[Chimera-users] Disulfide bonds

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 4 15:43:10 PST 2012


Hi Moritz,
There are several different ways... I'll mention a few.  You could select the two atoms from the Chimera window (Ctrl-click one, Shift-Ctrl-click the other) and then use command:

bond sel

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html>

The Command Line can be shown using the Favorites menu.  If the Cys atoms are not already displayed, try command:

disp :cys

Or instead of selecting, you could specify atoms by name, something like:

bond :25.a at sg :45.a at sg

... if the Cys were residue 25 and 45 in chain A. 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

Or, instead of commands you could use Build Structure (in menu under Tools... Structure Editing), the Adjust Bonds tab.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 4, 2012, at 7:12 AM, Moritz Bitzhenner wrote:

> Dear Chimera Users
> 
> I am fairly new to the program and I have a particular problem with the display of disulfide bonds. I have an amino acid sequence, I created a pdb-file with Expasys Swiss Model Workspace. I opened the pdb file with Chimera and coloured the ribbon structue (it looks amazing), I even did a movie of my rotating protein. But I cannot display the three disulfide bonds. 
> Is my pdb file lacking the CONECT information? How can I include them? With Swiss PDB Viewer (Deepviewer) I can show the bonds, but somehow I cannot transfer the information to the pdb file and Chimera.
> I also tried manually bonding the closest cysteins by selecting Cystein residues and "bond" in the command line. How do I select the two single atoms that I want to connect?
> I read through former similar questions in the list server but nothing helped so far.
> If you can find any time helping my case, it would be greatly appreciated.
> With best regards from Germany, Moritz
> 
> Here is the AA sequence:
> GEIDNNQCQICELLVKDIIEGLTANQSVEVIEHGLNLICDHIPLHVRVCKQFVDSNFQKIVQFIENHDDPQEICEKCGVC




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