Hi, I'm trying to measure the movement of a domain between two structures of the same protein. Here are the conditions: 1. There are two domains in each structure 2. I want to overlay the first domain and measure the rotation of the second domain 3. There are lots of structures, so I want to minimise the number of steps 4. I'd like to do this with a script and the --no_gui option on headless Chimera Here is my current script for the routine: open pdb1 open pdb2 match #1:1-50 #0:1-50 write format pdb relative #1 #0 t.pdb delete #1 open t.pdb match #1:55-80 #0:55-80 measure rotation #1 #0 delete #1 open pdb3 ... Is it possible to not have to write, delete, and open #1 after the first match step? If I don't do this, then the measure rotation #1 #0 will measure rotation of the initial match rather than the second match. Thanks for the help. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031
Hi Reza, The "match" command has a "show" option that gives both the transformation caused by that single "match" command relative to the previous position and the overall transformation. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> The first transformation is what you wanted, if I understand correctly. So if the information provided by match is sufficient, you could do something like this (using my own example because I don't have your proteins, but you can modify to your situation): open 1ggz open 1ahr match #1:4-70@ca #0:4-70@ca match #1:84-140@ca #0:84-140@ca show true close #1 In the Reply Log this gives the following information, which would be the individual-command transformation (which you were interested in) followed by the overall transformation. So your answer in this case would be 139.6 degrees. Executing match ['#1:84-140@ca', '#0:84-140@ca'], no iteration Motion of #1 in #0 coordinate system Matrix rotation and translation 0.82262091 0.53040723 -0.20484873 3.62409177 0.52981789 -0.58429031 0.61473396 -5.35565416 0.20636821 -0.61422553 -0.76166866 17.09651172 Axis -0.94832057 -0.31731354 -0.00045477 Axis point 0.00000000 0.03120861 9.69339429 Rotation angle (degrees) 139.61155749 Shift along axis -1.74515412 Motion of #1 original coordinates in #0 coordinate system Matrix rotation and translation -0.68295658 -0.27265659 0.67766414 39.52966567 0.17128697 0.84207891 0.51143317 -34.51544087 -0.71009231 0.46536169 -0.52840081 19.95150460 Axis -0.03160421 0.95197595 0.30453729 Axis point 25.66566934 0.00000000 6.71489755 Rotation angle (degrees) 133.20724233 Shift along axis -28.03119641 RMSD between 57 atom pairs is 0.906 angstroms Also I would use "close #1" in the script rather than "delete #1" but maybe that doesn't really matter. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 1, 2023, at 11:23 AM, Reza Khayat via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to measure the movement of a domain between two structures of the same protein. Here are the conditions: 1. There are two domains in each structure 2. I want to overlay the first domain and measure the rotation of the second domain 3. There are lots of structures, so I want to minimise the number of steps 4. I'd like to do this with a script and the --no_gui option on headless Chimera
Here is my current script for the routine: open pdb1 open pdb2 match #1:1-50 #0:1-50 write format pdb relative #1 #0 t.pdb delete #1 open t.pdb match #1:55-80 #0:55-80 measure rotation #1 #0 delete #1
open pdb3 ...
Is it possible to not have to write, delete, and open #1 after the first match step? If I don't do this, then the measure rotation #1 #0 will measure rotation of the initial match rather than the second match. Thanks for the help.
Best wishes, Reza
Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Hi Reza, Not sure you'll think this is simpler, but it avoids writing a temporary file. You open two copies of the second pdb, align one copy using domain 1 and the other using domain 2 and then measure the rotation between the two copies open pdb1 open pdb2 open pdb2 match #1:1-50 #0:1-50 match #2:55-80 #0:55-80 measure rotation #2 #1 close all By the way, I suggest you use ChimeraX. We have no funding for Chimera so you are more likely to get an answer to your question if it is about ChimeraX. All the above steps work in ChimeraX. Tom
On Aug 1, 2023, at 11:23 AM, Reza Khayat via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I'm trying to measure the movement of a domain between two structures of the same protein. Here are the conditions: 1. There are two domains in each structure 2. I want to overlay the first domain and measure the rotation of the second domain 3. There are lots of structures, so I want to minimise the number of steps 4. I'd like to do this with a script and the --no_gui option on headless Chimera
Here is my current script for the routine: open pdb1 open pdb2 match #1:1-50 #0:1-50 write format pdb relative #1 #0 t.pdb delete #1 open t.pdb match #1:55-80 #0:55-80 measure rotation #1 #0 delete #1
open pdb3 ...
Is it possible to not have to write, delete, and open #1 after the first match step? If I don't do this, then the measure rotation #1 #0 will measure rotation of the initial match rather than the second match. Thanks for the help.
Best wishes, Reza
Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 _______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
participants (3)
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Elaine Meng -
Reza Khayat -
Tom Goddard