rel="nofollow" target="_blank">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br></div><div dir="ltr">or, via email, send a message with subject or body 'help' to<br></div><div dir="ltr"> <a href="mailto:chimerax-users-request@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users-request@cgl.ucsf.edu</a><br></div><div dir="ltr"><br></div><div dir="ltr">You can reach the person managing the list at<br></div><div dir="ltr"> <a href="mailto:chimerax-users-owner@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users-owner@cgl.ucsf.edu</a><br></div><div dir="ltr"><br></div><div dir="ltr">When replying, please edit your Subject line so it is more specific<br></div><div dir="ltr">than "Re: Contents of ChimeraX-users digest..."<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">Today's Topics:<br></div><div dir="ltr"><br></div><div dir="ltr"> 1. independent centers of rotation (Elaine Meng)<br></div><div dir="ltr"> 2. Change the directory for data fetched from databases<br></div><div dir="ltr"> (Guillaume Gaullier)<br></div><div dir="ltr"> 3. Re: Change the directory for data fetched from databases<br></div><div dir="ltr"> (Tom Goddard)<br></div><div dir="ltr"> 4. Re: Change the directory for data fetched from databases<br></div><div dir="ltr"> (Guillaume Gaullier)<br></div><div dir="ltr"> 5. Re: Change the directory for data fetched from databases<br></div><div dir="ltr"> (Tristan Croll)<br></div><div dir="ltr"> 6. Re: Change the directory for data fetched from databases<br></div><div dir="ltr"> (Guillaume Gaullier)<br></div><div dir="ltr"> 7. PDB: 7OVR (Veler, Hana (NIH/NCI) [F])<br></div><div dir="ltr"> 8. Re: PDB: 7OVR (Elaine Meng)<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">----------------------------------------------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Message: 1<br></div><div dir="ltr">Date: Wed, 15 Dec 2021 12:51:58 -0800<br></div><div dir="ltr">From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" rel="nofollow" target="_blank">meng@cgl.ucsf.edu</a>><br></div><div dir="ltr">To: Abigail Jackson <<a href="mailto:ajackson@scripps.edu" rel="nofollow" target="_blank">ajackson@scripps.edu</a>><br></div><div dir="ltr">Cc: "<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>" <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Subject: [chimerax-users] independent centers of rotation<br></div><div dir="ltr">Message-ID: <<a href="mailto:90DEEA37-1BF5-4F52-AF35-DF81F0B4F273@cgl.ucsf.edu" rel="nofollow" target="_blank">90DEEA37-1BF5-4F52-AF35-DF81F0B4F273@cgl.ucsf.edu</a>><br></div><div dir="ltr">Content-Type: text/plain; charset=us-ascii<br></div><div dir="ltr"><br></div><div dir="ltr">Hi Abigail,<br></div><div dir="ltr">Ah, you're referring to the "independent centers of rotation" mode in Chimera. By default, the "tile" command in Chimera automatically turns it on.<br></div><div dir="ltr"><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/tile.html" rel="nofollow" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/tile.html</a>><br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><<a href="https://www.rbvi.ucsf.edu/chimerax/download.html" rel="nofollow" target="_blank">https://www.rbvi.ucsf.edu/chimerax/download.html</a>><br></div><div dir="ltr"><br></div><div dir="ltr">Sorry about that,<br></div><div dir="ltr">Elaine<br></div><div dir="ltr">-----<br></div><div dir="ltr">Elaine C. Meng, Ph.D. <br></div><div dir="ltr">UCSF Chimera(X) team<br></div><div dir="ltr">Department of Pharmaceutical Chemistry<br></div><div dir="ltr">University of California, San Francisco<br></div><div dir="ltr"><br></div><div dir="ltr">> On Dec 15, 2021, at 12:28 PM, Abigail Jackson via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br></div><div dir="ltr">> <br></div><div dir="ltr">> Hi there,<br></div><div dir="ltr">> 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?<br></div><div dir="ltr">> <br></div><div dir="ltr">> Hopefully that description makes sense. Thank you in advance for your help! <br></div><div dir="ltr">> Best,<br></div><div dir="ltr">> Abigail Jackson<br></div><div dir="ltr">> The Scripps Research Institute <br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Message: 2<br></div><div dir="ltr">Date: Thu, 16 Dec 2021 10:08:26 +0000<br></div><div dir="ltr">From: Guillaume Gaullier <<a href="mailto:guillaume.gaullier@icm.uu.se" rel="nofollow" target="_blank">guillaume.gaullier@icm.uu.se</a>><br></div><div dir="ltr">To: ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Subject: [chimerax-users] Change the directory for data fetched from<br></div><div dir="ltr"> databases<br></div><div dir="ltr">Message-ID: <<a href="mailto:7B64261E-92A8-45FF-BF14-0B597E14A98B@icm.uu.se" rel="nofollow" target="_blank">7B64261E-92A8-45FF-BF14-0B597E14A98B@icm.uu.se</a>><br></div><div dir="ltr">Content-Type: text/plain; charset="utf-8"<br></div><div dir="ltr"><br></div><div dir="ltr">Hello,<br></div><div dir="ltr"><br></div><div dir="ltr">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).