Aligning residue/ligand to foreground
Hello everyone,
In old Chimera, I was able to center the ligand to the foreground of view using "align ligand ~ligand" no matter the orientation, if the ligand is in view or not. Is there a comparable way in ChimeraX? The same command gives "expected a keyword" and using "view ligand" or "view sel-residues zalign sel" does not bring it to foreground if it's behind something else.
Thanks, Alex
Hi Alex, Yes, the commands are different in both form and functionality between the two programs. Currently the most similar thing in ChimeraX is to use "view" with "zalign" ... but the intent is to give 2 atoms to align along z, not the whole ligand. For example:
open 2gbp view zalign @c1 @c4
... or maybe ...
view ligand zalign @c1 @c4
...however, that requires knowing the atom names in the ligand and judiciously choosing the right ones.
I thought it might be useful if we could generalize that option to allow two multi-atom specifications (such as ligand and ~ligand) and then use the center of each for the axis alignment. We'll see what the other developers say (I'm not a programmer so I wouldn't be the one doing it.)
Even so, however, I don't think it would guarantee that there aren't other atoms in front of the ligand, for example if the pocket is completely buried. I also don't think that the Chimera approach you mentioned guarantees that either, although maybe in practice you haven't seen it happen.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 5, 2023, at 7:04 AM, Alexander Hung Lee via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello everyone,
In old Chimera, I was able to center the ligand to the foreground of view using "align ligand ~ligand" no matter the orientation, if the ligand is in view or not. Is there a comparable way in ChimeraX? The same command gives "expected a keyword" and using "view ligand" or "view sel-residues zalign sel" does not bring it to foreground if it's behind something else.
Thanks, Alex
Hi Alex, To make zalign take two multi-atom specifications would require a change to the syntax of the command, because consecutive specifications are basically one big specification (spaces are legal inside a spec), so the command wouldn't know how to divide the specification into two parts without some kind of keyword between the two. That doesn't mean it wouldn't be worth doing, but just that there's some additional things to consider. You can work around the problem right now by creating fake atoms at the center of the ligand and non-ligand and aligning on those, e.g.:
marker #100 pos ligand marker #101 pos ~ligand view ligand zalign #100 #101 close #100 #101
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Sep 5, 2023, at 10:17 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Alex, Yes, the commands are different in both form and functionality between the two programs. Currently the most similar thing in ChimeraX is to use "view" with "zalign" ... but the intent is to give 2 atoms to align along z, not the whole ligand. For example:
open 2gbp view zalign @c1 @c4
... or maybe ...
view ligand zalign @c1 @c4
...however, that requires knowing the atom names in the ligand and judiciously choosing the right ones.
I thought it might be useful if we could generalize that option to allow two multi-atom specifications (such as ligand and ~ligand) and then use the center of each for the axis alignment. We'll see what the other developers say (I'm not a programmer so I wouldn't be the one doing it.)
Even so, however, I don't think it would guarantee that there aren't other atoms in front of the ligand, for example if the pocket is completely buried. I also don't think that the Chimera approach you mentioned guarantees that either, although maybe in practice you haven't seen it happen.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 5, 2023, at 7:04 AM, Alexander Hung Lee via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello everyone,
In old Chimera, I was able to center the ligand to the foreground of view using "align ligand ~ligand" no matter the orientation, if the ligand is in view or not. Is there a comparable way in ChimeraX? The same command gives "expected a keyword" and using "view ligand" or "view sel-residues zalign sel" does not bring it to foreground if it's behind something else.
Thanks, Alex
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Hi Alex,
I added an option to the ChimeraX view zalign command so you can use two sets of atoms, for example,
view zalign ligand inFrontOf ~ligand
Here is another example showing chain B in front of a multi-chain structure #1
view zalign /B infrontof #1
It will be in tomorrow's ChimeraX builds dated September 6, 2023.
Tom
On Sep 5, 2023, at 7:04 AM, Alexander Hung Lee via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello everyone,
In old Chimera, I was able to center the ligand to the foreground of view using "align ligand ~ligand" no matter the orientation, if the ligand is in view or not. Is there a comparable way in ChimeraX? The same command gives "expected a keyword" and using "view ligand" or "view sel-residues zalign sel" does not bring it to foreground if it's behind something else.
Thanks, Alex _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu mailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (4)
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Alexander Hung Lee
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Elaine Meng
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Eric Pettersen
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Tom Goddard