Dear Chimera users, I obtained some dihedral angles around some rotatable bonds of my molecule's conformations. I used GA to get new sets of those torsions, now I need to convert them back to x,y,z coordinates (new conformations) Is it possible to do that in Chimera? Please help. Thank you. Chinh
Hi Chinh, You can change torsion angles using the Adjust Torsions GUI (in menu under Tools... Structure Editing) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust> ... or the rotation command <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html> If you have lots of values, you would probably want to script it, but it probably wouldn't be that easy/convenient since the commands (or python, if you do a python script) will need to specify the 4 atoms used to define each torsion. 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 Mar 22, 2013, at 12:33 AM, Chinh Su Tran To wrote:
Dear Chimera users,
I obtained some dihedral angles around some rotatable bonds of my molecule's conformations. I used GA to get new sets of those torsions, now I need to convert them back to x,y,z coordinates (new conformations)
Is it possible to do that in Chimera? Please help.
Thank you. Chinh
On Mar 22, 2013, at 10:51 AM, Elaine Meng wrote:
Hi Chinh, You can change torsion angles using the Adjust Torsions GUI (in menu under Tools... Structure Editing) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust>
... or the rotation command <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html>
If you have lots of values, you would probably want to script it, but it probably wouldn't be that easy/convenient since the commands (or python, if you do a python script) will need to specify the 4 atoms used to define each torsion.
What Elaine says is absolutely correct. What I would add though is that if the torsions you are changing are the phi, psi, or chi angles of standard amino acids, then adjusting them is somewhat easier since they are attributes of the residue and setting the attribute will change the torsion. For example, to change the phi angle of residue 14.A to 90 degrees: setattr r phi 90 :14.a --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Thanks Elaine. I'll have to script it because I have 10 torsions (for each of the 100 ligands) to change. Those 10 are generated from a GA program. I need to use the "rotation" command as you suggested. Do I have to WritePDB for every change of torsions to get the new conformation (new x,y,z coordinates) 'cause I need the new conformations to do DOCK for the next step? Dear Eric, My molecule is a drug (a small molecule). It is not a protein. I was wondering if changing that amount of torsions is too much. We're trying to do some optimizations using GA instead of running MD. Thank you and hope get more your advice. Regards, Chinh On Saturday, March 23, 2013, Eric Pettersen wrote:
On Mar 22, 2013, at 10:51 AM, Elaine Meng wrote:
Hi Chinh, You can change torsion angles using the Adjust Torsions GUI (in menu under Tools... Structure Editing) < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
... or the rotation command <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html>
If you have lots of values, you would probably want to script it, but it probably wouldn't be that easy/convenient since the commands (or python, if you do a python script) will need to specify the 4 atoms used to define each torsion.
What Elaine says is absolutely correct. What I would add though is that if the torsions you are changing are the phi, psi, or chi angles of standard amino acids, then adjusting them is somewhat easier since they are attributes of the residue and setting the attribute will change the torsion. For example, to change the phi angle of residue 14.A to 90 degrees:
setattr r phi 90 :14.a
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Hi Chinh, If you want a PDB file for each conformation, yes, you would have to use Write PDB (or command "write"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> Theoretically no number of rotations is too many. We just meant it would probably be too many to type in each command yourself. Instead you would prefer to script it in either Chimera commands or python, as mentioned in my previous message. Elaine On Mar 22, 2013, at 7:14 PM, Chinh Su Tran To wrote:
Thanks Elaine. I'll have to script it because I have 10 torsions (for each of the 100 ligands) to change. Those 10 are generated from a GA program. I need to use the "rotation" command as you suggested. Do I have to WritePDB for every change of torsions to get the new conformation (new x,y,z coordinates) 'cause I need the new conformations to do DOCK for the next step?
Dear Eric, My molecule is a drug (a small molecule). It is not a protein. I was wondering if changing that amount of torsions is too much. We're trying to do some optimizations using GA instead of running MD.
Thank you and hope get more your advice.
Regards, Chinh
On Saturday, March 23, 2013, Eric Pettersen wrote: On Mar 22, 2013, at 10:51 AM, Elaine Meng wrote:
Hi Chinh, You can change torsion angles using the Adjust Torsions GUI (in menu under Tools... Structure Editing) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust>
... or the rotation command <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html>
If you have lots of values, you would probably want to script it, but it probably wouldn't be that easy/convenient since the commands (or python, if you do a python script) will need to specify the 4 atoms used to define each torsion.
What Elaine says is absolutely correct. What I would add though is that if the torsions you are changing are the phi, psi, or chi angles of standard amino acids, then adjusting them is somewhat easier since they are attributes of the residue and setting the attribute will change the torsion. For example, to change the phi angle of residue 14.A to 90 degrees:
setattr r phi 90 :14.a
--Eric
thank you Elaine. On Sunday, March 24, 2013, Elaine Meng wrote:
Hi Chinh, If you want a PDB file for each conformation, yes, you would have to use Write PDB (or command "write"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>
Theoretically no number of rotations is too many. We just meant it would probably be too many to type in each command yourself. Instead you would prefer to script it in either Chimera commands or python, as mentioned in my previous message. Elaine
On Mar 22, 2013, at 7:14 PM, Chinh Su Tran To wrote:
Thanks Elaine. I'll have to script it because I have 10 torsions (for each of the 100 ligands) to change. Those 10 are generated from a GA program. I need to use the "rotation" command as you suggested. Do I have to WritePDB for every change of torsions to get the new conformation (new x,y,z coordinates) 'cause I need the new conformations to do DOCK for the next step?
Dear Eric, My molecule is a drug (a small molecule). It is not a protein. I was wondering if changing that amount of torsions is too much. We're trying to do some optimizations using GA instead of running MD.
Thank you and hope get more your advice.
Regards, Chinh
On Saturday, March 23, 2013, Eric Pettersen wrote: On Mar 22, 2013, at 10:51 AM, Elaine Meng wrote:
Hi Chinh, You can change torsion angles using the Adjust Torsions GUI (in menu under Tools... Structure Editing) < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...
... or the rotation command <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html>
If you have lots of values, you would probably want to script it, but
it probably wouldn't be that easy/convenient since the commands (or python, if you do a python script) will need to specify the 4 atoms used to define each torsion.
What Elaine says is absolutely correct. What I would add though is that if the torsions you are changing are the phi, psi, or chi angles of standard amino acids, then adjusting them is somewhat easier since they are attributes of the residue and setting the attribute will change the torsion. For example, to change the phi angle of residue 14.A to 90 degrees:
setattr r phi 90 :14.a
--Eric
participants (3)
-
Chinh Su Tran To -
Elaine Meng -
Eric Pettersen