[Chimera-users] Homology Modeling

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 17 14:50:58 PST 2013

Hi CE,
Different or missing chain IDs are not a problem, unless they somehow cause your specification to indicate different numbers of atoms in the two structures.  The example command I gave in the previous message had one structure with chain A and the other with no chain ID.  Different residue numbering is also not a problem, because you enter the numbers yourself in the match command.

> match   #1:482-513.A at ca   #0:212-243 at ca

However, a structure without chain IDs could cause a problem if it contains multiple chains and thus more than one residue with the same residue number.  Other common reasons for an error message like this:
(a) the specification syntax is simply wrong
(b) one structure has "alternate locations" (for example, 2fma residue 170.A) and thus multiple instances of the same atom/residue/chain name.  If I run into this, I usually delete the alternate locations (e.g. command "delete @.b" would delete all alternate locations B) and try again.

You can see how many atoms each specification generates with commands like:
select #1:482-513.A at ca
select #0:212-243 at ca

It is impossible to guess without having the actual structure and seeing the exact command that you used, sorry.

However, if you think it is related to chain ID, that can be changed using "Change Chain IDs" (in menu under Tools... Structure Editing) or command "changechain"

I hope this helps,
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 17, 2013, at 2:26 PM, Chinaza Egbuta wrote:

> Hi Elaine,
> Thank you for your prompt response.  Yes, the question is actually about 3D superposition.  I used the match command following the atom specification syntax described in <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>.  However,  I have been getting the following error message "Unequal number of atoms chosen for evaluation".   
> The two models I am comparing both have the same model number but the chains are different (one is "chain A" and the other is "principal chain").  This could be because the actual homology modeling was performed on the MOE platform (chemical computing) and the chain numbers are assigned differently.  Please could you let me know if I the error message is as a result of this nomenclature?  If yes, please could you provide me with information on how to change the chain number?
> Thank you!
> CE

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