[Chimera-users] superimposing an all-atom structure to a reduced one

Damien Larivière damien.lariviere at fourmentinguilbert.org
Tue Jan 10 04:03:47 PST 2012

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


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

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