[Chimera-users] Models or chain

hsosa at aecom.yu.edu hsosa at aecom.yu.edu
Sun Aug 31 06:54:31 PDT 2008

Hi Elaine,

The problem  I have is actually not whith chimera. itself.  I can 
display all the models etc nicely within it.  However, I want to make 
now a PDB file of a multi-protein complex in a format that can be 
deposited in the PDB database. Then I run into problems if the models 
are separated by Model ENDMDL lines or have chains with the same letter 
identifier. I was hoping to be able to generate a  multi-protein  PDB 
file from  my chimera fitting without having to manually edit a lot of 
lines in the multimodel PDB file. Any suggestions on how to best do this 
would be appreciated.



Elaine Meng wrote:
> Hi Hernando,
> Sorry, Chimera does not have an option for changing chain IDs.
> However, in Chimera I find it more convenient to work with structures 
> read as multiple models as opposed to multiple chains in a single model:
> - you can easily toggle which are shown and which are active (movable 
> with the mouse) using the Model Panel
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html
> - you can move one relative to another, whereas you cannot move one 
> chain relative to another chain in the same model
> - just like different chains, you can specify them independently in 
> commands, rainbow-color to give each its own color, etc.  In commands, 
> the different models read from a single PDB file are specified as 
> #0.1, #0.2, ... (and residues within them specified using something 
> like #0.1:23,350-355 )
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy 
> - further, each model can include several of its own chains, and it is 
> OK if another model in the same file also uses the same chain IDs, as 
> they are still distinguishable (#0.1:23.a is different than #0.2:23.a)
> Now I'm actually disappointed when a Web server gives me multiple 
> models as different chains in a single model, because it is less 
> convenient.
> I do agree there may be situations in which you want the models as 
> different chains, such as for input to another program, but currently 
> Chimera does not include that type of editing.
> Best,
> Elaine
> -----
> 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
>                      http://www.cgl.ucsf.edu/home/meng/index.html

Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone	(718) 430-3456
FAX	(718) 430-8819
email	hsosa at aecom.yu.edu

More information about the Chimera-users mailing list