Saving a moved PDB only moved in a new session
Hi all I am working with chimera, and I have a map and a pdb. 1) I have split the pdb into several fragments in order to fit them into the map 2) I have successfully moved the PDBs and fitted them into the map 3) I have "write each PDB" "relative to the map, which seems to make sense :) 4) In the current session I keep the map and the moved PDB open ...plus I open the just saved "wrote PDB" (intended to be on the same position I moved it). To me both, the opened PDB (which I have moved) and the just saved PDB, might be in the same position, fitting into the map... But... the just save-written PDB is clearly somewhere else... :( 5) But... If I make a NEW session, opening the map and the "wrote PDB", everything make sense, and the PDB is where I in fact moved to keep it fitted... Why is that that in the current session the written-PDB is not where it was "moved"; but when a new session is opened it is displayed where it was moved? It seems that everything works fine, it is just a bit confusing to me. Thanks in advanced! Marta
Hi Maria, It makes sense to me. When you save “relative to map” it means if you open the map and then all those PDBs they will be in the right position relative to the map. However, in the current session, you have rotated/zoomed the view interactively (moving the map from its original position), and when you open the PDBs it does automatically apply all those other changes unless the map is the lowest-ID model. When you start a new session you haven’t moved the map around yet. Here’s a more advanced suggestion that you could ignore (and I’m not even 100% sure it would work): Maybe in the current session you can bring the saved PDBs to the right positions relative to the map by additionallly applying whatever transformations you had done manually to the map with the matrixcopy command. E.g. if map is #5 and one of the saved PDBs was opened as #6, it may work to use command matrixcopy #5 #6 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2018, at 2:37 AM, Marta Perez Illana <marta.perez@cnb.csic.es> wrote:
Hi all
I am working with chimera, and I have a map and a pdb.
1) I have split the pdb into several fragments in order to fit them into the map
2) I have successfully moved the PDBs and fitted them into the map
3) I have "write each PDB" "relative to the map, which seems to make sense :)
4) In the current session I keep the map and the moved PDB open ...plus I open the just saved "wrote PDB" (intended to be on the same position I moved it).
To me both, the opened PDB (which I have moved) and the just saved PDB, might be in the same position, fitting into the map... But... the just save-written PDB is clearly somewhere else... :(
5) But... If I make a NEW session, opening the map and the "wrote PDB", everything make sense, and the PDB is where I in fact moved to keep it fitted...
Why is that that in the current session the written-PDB is not where it was "moved"; but when a new session is opened it is displayed where it was moved?
It seems that everything works fine, it is just a bit confusing to me. Thanks in advanced!
Marta
participants (2)
-
Elaine Meng -
Marta Perez Illana