<br></div><div dir="ltr"><br></div><div dir="ltr">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).<br></div><div dir="ltr"><br></div><div dir="ltr">Thank you,<br></div><div dir="ltr"><br></div><div dir="ltr">Guillaume<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">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: <a href="http://www.uu.se/om-uu/dataskydd-personuppgifter/" rel="nofollow" target="_blank">http://www.uu.se/om-uu/dataskydd-personuppgifter/</a><br></div><div dir="ltr"><br></div><div dir="ltr">E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: <a href="http://www.uu.se/en/about-uu/data-protection-policy" rel="nofollow" target="_blank">http://www.uu.se/en/about-uu/data-protection-policy</a><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Message: 3<br></div><div dir="ltr">Date: Thu, 16 Dec 2021 14:50:25 -0800<br></div><div dir="ltr">From: Tom Goddard <<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a>><br></div><div dir="ltr">To: Guillaume Gaullier <<a href="mailto:guillaume.gaullier@icm.uu.se" rel="nofollow" target="_blank">guillaume.gaullier@icm.uu.se</a>><br></div><div dir="ltr">Cc: ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Subject: Re: [chimerax-users] Change the directory for data fetched<br></div><div dir="ltr"> from databases<br></div><div dir="ltr">Message-ID: <<a href="mailto:8D292E49-13E7-4DF0-9B94-7EAC424DA7D0@sonic.net" rel="nofollow" target="_blank">8D292E49-13E7-4DF0-9B94-7EAC424DA7D0@sonic.net</a>><br></div><div dir="ltr">Content-Type: text/plain; charset=utf-8<br></div><div dir="ltr"><br></div><div dir="ltr">Hi Guillaume,<br></div><div dir="ltr"><br></div><div dir="ltr"> There is no setting to change the location where ChimeraX caches fetched files. It is always<br></div><div dir="ltr"><br></div><div dir="ltr"> ~/Downloads/ChimeraX<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux)<br></div><div dir="ltr"><br></div><div dir="ltr"> chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py<br></div><div dir="ltr"><br></div><div dir="ltr">making<br></div><div dir="ltr"><br></div><div dir="ltr"> _cache_dirs = ['/usr/local/chimerax_fetch']<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr"> Tom<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">> On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br></div><div dir="ltr">> <br></div><div dir="ltr">> Hello,<br></div><div dir="ltr">> <br></div><div dir="ltr">> 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).<br></div><div dir="ltr">> <br></div><div dir="ltr">> 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).<br></div><div dir="ltr">> <br></div><div dir="ltr">> Thank you,<br></div><div dir="ltr">> <br></div><div dir="ltr">> Guillaume<br></div><div dir="ltr">> <br></div><div dir="ltr">> <br></div><div dir="ltr">> <br></div><div dir="ltr">> <br></div><div dir="ltr">> <br></div><div dir="ltr">> <br></div><div dir="ltr">> <br></div><div dir="ltr">> <br></div><div dir="ltr">> <br></div><div dir="ltr">> 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: <a href="http://www.uu.se/om-uu/dataskydd-personuppgifter/" rel="nofollow" target="_blank">http://www.uu.se/om-uu/dataskydd-personuppgifter/</a><br></div><div dir="ltr">> <br></div><div dir="ltr">> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: <a href="http://www.uu.se/en/about-uu/data-protection-policy" rel="nofollow" target="_blank">http://www.uu.se/en/about-uu/data-protection-policy</a><br></div><div dir="ltr">> <br></div><div dir="ltr">> _______________________________________________<br></div><div dir="ltr">> ChimeraX-users mailing list<br></div><div dir="ltr">> <a href="mailto:ChimeraX-users@cgl.ucsf.edu" rel="nofollow" target="_blank">ChimeraX-users@cgl.ucsf.edu</a><br></div><div dir="ltr">> Manage subscription:<br></div><div dir="ltr">> <a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" rel="nofollow" target="_blank">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br></div><div dir="ltr">> <br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Message: 4<br></div><div dir="ltr">Date: Fri, 17 Dec 2021 08:40:06 +0000<br></div><div dir="ltr">From: Guillaume Gaullier <<a