[Chimera-users] superimposing proteins on co-factor

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 7 10:01:04 PST 2006

Hi Boaz,
There are two main issues that might complicate your analysis:

(1) extra chains or copies of the protein and cofactor within the  
same PDB file
(2) differences in how the cofactor residue is named and its atoms  
are named

For issue (1), you could decide which protein chain(s) you want to  
work with and delete the others to simplify the situation.  Some PDB  
files are cooperative and give the cofactor molecules chain IDs that  
match the corresponding protein (residue HEM in chain A is bound to  
protein chain A, B in B, etc.), in which case it is pretty easy to  
select whole chains and delete them.  Other PDB files are less  
conveniently arranged, with cofactor molecules given no chain ID or  
different chain IDs than the proteins that bind them, so even after  
you delete extra protein chains, there are a bunch of extra cofactor  
molecules floating around. At this point, I usually select atoms in  
each of those from the graphics window with Ctrl-Shift-click, hit up  
arrow to promote the selection to the entire residues, and then  
delete the selection. The reason you would want to delete extra  
copies is that if you use the name of the cofactor for matching, that  
will specify all existing copies, resulting in unequal numbers of  
atoms to be matched in the two structures.

Issue (2) can be even more taxing. IF the cofactor residue has the  
same name and its atoms have the same names and are in the same  
orders in all pairs of structures to be compared, you could then use  
EnsembleMatch.  You'd specify the cofactor residue as the atoms to  
match, e.g.
(residues named FAD).  Another approach in this situation would be to  
use the match command, e.g.
    command> match #1:fad #0:fad
(match FAD in model 1 to FAD in model 0). This would reorient the  
entire contents of model 1 to best fit the specified atoms. The  
drawback is that sometimes the residues and/or their atoms are named  
differently or the atoms are in different orders.  Rather than  
peering at the files, you might want to try EnsembleMatch or the  
match command and see whether the resulting fit and RMSD value are as  
expected.  If not, then the atom naming issue is probably to blame.

When the atoms are named differently, you can still use the match  
command, but you would either have to name all the atoms in  
corresponding orders, or pick them in the same orders (first in one  
model and then the other) from the graphics window with Ctrl-Shift- 
click; both of these approaches are described in the man page for  

This page also describes the iteration option, which could be helpful  
if the cofactor is in different conformations in the different  

I hope this helps,

On Mar 7, 2006, at 2:58 AM, Boaz Shaanan wrote:

> Hi Chimera prople,
>  If I want to superimpose proteins on their co-factors (or part of
> them), is ensembleMatch the way to go or are there other ways to do  
> this
> ? I'd appreciate your advice.
>    Regards,
>                Boaz
> -- 
> *************************************************************
> Boaz Shaanan, Ph.D.
> Associate Prof.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> Phone: 972-8-647-2220   e-mail:bshaanan at bgu.ac.il
> Fax:   972-8-647-2992 or 972-8-646-1710
> *************************************************************
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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