[Chimera-users] Newbie Questions

[Elaine Meng]

Hi Shafrir,
(1) The write command that you gave should have worked to write the  
file without bringing up a save dialog.  I just tried this in version  
1.2199 on the mac and it worked correctly.  You could send more  
information on this problem (version used, platform, any error  
messages) to chimera-bugs at cgl.ucsf.edu

Although there is no command to split a model in the released  
Chimera, you can download an "experimental feature" to do it.   
Instead of putting a *selected* chain into a different model,  
however, it puts each chain in the original file into a separate  
model. The split command is about the fourth thing on the  
experimental features page:
http://www.cgl.ucsf.edu/chimera/experimental/experimental.html

Actually, I'm not sure what your script is doing, so another possible  
approach would be to delete the rest of the chains, resulting in a  
model with only your chain of interest.  For example:
command> sel :.a
command> sel invert sel
command> delete sel

(2) To assign secondary structure arbitrarily (without using the  
ksdssp program), select the residues of interest, and click the  
button on the lower right corner of Chimera to open the Selection  
Inspector.  In the Selection Inspector, change to Inspect Residue,  
then set "in helix" to false and "in strand" to true.  If you wanted  
to save (write) the file for later, the changed assignments will be  
reflected in the HELIX and SHEET records.

I hope this helps,
Elaine

p.s. no need to send the mail twice (delay is only because our  
moderator has to approve the message sometimes)


On Apr 7, 2006, at 1:17 PM, Shafrir, Yinon ((NIH/NCI)) [F] wrote:

> Hi there!
>
>
>
> I have two questions regarding using Chimera.
>
>
>
> How do you break a molecule to different models using the command  
> line?
>
> I have a protein composed of 4 chains. It loads as one piece and  
> designated model 0
>
>
>
> I then select a single chain and I want to designate it as a new  
> model. How do I do that using the command line (so I can write a  
> script)?
>
>
>
> Also, when I select the chain and use the write command in this  
> manner “write selected su1.pdb”  the save dialog box pops up (even  
> though I designated a filename)
>
> When I try “write selected 0 su1.pdb” nothing happens.
>
>
>
>
>
> My other question is:
>
> How can you force chimera to assign secondary type display to  
> residues without editing the PDB file first?
>
> Say I want to show 30 residues that are not detected by ksdssp as  
> beta sheets. Still, I want to represent them as beta sheets. Do I  
> need to edit the pdb file?
>
>
>
>
>
> Best regards
>
> Yinon Shafrir
>
>
>
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> Chimera-users at cgl.ucsf.edu
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-----
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