href="mailto:guillaume.gaullier@icm.uu.se" rel="nofollow" target="_blank">guillaume.gaullier@icm.uu.se</a>><br></div><div dir="ltr">To: Tom Goddard <<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a>><br></div><div dir="ltr">Cc: ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Subject: Re: [chimerax-users] Change the directory for data fetched<br></div><div dir="ltr"> from databases<br></div><div dir="ltr">Message-ID: <<a href="mailto:ED531B0A-5F66-4E86-920E-565966A5D8A3@icm.uu.se" rel="nofollow" target="_blank">ED531B0A-5F66-4E86-920E-565966A5D8A3@icm.uu.se</a>><br></div><div dir="ltr">Content-Type: text/plain; charset="utf-8"<br></div><div dir="ltr"><br></div><div dir="ltr">Hi Tom,<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">Thank you for your answer.<br></div><div dir="ltr">Cheers,<br></div><div dir="ltr"><br></div><div dir="ltr">Guillaume<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">On 16 Dec 2021, at 23:50, Tom Goddard <<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a><mailto:<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a>>> wrote:<br></div><div dir="ltr"><br></div><div dir="ltr">Hi Guillaume,<br></div><div dir="ltr"><br></div><div dir="ltr"> There is no setting to change the location where ChimeraX caches fetched files. It is always<br></div><div dir="ltr"><br></div><div dir="ltr">~/Downloads/ChimeraX<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux)<br></div><div dir="ltr"><br></div><div dir="ltr">chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py<br></div><div dir="ltr"><br></div><div dir="ltr">making<br></div><div dir="ltr"><br></div><div dir="ltr">_cache_dirs = ['/usr/local/chimerax_fetch']<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">Tom<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a><mailto:<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>>> wrote:<br></div><div dir="ltr"><br></div><div dir="ltr">Hello,<br></div><div dir="ltr"><br></div><div dir="ltr">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).<br></div><div dir="ltr"><br></div><div dir="ltr">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).<br></div><div dir="ltr"><br></div><div dir="ltr">Thank you,<br></div><div dir="ltr"><br></div><div dir="ltr">Guillaume<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">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: <a href="http://www.uu.se/om-uu/dataskydd-personuppgifter/" rel="nofollow" target="_blank">http://www.uu.se/om-uu/dataskydd-personuppgifter/</a><br></div><div dir="ltr"><br></div><div dir="ltr">E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: <a href="http://www.uu.se/en/about-uu/data-protection-policy" rel="nofollow" target="_blank">http://www.uu.se/en/about-uu/data-protection-policy</a><br></div><div dir="ltr"><br></div><div dir="ltr">_______________________________________________<br></div><div dir="ltr">ChimeraX-users mailing list<br></div><div dir="ltr"><a href="mailto:ChimeraX-users@cgl.ucsf.edu" rel="nofollow" target="_blank">ChimeraX-users@cgl.ucsf.edu</a><mailto:<a href="mailto:ChimeraX-users@cgl.ucsf.edu" rel="nofollow" target="_blank">ChimeraX-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Manage subscription:<br></div><div dir="ltr"><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" rel="nofollow" target="_blank">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">-------------- next part --------------<br></div><div dir="ltr">An HTML attachment was scrubbed...<br></div><div dir="ltr">URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211217/be050f17/attachment-0001.html" rel="nofollow" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211217/be050f17/attachment-0001.html</a>><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Message: 5<br></div><div dir="ltr">Date: Fri, 17 Dec 2021 09:11:45 +0000<br></div><div dir="ltr">From: Tristan Croll <<a href="mailto:tic20@cam.ac.uk" rel="nofollow" target="_blank">tic20@cam.ac.uk</a>><br></div><div dir="ltr">To: goddard <<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a>>, Guillaume Gaullier<br></div><div dir="ltr"> <<a href="mailto:guillaume.gaullier@icm.uu.se" rel="nofollow" target="_blank">guillaume.gaullier@icm.uu.se</a>><br></div><div dir="ltr">Cc: ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Subject: Re: [chimerax-users] Change the directory for data fetched<br></div><div dir="ltr"> from databases<br></div><div dir="ltr">Message-ID:<br></div><div dir="ltr"> <<a href="mailto:CWXP265MB3318E17B89A1971E1C5B40F0F5789@CWXP265MB3318.GBRP265.PROD.OUTLOOK.COM" rel="nofollow" target="_blank">CWXP265MB3318E17B89A1971E1C5B40F0F5789@CWXP265MB3318.GBRP265.PROD.OUTLOOK.COM</a>><br></div><div