Save multiple fitted maps in Chimera
Dear Chimera team and users, I am trying fit hundreds of protein density maps into a tomogram by manually adjusting their positions. After the placement, I found I can't save all the maps together in a single mrc file. Is there anyway to do so? Or is there a way to extract the relative orientations of the individual models? Thank you! Best, Huabin ________________________________ UT Southwestern Medical Center The future of medicine, today.
Dear Huabin, You could save a Chimera session, but you'd also need to keep the input tomogram files and density map files in their current locations since the session file does not include them. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sessions.html> For saving multiple maps to one file, I believe the only choice is "Chimera map format" <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#chimap> HOWEVER, as I understand it, simply saving a map to a file does not preserve any rotations and translations of that map such as from fitting. So first you may need to resample each density map to create a new density map in the new orientation, as discussed here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting> 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 13, 2021, at 11:59 AM, Huabin Zhou via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera team and users, I am trying fit hundreds of protein density maps into a tomogram by manually adjusting their positions. After the placement, I found I can't save all the maps together in a single mrc file. Is there anyway to do so? Or is there a way to extract the relative orientations of the individual models? Thank you! Best, Huabin
If you use ChimeraX instead (which has the same fitting capabilities), saving a ChimeraX session has an option to include density maps in the file. However, it sounds like that might be an extremely huge file, perhaps impractically large. In general, however, ChimeraX is much better/faster for working with large data than Chimera. ChimeraX sessions: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> ChimeraX homepage, download quick link is on the left <https://www.rbvi.ucsf.edu/chimerax/index.html> Elaine
On Dec 13, 2021, at 12:14 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Huabin, You could save a Chimera session, but you'd also need to keep the input tomogram files and density map files in their current locations since the session file does not include them. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sessions.html>
For saving multiple maps to one file, I believe the only choice is "Chimera map format" <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#chimap>
HOWEVER, as I understand it, simply saving a map to a file does not preserve any rotations and translations of that map such as from fitting. So first you may need to resample each density map to create a new density map in the new orientation, as discussed here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>
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 13, 2021, at 11:59 AM, Huabin Zhou via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera team and users, I am trying fit hundreds of protein density maps into a tomogram by manually adjusting their positions. After the placement, I found I can't save all the maps together in a single mrc file. Is there anyway to do so? Or is there a way to extract the relative orientations of the individual models? Thank you! Best, Huabin
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Elaine, Thank you so much for your quick reply. The ChimeraX is much faster than Chimera. With vol resample, I was able to get the new individual map on fitted positions. BTW, for any other user's future reference, Clara Altomare pointed out the following command could add multiple density map together: vop add #1-99 Thanks, Huabin ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 13 December 2021 14:23 To: Chimera <chimera-users@cgl.ucsf.edu>; Huabin Zhou <Huabin.Zhou@UTSouthwestern.edu> Subject: Re: [Chimera-users] Save multiple fitted maps in Chimera EXTERNAL MAIL If you use ChimeraX instead (which has the same fitting capabilities), saving a ChimeraX session has an option to include density maps in the file. However, it sounds like that might be an extremely huge file, perhaps impractically large. In general, however, ChimeraX is much better/faster for working with large data than Chimera. ChimeraX sessions: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> ChimeraX homepage, download quick link is on the left <https://www.rbvi.ucsf.edu/chimerax/index.html> Elaine
On Dec 13, 2021, at 12:14 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Huabin, You could save a Chimera session, but you'd also need to keep the input tomogram files and density map files in their current locations since the session file does not include them. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sessions.html>
For saving multiple maps to one file, I believe the only choice is "Chimera map format" <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#chimap>
HOWEVER, as I understand it, simply saving a map to a file does not preserve any rotations and translations of that map such as from fitting. So first you may need to resample each density map to create a new density map in the new orientation, as discussed here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>
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 13, 2021, at 11:59 AM, Huabin Zhou via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera team and users, I am trying fit hundreds of protein density maps into a tomogram by manually adjusting their positions. After the placement, I found I can't save all the maps together in a single mrc file. Is there anyway to do so? Or is there a way to extract the relative orientations of the individual models? Thank you! Best, Huabin
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today.
Thanks for mentioning "vop add," since I forgot to include it! It does the adding and resampling all at once. ChimeraX and Chimera both have this command, although in ChimeraX it is documented as "volume add": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add> Elaine
On Dec 13, 2021, at 1:25 PM, Huabin Zhou <Huabin.Zhou@UTSouthwestern.edu> wrote:
Dear Elaine,
Thank you so much for your quick reply. The ChimeraX is much faster than Chimera. With vol resample, I was able to get the new individual map on fitted positions.
BTW, for any other user's future reference, Clara Altomare pointed out the following command could add multiple density map together: vop add #1-99
Thanks,
Huabin
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 13 December 2021 14:23 To: Chimera <chimera-users@cgl.ucsf.edu>; Huabin Zhou <Huabin.Zhou@UTSouthwestern.edu> Subject: Re: [Chimera-users] Save multiple fitted maps in Chimera
EXTERNAL MAIL
If you use ChimeraX instead (which has the same fitting capabilities), saving a ChimeraX session has an option to include density maps in the file. However, it sounds like that might be an extremely huge file, perhaps impractically large.
In general, however, ChimeraX is much better/faster for working with large data than Chimera.
ChimeraX sessions: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session>
ChimeraX homepage, download quick link is on the left <https://www.rbvi.ucsf.edu/chimerax/index.html>
Elaine
On Dec 13, 2021, at 12:14 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Huabin, You could save a Chimera session, but you'd also need to keep the input tomogram files and density map files in their current locations since the session file does not include them. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sessions.html>
For saving multiple maps to one file, I believe the only choice is "Chimera map format" <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#chimap>
HOWEVER, as I understand it, simply saving a map to a file does not preserve any rotations and translations of that map such as from fitting. So first you may need to resample each density map to create a new density map in the new orientation, as discussed here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>
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 13, 2021, at 11:59 AM, Huabin Zhou via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera team and users, I am trying fit hundreds of protein density maps into a tomogram by manually adjusting their positions. After the placement, I found I can't save all the maps together in a single mrc file. Is there anyway to do so? Or is there a way to extract the relative orientations of the individual models? Thank you! Best, Huabin
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.
UT Southwestern Medical Center The future of medicine, today.
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Elaine Meng -
Huabin Zhou