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
Subject: [chimerax-users] independent centers of rotation
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.
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.
Sorry about that,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
>
> 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
Subject: [chimerax-users] Change the directory for data fetched from
databases
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
------------------------------
Message: 3
Date: Thu, 16 Dec 2021 14:50:25 -0800
Subject: Re: [chimerax-users] Change the directory for data fetched
from databases
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
>
> 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
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> ChimeraX-users mailing list
> Manage subscription:
>
------------------------------
Message: 4
Date: Fri, 17 Dec 2021 08:40:06 +0000
Subject: Re: [chimerax-users] Change the directory for data fetched
from databases
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
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
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: 5
Date: Fri, 17 Dec 2021 09:11:45 +0000
Subject: Re: [chimerax-users] Change the directory for data fetched
from databases
Message-ID:
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
________________________________
Sent: 17 December 2021 08:40
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
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
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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Manage subscription:
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Message: 6
Date: Fri, 17 Dec 2021 09:14:32 +0000
Subject: Re: [chimerax-users] Change the directory for data fetched
from databases
Content-Type: text/plain; charset="utf-8"
Very simple indeed, I should have thought of that first. Thank you Tristan. :-)
Guillaume
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
________________________________
Sent: 17 December 2021 08:40
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
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
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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ChimeraX-users mailing list
Manage subscription:
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Message: 7
Date: Fri, 17 Dec 2021 17:18:57 +0000
Subject: [chimerax-users] PDB: 7OVR
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
Subject: Re: [chimerax-users] PDB: 7OVR
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
>
> 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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