dir="ltr"> <br></div><div dir="ltr">Content-Type: text/plain; charset="windows-1252"<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">-- Tristan<br></div><div dir="ltr">________________________________<br></div><div dir="ltr">From: ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users-bounces@cgl.ucsf.edu</a>> on behalf of Guillaume Gaullier via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Sent: 17 December 2021 08:40<br></div><div dir="ltr">To: goddard <<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a>><br></div><div dir="ltr">Cc: ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Subject: Re: [chimerax-users] Change the directory for data fetched from databases<br></div><div dir="ltr"><br></div><div dir="ltr">Hi Tom,<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">Thank you for your answer.<br></div><div dir="ltr">Cheers,<br></div><div dir="ltr"><br></div><div dir="ltr">Guillaume<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">On 16 Dec 2021, at 23:50, Tom Goddard <<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a><mailto:<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a>>> wrote:<br></div><div dir="ltr"><br></div><div dir="ltr">Hi Guillaume,<br></div><div dir="ltr"><br></div><div dir="ltr"> There is no setting to change the location where ChimeraX caches fetched files. It is always<br></div><div dir="ltr"><br></div><div dir="ltr">~/Downloads/ChimeraX<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux)<br></div><div dir="ltr"><br></div><div dir="ltr">chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py<br></div><div dir="ltr"><br></div><div dir="ltr">making<br></div><div dir="ltr"><br></div><div dir="ltr">_cache_dirs = ['/usr/local/chimerax_fetch']<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">Tom<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a><mailto:<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>>> wrote:<br></div><div dir="ltr"><br></div><div dir="ltr">Hello,<br></div><div dir="ltr"><br></div><div dir="ltr">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).<br></div><div dir="ltr"><br></div><div dir="ltr">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).<br></div><div dir="ltr"><br></div><div dir="ltr">Thank you,<br></div><div dir="ltr"><br></div><div dir="ltr">Guillaume<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">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: <a href="http://www.uu.se/om-uu/dataskydd-personuppgifter/" rel="nofollow" target="_blank">http://www.uu.se/om-uu/dataskydd-personuppgifter/</a><br></div><div dir="ltr"><br></div><div dir="ltr">E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: <a href="http://www.uu.se/en/about-uu/data-protection-policy" rel="nofollow" target="_blank">http://www.uu.se/en/about-uu/data-protection-policy</a><br></div><div dir="ltr"><br></div><div dir="ltr">_______________________________________________<br></div><div dir="ltr">ChimeraX-users mailing list<br></div><div dir="ltr"><a href="mailto:ChimeraX-users@cgl.ucsf.edu" rel="nofollow" target="_blank">ChimeraX-users@cgl.ucsf.edu</a><mailto:<a href="mailto:ChimeraX-users@cgl.ucsf.edu" rel="nofollow" target="_blank">ChimeraX-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Manage subscription:<br></div><div dir="ltr"><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" rel="nofollow" target="_blank">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">-------------- next part --------------<br></div><div dir="ltr">An HTML attachment was scrubbed...<br></div><div dir="ltr">URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211217/4dc43f3a/attachment-0001.html" rel="nofollow" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211217/4dc43f3a/attachment-0001.html</a>><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Message: 6<br></div><div dir="ltr">Date: Fri, 17 Dec 2021 09:14:32 +0000<br></div><div dir="ltr">From: Guillaume Gaullier <<a href="mailto:guillaume.gaullier@icm.uu.se" rel="nofollow" target="_blank">guillaume.gaullier@icm.uu.se</a>><br></div><div dir="ltr">To: Tristan Croll <<a href="mailto:tic20@CAM.AC.UK" rel="nofollow" target="_blank">tic20@CAM.AC.UK</a>><br></div><div dir="ltr">Cc: ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Subject: Re: [chimerax-users] Change the directory for data fetched<br></div><div dir="ltr"> from databases<br></div><div dir="ltr">Message-ID: <<a href="mailto:E19B97E0-98D3-4FE4-8EB9-D591BC947449@icm.uu.se" rel="nofollow" target="_blank">E19B97E0-98D3-4FE4-8EB9-D591BC947449@icm.uu.se</a>><br></div><div