I'm wondering if there's a way to determine hbond formation during a trajectory in a similar way to the way the Plot distances tool in MD Movie/Analysis works.
Or dumb values to a file.
Many thanks in advance for any suggestions
Regards
George
Hi George, For dumping results to a file, please see this previous post:
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007044.html%...
For plotting, I don't know what you wanted on the Y axis, but the MD Movie plotting currently only includes distances, angles, and dihedrals. Of course, you could plot the distance between the H-bonding atoms.
Regards, 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 26, 2012, at 9:14 AM, George Tzotzos wrote:
I'm wondering if there's a way to determine hbond formation during a trajectory in a similar way to the way the Plot distances tool in MD Movie/Analysis works.
Or dumb values to a file.
Many thanks in advance for any suggestions
Regards
George
Hi
I'm trying to align two structures each containing 3 chains using only one specific chain (in each of the two pdb files) and then move the whole molecule as a unit (i.e. the 3 chains together). The problem I'm having is that only the selected chain is aligned and the other two are left in place. The problem may be due to the fact that the 3 chains in the pdb file are different models 1.1.,1.2,1.3 (but still with different chain character identifiers). How can I change this behavior so that all the chains or models move together as a unit according to the alignment of a single chain (model)?
Thanks
Hernando
Hi Hernando, I think you can bring the other two into place with the command matrixcopy. For example, if #1.2 was the one that moved, after matchmaker try:
matrixcopy #1.2 #1.1 matrixcopy #1.2 #1.3
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html
to move the other two.
Another possibility would be to combine #1.1-#1.3 into a single model before running matchmaker. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html
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 26, 2012, at 3:21 PM, Hernando J Sosa wrote:
Hi I'm trying to align two structures each containing 3 chains using only one specific chain (in each of the two pdb files) and then move the whole molecule as a unit (i.e. the 3 chains together). The problem I'm having is that only the selected chain is aligned and the other two are left in place. The problem may be due to the fact that the 3 chains in the pdb file are different models 1.1.,1.2,1.3 (but still with different chain character identifiers). How can I change this behavior so that all the chains or models move together as a unit according to the alignment of a single chain (model)? Thanks Hernando
Another possibility would be to combine #1.1-#1.3 into a single model before running matchmaker. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html
I used this and worked. Thanks a lot
Hernando
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, March 26, 2012 6:37 PM To: Hernando J Sosa Cc: UCSF Chimera Mailing List Subject: Re: [Chimera-users] Matchmaker
Hi Hernando, I think you can bring the other two into place with the command matrixcopy. For example, if #1.2 was the one that moved, after matchmaker try:
matrixcopy #1.2 #1.1 matrixcopy #1.2 #1.3
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html
to move the other two.
Another possibility would be to combine #1.1-#1.3 into a single model before running matchmaker. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html
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 26, 2012, at 3:21 PM, Hernando J Sosa wrote:
Hi I'm trying to align two structures each containing 3 chains using only one specific chain (in each of the two pdb files) and then move the whole molecule as a unit (i.e. the 3 chains together). The problem I'm having is that only the selected chain is aligned and the other two are left in place. The problem may be due to the fact that the 3 chains in the pdb file are different models 1.1.,1.2,1.3 (but still with different chain character identifiers). How can I change this behavior so that all the chains or models move together as a unit according to the alignment of a single chain (model)? Thanks Hernando
participants (3)
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Elaine Meng -
George Tzotzos -
Hernando J Sosa