[Chimera-users] Question about disulfide bonds and energy minimization

Steven Douglas Aird steven.aird at oist.jp
Fri Jul 20 01:41:01 PDT 2018

Dear Elaine,

For the first time in about three years, I need to do a little more modeling.   We sequenced an NADase and I used Galaxy to create a model using a known CD38 structure as a template (attached).  Chimera displayed everything, but the disulfide bonds, of course.  So I entered the specifications for those manually into the PDB file (attached).  Two of the disulfides displayed properly, but four appear as thin dashed lines.  At least one, at the C-terminus is clearly way too long.

I tried to do an energy minimization, but while Chimera executed the steps, nothing in the structure moved.  It used to be that one could watch the structure flex as it assumed the most energetically favorable conformation, but not this time, yet some of the disulfide bond lengths are clearly wrong.

I also tried to use the set length command, in the forms:  set length 2.05 / Set Length [2.05]  but Chimera does not like either of these commands.  If the manual included examples of the command format for each command, that would be really useful, because it is not clear where the syntax problem lies.

As always, thanks for your help!

Sincerely yours,


Steven D. Aird
Technical Editor
Faculty Affairs Office
Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son
Kunigami-gun, Okinawa-ken
Japan  904-0495

Phone:  098-982-3584
Cell:  080-4154-9504
Email:  steven.aird at oist.jp<mailto:steven.aird at oist.jp>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180720/93915cf7/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: M suri M1.py
Type: text/x-python-script
Size: 263975 bytes
Desc: M suri M1.py
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180720/93915cf7/attachment.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: model_1.pdb
Type: application/octet-stream
Size: 166228 bytes
Desc: model_1.pdb
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180720/93915cf7/attachment.obj>

More information about the Chimera-users mailing list