[Chimera-users] Creating abridged multimer

[Elaine Meng]

Hi Francesco,
If I understand correctly, you have a structure with a single copy,  
but there are some parts you don't want to duplicate in the  
multimer.  You didn't say whether you are deleting part of the  
protein, or some other subunits, or ligands, but I will try to answer  
generally.

You also did not say what method you would be using to assemble the  
multimer. I mentioned PQS fetch, Unit Cell, and Multiscale Models in  
this previous message to you:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-October/001897.html

Another possibility is a "manual" approach where you open the  
structure multiple times and move the copies around yourself, or  
superimpose them on some other structure already available as a  
multimer that you believe is similar.

With PQS fetch, the only choice is to perform the deletions from the  
already assembled multimer.  With Unit Cell and Multiscale Models, I  
don't think it matters whether you delete the extra atoms before or  
after.  With the manual approach, deleting before assembling the  
multimer would be better, as it would make the display less  
confusing, especially if you are doing clash checking while moving  
things around.

Whether the file header is appropriate for the abridged subunit and/ 
or multimer depends on the file, of course, but also on what you want  
to do with that file.  Often the header is merely for your own  
information and will have no effect on your subsequent work.  Some  
tools will make use of symmetry matrix, HELIX/STRAND, and/or SEQRES  
information.  Even if you delete the header entirely, however,  
Chimera will cope, for example by recomputing helix and strand  
assignments.

I hope this helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html

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On Jul 12, 2008, at 10:38 AM, Francesco Pietra wrote:

> I am posting again after having once again subscribed
>
> In order to create an abridged multimer made of non covalently bound
> subunits (from available pdb of subunit) which is the preferable
> route?
>
> (1) Load the monomer, delete substructures, and then assemble an
> abridged multimer? Are the headers furnished with the monomer OK for
> the
> abridged subunit?
>
> (2) Build the unabridged multimer and proceed to simplify each subunit
> the same way?
>
> Thanks
>
> francesco pietra