[Chimera-users] chain selection in a multi-conformatin pdb file.

Elaine Meng meng at cgl.ucsf.edu
Wed May 9 09:22:18 PDT 2007

Hi Hong,
1. Yes, you can definitely get rid of the parts you are not  
interested in.

(A) Your example is an NMR structure, where the PDB file has multiple  
models.  If you open the Model Panel (under Favorites) you can see  
the numbering of those models: for 1x95, there are models #0.1-0.15.   
In the Model Panel, click the line on the left for the structure you  
want to keep and then click "show only" on the right; this hides all  
the others.  Or, if you really want to delete the others instead of  
just hiding them, choose their lines (using clicking, dragging, and/ 
or Ctrl-click to add/subtract) and then click "close" on the right  
side of the Model Panel (NOT the Close button at the bottom of that  
panel!).  Or, you can do it in one step with a simple command; the  
following example keeps #0.1 and deletes the others:
    delete #0.2-end

(B) Sometimes there are more chains than you want even in a single  
model.  In that case, you can select the parts you want to delete and  
then use "Actions... Atoms/Bonds... delete", or select what you want  
to keep and then invert the selections with "Select... Invert (all  
models)" before deleting.  Similar to the example above, you can also  
use the "delete" command.

2. Chimera does not build DNA/RNA, although we would like to add that  
in the future.

The following web server will build nucleic acid helices (I haven't  
tried it yet):
It probably would just build the whole thing rather than adding to an  
existing structure, however.

I hope this helps,
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

On May 8, 2007, at 10:01 PM, Hong Liang wrote:
> 1. If a pdb file contains more then one struture, how can I select  
> and keep just one and get rid of  the rest.  Such as  1X95.  It is  
> a big mess after Chimera load the the DNA pdb structure.  How can I  
> leave just  one double helix?
> 2. Can Chimera do the extension of DNA.  Such as 1X95 has the  
> hexamer with the sequence of ATGCAT, can Chimera double it to a  
> dodecamer with a sequence ATGCATATGCAT?  It Chimera can not do  
> that, do you know which software has such a function.  I tried  
> PyMol but did not get what I wanted.

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