[Chimera-users] save/reset/new PDB

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 2 14:10:28 PDT 2009

Hi Matt,
If the new structure is sufficiently well matched to the old one when  
they are in the default (untransformed) positions, then after you  
reset to the various positions, you can bring the new one in by  
applying the same transform as is used for the older similar structure.

For example, if your older similar structure is model 3 and the newer  
one is model 10, and you have just reset to a position that leaves the  
new model stranded, try the command

matrixcopy 3 10

to bring 10 into the proper position.

How "reset" dealt with new models not in the original saved position  
was improved (after release 1.3) so that the new models will maintain  
their transformation relative to the lowest-numbered model that was  
included in the position.  I guess your older similar model is not the  
lowest-numbered.  Or, if it is, you could try using a recent daily  
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 2, 2009, at 1:52 PM, Matthew Dougherty wrote:

> I am trying to incorporate a new pdb structure into an existing
> session file that has a number of savepos view_names.
> The new pdb file that is pretty much the same as the old pdb file,
> just a few side chains moved.
> So in reset default, they are pretty much sync'd up.
> when I try some of the other view_names, the new pdb structure does
> not match.
> Its as though the same transformations used in the old PDB structure
> are not being applied to the new PDB structure.
> How can I sync the new PDB structure to the various view_names?
> thanks, Matt

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