Hello Do you know if there is a way to set interatomic distances to a certain value in chimera (rather than measuring them)? Basically what I want to do is rotate/translate a peptide with respect to a protein so that a set of interatomic distances between the two are satisfied Many thanks! George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568
Hi George, Sorry, there is nothing like that. You would have to use some other program for satisfaction of multiple constraints/restraints. With Chimera, it would probably be difficult depending on the number of constraints, but you could measure the various distances and then move one structure relative to the other; the distance values will update automatically. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 18, 2013, at 9:16 AM, "George Patargias" <gpat@bioacademy.gr> wrote:
Hello Do you know if there is a way to set interatomic distances to a certain value in chimera (rather than measuring them)?
Basically what I want to do is rotate/translate a peptide with respect to a protein so that a set of interatomic distances between the two are satisfied Many thanks! George
Hi George, If you know Python programming, it wouldn't be too hard to change the Chimera distance-montoring code so that distance monitors change colors depending on whether the corresponding constraint is satisfied/violated, if that would help. That code is in <chimera installation>/share/StructMeasure/DistMonitor.py, specifically the addDistance and updateDistance routines. --Eric Eric Pettersen UCSF Computer Graphics Lab On Nov 18, 2013, at 11:56 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, Sorry, there is nothing like that. You would have to use some other program for satisfaction of multiple constraints/restraints.
With Chimera, it would probably be difficult depending on the number of constraints, but you could measure the various distances and then move one structure relative to the other; the distance values will update automatically. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 18, 2013, at 9:16 AM, "George Patargias" <gpat@bioacademy.gr> wrote:
Hello Do you know if there is a way to set interatomic distances to a certain value in chimera (rather than measuring them)?
Basically what I want to do is rotate/translate a peptide with respect to a protein so that a set of interatomic distances between the two are satisfied Many thanks! George
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Hello Elaine and Eric Many thanks for your useful comments! George
Hi George, If you know Python programming, it wouldn't be too hard to change the Chimera distance-montoring code so that distance monitors change colors depending on whether the corresponding constraint is satisfied/violated, if that would help. That code is in <chimera installation>/share/StructMeasure/DistMonitor.py, specifically the addDistance and updateDistance routines.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 18, 2013, at 11:56 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, Sorry, there is nothing like that. You would have to use some other program for satisfaction of multiple constraints/restraints.
With Chimera, it would probably be difficult depending on the number of constraints, but you could measure the various distances and then move one structure relative to the other; the distance values will update automatically. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 18, 2013, at 9:16 AM, "George Patargias" <gpat@bioacademy.gr> wrote:
Hello Do you know if there is a way to set interatomic distances to a certain value in chimera (rather than measuring them)?
Basically what I want to do is rotate/translate a peptide with respect to a protein so that a set of interatomic distances between the two are satisfied Many thanks! George
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568
participants (3)
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Elaine Meng -
Eric Pettersen -
George Patargias