Save PDB relative to map - does not store relative postion
Hello, I am running into an issue with saving pdb coordinates and their relative postioning. I am fitting an atomic model into a map model, explicitly the atomic model is rotated and translated into the map using fitmap (local optimization, rigid body fitting). Once the fit is complete, the atomic model is saved as a PDB file with the checkmark set on "Save relative to model...", here I have chosen the map the atomic model has just been fit to. This is, I think, in accordance with what is adviced in the doc of the "Fit in Map" Tool. However, when I reopen said atomic model and map in a new chimerax session (loading the map and loading the pdb file just saved relative to this map), none of the rotational and translational information is kept and the map and atomic model are in no meaning full spatial relationship. I wanted to use this procedure to prepare for cryofit and/or real space refinement in phenix, so I would like to use map and pdb for another software. As is mentioned in the doc of the "Fit in Map" Tool, volume files generally do not store rotation, thus the pdb file should be chosen to capture the rotational and translation information. Am I understanding something wrongly here or how come that the postioning is completely off when I reload map and model? Thank you for your help. Best regards, Dennis --------------------------------------------- Dennis Dannecker Master Student of Biochemistry Department of Chemistry Faculty of Mathematics and Natural Sciences University of Cologne Albertus-Magnus-Platz 50923 Cologne, Germany
Hi Dennis, It sounds like you did exactly the right thing. However, I cannot reproduce this problem. e.g. commands fit #1 in #3 save test.pdb models #1 rel #3 ... then closing all and reopening map (which was #3) and test.pdb, the PDB structure is in its new, fit position relative to the map. In a completely separate test, I also tried saving the fit pdb with the File menu instead of the "save" comand after fitting, choosing the "relative to" option with the map model specified. Again, closing everything and reopening gives the PDB in its new fit position relative to the map. The only confusing thing I can think of is that the map contour level may be different when you reopen it so it might look different. However, as far as I can tell, structure saving "relative to" is working correctly. I could also say to make sure you have a recent ChimeraX, since sometimes bugs have been fixed, but I don't think there has been any change to this highly used feature for a long time. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 2, 2024, at 3:55 PM, Dennis Dannecker via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am running into an issue with saving pdb coordinates and their relative postioning.
I am fitting an atomic model into a map model, explicitly the atomic model is rotated and translated into the map using fitmap (local optimization, rigid body fitting). Once the fit is complete, the atomic model is saved as a PDB file with the checkmark set on "Save relative to model...", here I have chosen the map the atomic model has just been fit to. This is, I think, in accordance with what is adviced in the doc of the "Fit in Map" Tool.
However, when I reopen said atomic model and map in a new chimerax session (loading the map and loading the pdb file just saved relative to this map), none of the rotational and translational information is kept and the map and atomic model are in no meaning full spatial relationship.
I wanted to use this procedure to prepare for cryofit and/or real space refinement in phenix, so I would like to use map and pdb for another software. As is mentioned in the doc of the "Fit in Map" Tool, volume files generally do not store rotation, thus the pdb file should be chosen to capture the rotational and translation information.
Am I understanding something wrongly here or how come that the postioning is completely off when I reload map and model?
Thank you for your help.
Best regards,
Dennis
If you still believe there is a bug with your specific situation, we recommend using menu: Help... Report a Bug insteaad of sending email. Please include all relevant information in the bug-reporting dialog and also the data (e.g. attach a session) unless it is data that has to remain private. Thanks, Elaine
On Feb 2, 2024, at 4:20 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dennis, It sounds like you did exactly the right thing. However, I cannot reproduce this problem.
e.g. commands
fit #1 in #3 save test.pdb models #1 rel #3
... then closing all and reopening map (which was #3) and test.pdb, the PDB structure is in its new, fit position relative to the map.
In a completely separate test, I also tried saving the fit pdb with the File menu instead of the "save" comand after fitting, choosing the "relative to" option with the map model specified. Again, closing everything and reopening gives the PDB in its new fit position relative to the map.
The only confusing thing I can think of is that the map contour level may be different when you reopen it so it might look different. However, as far as I can tell, structure saving "relative to" is working correctly.
I could also say to make sure you have a recent ChimeraX, since sometimes bugs have been fixed, but I don't think there has been any change to this highly used feature for a long time.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 2, 2024, at 3:55 PM, Dennis Dannecker via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am running into an issue with saving pdb coordinates and their relative postioning.
I am fitting an atomic model into a map model, explicitly the atomic model is rotated and translated into the map using fitmap (local optimization, rigid body fitting). Once the fit is complete, the atomic model is saved as a PDB file with the checkmark set on "Save relative to model...", here I have chosen the map the atomic model has just been fit to. This is, I think, in accordance with what is adviced in the doc of the "Fit in Map" Tool.
However, when I reopen said atomic model and map in a new chimerax session (loading the map and loading the pdb file just saved relative to this map), none of the rotational and translational information is kept and the map and atomic model are in no meaning full spatial relationship.
I wanted to use this procedure to prepare for cryofit and/or real space refinement in phenix, so I would like to use map and pdb for another software. As is mentioned in the doc of the "Fit in Map" Tool, volume files generally do not store rotation, thus the pdb file should be chosen to capture the rotational and translation information.
Am I understanding something wrongly here or how come that the postioning is completely off when I reload map and model?
Thank you for your help.
Best regards,
Dennis
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participants (2)
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Dennis Dannecker -
Elaine Meng