[Chimera-users] Newbie Questions
meng at cgl.ucsf.edu
Mon Apr 10 09:35:49 PDT 2006
(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:
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,
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
> 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
> 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
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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
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