dir="ltr">Content-Type: text/plain; charset="utf-8"<br></div><div dir="ltr"><br></div><div dir="ltr">Very simple indeed, I should have thought of that first. Thank you Tristan. :-)<br></div><div dir="ltr"><br></div><div dir="ltr">Guillaume<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">On 17 Dec 2021, at 10:11, Tristan Croll <<a href="mailto:tic20@CAM.AC.UK" rel="nofollow" target="_blank">tic20@CAM.AC.UK</a><mailto:<a href="mailto:tic20@CAM.AC.UK" rel="nofollow" target="_blank">tic20@CAM.AC.UK</a>>> wrote:<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">-- Tristan<br></div><div dir="ltr">________________________________<br></div><div dir="ltr">From: ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users-bounces@cgl.ucsf.edu</a><mailto:<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users-bounces@cgl.ucsf.edu</a>>> on behalf of Guillaume Gaullier via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a><mailto:<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>>><br></div><div dir="ltr">Sent: 17 December 2021 08:40<br></div><div dir="ltr">To: goddard <<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a><mailto:<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a>>><br></div><div dir="ltr">Cc: ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a><mailto:<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>>><br></div><div dir="ltr">Subject: Re: [chimerax-users] Change the directory for data fetched from databases<br></div><div dir="ltr"><br></div><div dir="ltr">Hi Tom,<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">Thank you for your answer.<br></div><div dir="ltr">Cheers,<br></div><div dir="ltr"><br></div><div dir="ltr">Guillaume<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">On 16 Dec 2021, at 23:50, Tom Goddard <<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a><mailto:<a href="mailto:goddard@sonic.net" rel="nofollow" target="_blank">goddard@sonic.net</a>>> wrote:<br></div><div dir="ltr"><br></div><div dir="ltr">Hi Guillaume,<br></div><div dir="ltr"><br></div><div dir="ltr"> There is no setting to change the location where ChimeraX caches fetched files. It is always<br></div><div dir="ltr"><br></div><div dir="ltr">~/Downloads/ChimeraX<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">You could modify the ChimeraX application file, a file in the distribution (here's the path for Linux)<br></div><div dir="ltr"><br></div><div dir="ltr">chimerax/lib/python3.9/site-packages/chimerax/core/fetch.py<br></div><div dir="ltr"><br></div><div dir="ltr">making<br></div><div dir="ltr"><br></div><div dir="ltr">_cache_dirs = ['/usr/local/chimerax_fetch']<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">Tom<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">On Dec 16, 2021, at 2:08 AM, Guillaume Gaullier via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a><mailto:<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>>> wrote:<br></div><div dir="ltr"><br></div><div dir="ltr">Hello,<br></div><div dir="ltr"><br></div><div dir="ltr">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).<br></div><div dir="ltr"><br></div><div dir="ltr">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).<br></div><div dir="ltr"><br></div><div dir="ltr">Thank you,<br></div><div dir="ltr"><br></div><div dir="ltr">Guillaume<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">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: <a href="http://www.uu.se/om-uu/dataskydd-personuppgifter/" rel="nofollow" target="_blank">http://www.uu.se/om-uu/dataskydd-personuppgifter/</a><br></div><div dir="ltr"><br></div><div dir="ltr">E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: <a href="http://www.uu.se/en/about-uu/data-protection-policy" rel="nofollow" target="_blank">http://www.uu.se/en/about-uu/data-protection-policy</a><br></div><div dir="ltr"><br></div><div dir="ltr">_______________________________________________<br></div><div dir="ltr">ChimeraX-users mailing list<br></div><div dir="ltr"><a href="mailto:ChimeraX-users@cgl.ucsf.edu" rel="nofollow" target="_blank">ChimeraX-users@cgl.ucsf.edu</a><mailto:<a href="mailto:ChimeraX-users@cgl.ucsf.edu" rel="nofollow" target="_blank">ChimeraX-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Manage subscription:<br></div><div dir="ltr"><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" rel="nofollow" target="_blank">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br></div><div dir="ltr"><br></div><div dir="ltr">-------------- next part --------------<br></div><div dir="ltr">An HTML attachment was scrubbed...