superimposing an all-atom structure to a reduced one
Dear all, I have two instances of the same protein. One is the original pdb structure which has been locally deformed and saved as the second pdb structure. I would like to match the 2 pdb structures. However, one structure is a reduced version of the other in that it contains only the carbon-alpha trace plus one or two atoms of the side chain. I get an error message when I use MatchMatcher. What can I do to superimpose the all-atom structure onto the reduced one? Many thanks for your help! Damien ps: I can join the two pdb structures if necessary
Hi Damien, There must be some other problem. I tried MatchMaker to superimpose an all-atom structure on a CA-only structure, and it worked. Example: open 1gix del ~ :.w open 2vqe del #1 & ~ :.t preset apply int 2 mm #0 #1 focus I also tried the other way around (mm #1 #0). However, if you have a recipe for getting the problem, please use "Help... Report a Bug" in the Chimera menu and include instructions on how to reproduce it. Thanks, 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 Jan 9, 2012, at 9:41 AM, Damien Larivière wrote:
Dear all, I have two instances of the same protein. One is the original pdb structure which has been locally deformed and saved as the second pdb structure.
I would like to match the 2 pdb structures. However, one structure is a reduced version of the other in that it contains only the carbon-alpha trace plus one or two atoms of the side chain.
I get an error message when I use MatchMatcher. What can I do to superimpose the all-atom structure onto the reduced one?
Many thanks for your help!
Damien
ps: I can join the two pdb structures if necessary
Dear Elaine, Effectively the pdb format for the reduced protein is not correct. This is probably the source of the error. I try again. Thanks for your help Damien On 09/01/2012 20:48, Elaine Meng wrote:
Hi Damien, There must be some other problem. I tried MatchMaker to superimpose an all-atom structure on a CA-only structure, and it worked. Example:
open 1gix del ~ :.w open 2vqe del #1& ~ :.t preset apply int 2 mm #0 #1 focus
I also tried the other way around (mm #1 #0). However, if you have a recipe for getting the problem, please use "Help... Report a Bug" in the Chimera menu and include instructions on how to reproduce it. Thanks, 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 Jan 9, 2012, at 9:41 AM, Damien Larivière wrote:
Dear all, I have two instances of the same protein. One is the original pdb structure which has been locally deformed and saved as the second pdb structure.
I would like to match the 2 pdb structures. However, one structure is a reduced version of the other in that it contains only the carbon-alpha trace plus one or two atoms of the side chain.
I get an error message when I use MatchMatcher. What can I do to superimpose the all-atom structure onto the reduced one?
Many thanks for your help!
Damien
ps: I can join the two pdb structures if necessary
participants (2)
-
Damien Larivière -
Elaine Meng