[Chimera-users] Merge PDB Question

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 28 10:38:00 PDT 2006

Hi Jared,
Currently you cannot bond different models, and the only way to  
"merge" is to put the atoms in the same file before opening it.   
There are actually other reasons your command wouldn't work:

- seems to me that there is no model 1, only 1.1, 1.2, 1.3 and 1.4,  
so the first part would specify zero atoms
- the ampersand & stands for intersection (logical AND, not english  
and) and should be omitted, e.g.
   command: bond #1.1:504.b at c #1.1:505.b at n

What I've done in the past to handle similar cases (splicing stuff  
from an NMR structure onto a Xray structure) is to first put the tail  
(with a few extra residues to overlap with residues that are already  
present) into a file by itself.  Then I open that new file, so it  
will be a new, separate model.  I then match that model onto the  
original model using atoms in the overlapping part.  Then, write out  
another PDB file of the tail relative to the untransformed original  
model.  Using text-editing, remove the part that overlaps since it  
was just there for positioning purposes.  FINALLY (text-editing  
again) make another PDB file that combines the new tail with the  
original protein.  They may need to have the same chain ID as well.   
Sorry this is such a long process.  If you think you can hand- 
position the tail sufficiently well you could skip the parts about  
having the extra atoms, using them for matching, and deleting them.

If you remove any intervening TER, the bond will already be there  
when  you open the new file.

I hope this helps,

On Sep 28, 2006, at 10:13 AM, Jared Godar wrote:

> I have an incomplete pdb crystal structure of a homohexameric  
> protein containing six ~25AA tails.  In the incomplete model, two  
> of these six tails are complete (A and F)  and the other four are  
> truncated at various positions (B,C,D, and E).  I have used the  
> either the A or F complete tails as templates and generated  
> appropriate length segments to compleate each of the truncated B-E  
> tails by selecting the appropriate residues and saving the selected  
> atoms as a new PDB.  Currently, I have all six tails completed and  
> saved as a single PDB.  I would like to use the Bond command to  
> covalently link the extended chains, but my single PDB is  
> segregated into models 1.1, 1.2, 1.3, 1.4, and 1.5.  When I use the  
> Bond command as follows "bond #1:504.b at c & #1.3:505.a at n", I get an  
> error that only one atom is selected.  Does Chimera consider #1 and  
> #1.1 to be different models?  If so, how can I merge these 5 models  
> into one to allow me to create the bond?
> Thanks,
> Jared
> -- 
> Jared A. Godar
> Graduate Student: Stewart Lab
> Vanderbilt University Medical Center
> Department of Molecular Physiology & Biophysics
> 708 Light Hall
> 2215 Garland Ave.
> Nashville, TN 37232-0615
> Work: 615.322.7898
> Fax:   615.322.7236
> jared.godar at vanderbilt.edu
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20060928/2a3f2b57/attachment.html>

More information about the Chimera-users mailing list