<br></div><div dir="ltr">URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211217/e20e526f/attachment-0001.html" rel="nofollow" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211217/e20e526f/attachment-0001.html</a>><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Message: 7<br></div><div dir="ltr">Date: Fri, 17 Dec 2021 17:18:57 +0000<br></div><div dir="ltr">From: "Veler, Hana (NIH/NCI) [F]" <<a href="mailto:hana.veler@nih.gov" rel="nofollow" target="_blank">hana.veler@nih.gov</a>><br></div><div dir="ltr">To: "<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>" <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Subject: [chimerax-users] PDB: 7OVR<br></div><div dir="ltr">Message-ID: <<a href="mailto:387A4521-19AF-4D23-8BA8-6DB6DD300F3B@contoso.com" rel="nofollow" target="_blank">387A4521-19AF-4D23-8BA8-6DB6DD300F3B@contoso.com</a>><br></div><div dir="ltr">Content-Type: text/plain; charset="utf-8"<br></div><div dir="ltr"><br></div><div dir="ltr">To whom it may concern,<br></div><div dir="ltr"><br></div><div dir="ltr">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.<br></div><div dir="ltr"><br></div><div dir="ltr">Would you know what could be the cause?<br></div><div dir="ltr"><br></div><div dir="ltr">Thanks,<br></div><div dir="ltr">Hana<br></div><div dir="ltr">-------------- next part --------------<br></div><div dir="ltr">An HTML attachment was scrubbed...<br></div><div dir="ltr">URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211217/9bc1ca40/attachment-0001.html" rel="nofollow" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211217/9bc1ca40/attachment-0001.html</a>><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Message: 8<br></div><div dir="ltr">Date: Fri, 17 Dec 2021 09:23:32 -0800<br></div><div dir="ltr">From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" rel="nofollow" target="_blank">meng@cgl.ucsf.edu</a>><br></div><div dir="ltr">To: "Veler, Hana (NIH/NCI) [F]" <<a href="mailto:hana.veler@nih.gov" rel="nofollow" target="_blank">hana.veler@nih.gov</a>><br></div><div dir="ltr">Cc: "<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>" <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br></div><div dir="ltr">Subject: Re: [chimerax-users] PDB: 7OVR<br></div><div dir="ltr">Message-ID: <<a href="mailto:8FE6FF2D-AAF7-46A6-8997-FD73E7910BE8@cgl.ucsf.edu" rel="nofollow" target="_blank">8FE6FF2D-AAF7-46A6-8997-FD73E7910BE8@cgl.ucsf.edu</a>><br></div><div dir="ltr">Content-Type: text/plain; charset=utf-8<br></div><div dir="ltr"><br></div><div dir="ltr">Hello Hana,<br></div><div dir="ltr">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?<br></div><div dir="ltr"><br></div><div dir="ltr">Also, when I open structure 7ovr in ChimeraX, all of the atoms are shown already. <br></div><div dir="ltr"><br></div><div dir="ltr">I hope this helps,<br></div><div dir="ltr">Elaine<br></div><div dir="ltr">-----<br></div><div dir="ltr">Elaine C. Meng, Ph.D. <br></div><div dir="ltr">UCSF Chimera(X) team<br></div><div dir="ltr">Department of Pharmaceutical Chemistry<br></div><div dir="ltr">University of California, San Francisco<br></div><div dir="ltr"><br></div><div dir="ltr">> On Dec 17, 2021, at 9:18 AM, Veler, Hana (NIH/NCI) [F] via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" rel="nofollow" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br></div><div dir="ltr">> <br></div><div dir="ltr">> To whom it may concern,<br></div><div dir="ltr">> <br></div><div dir="ltr">> 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.<br></div><div dir="ltr">> <br></div><div dir="ltr">> Would you know what could be the cause? <br></div><div dir="ltr">> <br></div><div dir="ltr">> Thanks,<br></div><div dir="ltr">> Hana <br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">Subject: Digest Footer<br></div><div dir="ltr"><br></div><div dir="ltr">_______________________________________________<br></div><div dir="ltr">ChimeraX-users mailing list<br></div><div dir="ltr"><a href="mailto:ChimeraX-users@cgl.ucsf.edu" rel="nofollow" target="_blank">ChimeraX-users@cgl.ucsf.edu</a><br></div><div dir="ltr">Manage subscription:<br></div><div dir="ltr"><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" rel="nofollow" target="_blank">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">------------------------------<br></div><div dir="ltr"><br></div><div dir="ltr">End of ChimeraX-users Digest, Vol 60, Issue 7<br></div><div dir="ltr">*********************************************<br></div></div>
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