[Chimera-users] chimera question

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 9 13:32:51 PST 2005

On Nov 9, 2005, at 12:34 PM, cjamesgrant at earthlink.net wrote:

> Does chimera have the capability of automatically connecting the  
> elements of a protein to reveal its overall shape.  I am trying to  
> determine the amino acid sequence of the attached protein, but I am  
> having a hard time visualizing how the elements are connected to  
> each other.  I am new to this program, so any help would be greatly  
> appreciated.
> Thank you,
> C Grant
> <Sequence_A.pdb>

Hi there,
There are a lot of problems with that PDB file!  Chimera will  
automatically connect atoms, except that this file has TER between  
each atom, forcing it to not include any bonds.  Additional problems  
are that each atom is given a different residue number.  It looks  
like these are normal amino acid residues, but instead of their usual  
names, the residue name throughout the file is PPP.  I edited the  
whole file to be residue number 1 and removed all the TER lines,  
which is technically still very incorrect, but now you can visually  
tell the sequence of the peptide.  The edited file is attached. To be  
technically correct you would have to name and number the residues  
correctly (looks like there are 14 of them).
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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: temp.pdb
Type: application/octet-stream
Size: 9243 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20051109/cd973e08/attachment.obj>
-------------- next part --------------

More information about the Chimera-users mailing list