Orientation and pre-superimposition of the PDB
Dear Chimera Users!
I am dealing with some script that use Chimera X to make a very nice images of the RMSF mapped to the PDB in B-factor column (produced by gromacs as the result of MD simulation).
The problem that when I map RMSF onto structure for several different systems (e.g. the different conformations of the same protein) the pdb produced by gmx rmsf in different orientation so Chimera use it for image and the positions of the structure are not the same (thus not being aligned, see the image for example!)
Would it be possible by means of some Chimera-X comands to orient pdbs in order to align them in the same way? E.g. I open (in bash loop) many pdbs (the same protein but in different states, which are not aligned before, but I need that on the final images the positions for each PDB would be the same (thus to avoid pre-align the PDBs before opening them in ChimeraX!
Thanks in advance!
Hi James, The problem is how to tell ChimeraX (and the problem would be the same in Chimera) what orientation is the “same” … What I would do is keep one reference structure open at all times, but hide it. Then when you open the different structures for display, you can match them to the (hidden) reference structure using whatever superposition method works best for you, either:
- matchmaker command, which figures out the pairing for you based on sequence alignment http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
- align command, for which you have to specify the atoms to pair yourself http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.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 Jun 27, 2019, at 2:08 AM, James Starlight jmsstarlight@gmail.com wrote:
Dear Chimera Users!
I am dealing with some script that use Chimera X to make a very nice images of the RMSF mapped to the PDB in B-factor column (produced by gromacs as the result of MD simulation).
The problem that when I map RMSF onto structure for several different systems (e.g. the different conformations of the same protein) the pdb produced by gmx rmsf in different orientation so Chimera use it for image and the positions of the structure are not the same (thus not being aligned, see the image for example!)
Would it be possible by means of some Chimera-X comands to orient pdbs in order to align them in the same way? E.g. I open (in bash loop) many pdbs (the same protein but in different states, which are not aligned before, but I need that on the final images the positions for each PDB would be the same (thus to avoid pre-align the PDBs before opening them in ChimeraX!
Thanks in advance!
Yes, thank you so much Elaine!
I also thought about reference.pdb, which would be usefull for the structural matching. Could you precise- what is 'hidden' reference?
Assuming that each time while looping pdbs, I load a new pdb (with b-factors info) + the (same) reference pdb (which is going to be used for matching of each pdb and should not be normally displayed, since I am taking a screenshot at the end). Could you just show commands of Chimera-X that mau be used as an example to
1) While having loaded 2 PDBs: to match target pdb (all of them have the same suffix, called B-factors-*.pdb) to the reference.pdb e.g. using C-alpha trace; 2) remove or hide reference pdb (not sure how to do it properly in this case, since on the next step I take a screenshot of the aligned PDB. probably I also should to focus camera on the aligned PDB.
Thank you in advance!
Gleb
чт, 27 июн. 2019 г. в 18:59, Elaine Meng meng@cgl.ucsf.edu:
Hi James, The problem is how to tell ChimeraX (and the problem would be the same in Chimera) what orientation is the “same” … What I would do is keep one reference structure open at all times, but hide it. Then when you open the different structures for display, you can match them to the (hidden) reference structure using whatever superposition method works best for you, either:
- matchmaker command, which figures out the pairing for you based on sequence alignment
http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
- align command, for which you have to specify the atoms to pair yourself
http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.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 Jun 27, 2019, at 2:08 AM, James Starlight jmsstarlight@gmail.com wrote:
Dear Chimera Users!
I am dealing with some script that use Chimera X to make a very nice images of the RMSF mapped to the PDB in B-factor column (produced by gromacs as the result of MD simulation).
The problem that when I map RMSF onto structure for several different systems (e.g. the different conformations of the same protein) the pdb produced by gmx rmsf in different orientation so Chimera use it for image and the positions of the structure are not the same (thus not being aligned, see the image for example!)
Would it be possible by means of some Chimera-X comands to orient pdbs in order to align them in the same way? E.g. I open (in bash loop) many pdbs (the same protein but in different states, which are not aligned before, but I need that on the final images the positions for each PDB would be the same (thus to avoid pre-align the PDBs before opening them in ChimeraX!
Thanks in advance!
Hi Gleb, My phrase “hidden reference” does not mean anything special. It just means to hide (undisplay) the model used as the reference for matching.
I only know ChimeraX commands, somebody else would have to respond about scripting for looping. Here are some example ChimeraX commands:
open reference.pdb [… set the view how you like, could be done interactively with mouse, then save session if you want to keep it for later…] hide #1 models open display1.pdb mm #2 to #1 [… do all the coloring or style/display changes and image saving …] close #2 open display2.pdb mm #2 to #1 [… do all the coloring or style/display changes and image saving …]
etc.
As previously mentioned, using “mm” (= matchmaker) to superimpose assumes the proteins have the same or at least similar sequences, enough to align them. If “mm” doesn’t work, you will have to figure out which atoms appear in all your structures and can be used in an “align” command.
Assuming all the proteins are about the same in terms of size/shape you could just manually position and zoom the reference PDB how you like, and then never move anything after that. You never close the reference.
If some of the proteins are much bigger, e.g. have some extra domains or other chains, you could use “view” after each superposition (similar to Chimera focus), but that might zoom out too much, and then you’d have to experiment with adding a “zoom” command after that.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html
I hope this helps, Elaine
On Jun 27, 2019, at 11:08 AM, James Starlight jmsstarlight@gmail.com wrote:
Yes, thank you so much Elaine!
I also thought about reference.pdb, which would be usefull for the structural matching. Could you precise- what is 'hidden' reference?
Assuming that each time while looping pdbs, I load a new pdb (with b-factors info) + the (same) reference pdb (which is going to be used for matching of each pdb and should not be normally displayed, since I am taking a screenshot at the end). Could you just show commands of Chimera-X that mau be used as an example to
- While having loaded 2 PDBs: to match target pdb (all of them have
the same suffix, called B-factors-*.pdb) to the reference.pdb e.g. using C-alpha trace; 2) remove or hide reference pdb (not sure how to do it properly in this case, since on the next step I take a screenshot of the aligned PDB. probably I also should to focus camera on the aligned PDB.
Thank you in advance!
Gleb
чт, 27 июн. 2019 г. в 18:59, Elaine Meng meng@cgl.ucsf.edu:
Hi James, The problem is how to tell ChimeraX (and the problem would be the same in Chimera) what orientation is the “same” … What I would do is keep one reference structure open at all times, but hide it. Then when you open the different structures for display, you can match them to the (hidden) reference structure using whatever superposition method works best for you, either:
- matchmaker command, which figures out the pairing for you based on sequence alignment
http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
- align command, for which you have to specify the atoms to pair yourself
http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.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 Jun 27, 2019, at 2:08 AM, James Starlight jmsstarlight@gmail.com wrote:
Dear Chimera Users!
I am dealing with some script that use Chimera X to make a very nice images of the RMSF mapped to the PDB in B-factor column (produced by gromacs as the result of MD simulation).
The problem that when I map RMSF onto structure for several different systems (e.g. the different conformations of the same protein) the pdb produced by gmx rmsf in different orientation so Chimera use it for image and the positions of the structure are not the same (thus not being aligned, see the image for example!)
Would it be possible by means of some Chimera-X comands to orient pdbs in order to align them in the same way? E.g. I open (in bash loop) many pdbs (the same protein but in different states, which are not aligned before, but I need that on the final images the positions for each PDB would be the same (thus to avoid pre-align the PDBs before opening them in ChimeraX!
Thanks in advance!
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Yes, this solution is exacrly what I was looking for! Thank you so much, Elaine!
James
чт, 27 июн. 2019 г. в 21:56, Elaine Meng meng@cgl.ucsf.edu:
Hi Gleb, My phrase “hidden reference” does not mean anything special. It just means to hide (undisplay) the model used as the reference for matching.
I only know ChimeraX commands, somebody else would have to respond about scripting for looping. Here are some example ChimeraX commands:
open reference.pdb [… set the view how you like, could be done interactively with mouse, then save session if you want to keep it for later…] hide #1 models open display1.pdb mm #2 to #1 [… do all the coloring or style/display changes and image saving …] close #2 open display2.pdb mm #2 to #1 [… do all the coloring or style/display changes and image saving …]
etc.
As previously mentioned, using “mm” (= matchmaker) to superimpose assumes the proteins have the same or at least similar sequences, enough to align them. If “mm” doesn’t work, you will have to figure out which atoms appear in all your structures and can be used in an “align” command.
Assuming all the proteins are about the same in terms of size/shape you could just manually position and zoom the reference PDB how you like, and then never move anything after that. You never close the reference.
If some of the proteins are much bigger, e.g. have some extra domains or other chains, you could use “view” after each superposition (similar to Chimera focus), but that might zoom out too much, and then you’d have to experiment with adding a “zoom” command after that.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html
I hope this helps, Elaine
On Jun 27, 2019, at 11:08 AM, James Starlight jmsstarlight@gmail.com wrote:
Yes, thank you so much Elaine!
I also thought about reference.pdb, which would be usefull for the structural matching. Could you precise- what is 'hidden' reference?
Assuming that each time while looping pdbs, I load a new pdb (with b-factors info) + the (same) reference pdb (which is going to be used for matching of each pdb and should not be normally displayed, since I am taking a screenshot at the end). Could you just show commands of Chimera-X that mau be used as an example to
- While having loaded 2 PDBs: to match target pdb (all of them have
the same suffix, called B-factors-*.pdb) to the reference.pdb e.g. using C-alpha trace; 2) remove or hide reference pdb (not sure how to do it properly in this case, since on the next step I take a screenshot of the aligned PDB. probably I also should to focus camera on the aligned PDB.
Thank you in advance!
Gleb
чт, 27 июн. 2019 г. в 18:59, Elaine Meng meng@cgl.ucsf.edu:
Hi James, The problem is how to tell ChimeraX (and the problem would be the same in Chimera) what orientation is the “same” … What I would do is keep one reference structure open at all times, but hide it. Then when you open the different structures for display, you can match them to the (hidden) reference structure using whatever superposition method works best for you, either:
- matchmaker command, which figures out the pairing for you based on sequence alignment
http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
- align command, for which you have to specify the atoms to pair yourself
http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.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 Jun 27, 2019, at 2:08 AM, James Starlight jmsstarlight@gmail.com wrote:
Dear Chimera Users!
I am dealing with some script that use Chimera X to make a very nice images of the RMSF mapped to the PDB in B-factor column (produced by gromacs as the result of MD simulation).
The problem that when I map RMSF onto structure for several different systems (e.g. the different conformations of the same protein) the pdb produced by gmx rmsf in different orientation so Chimera use it for image and the positions of the structure are not the same (thus not being aligned, see the image for example!)
Would it be possible by means of some Chimera-X comands to orient pdbs in order to align them in the same way? E.g. I open (in bash loop) many pdbs (the same protein but in different states, which are not aligned before, but I need that on the final images the positions for each PDB would be the same (thus to avoid pre-align the PDBs before opening them in ChimeraX!
Thanks in advance!
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
-
Elaine Meng -
James Starlight