[Chimera-users] Just starting out

burt.goldberg at gmail.com burt.goldberg at gmail.com
Sat Jun 1 09:34:45 PDT 2013

Dear all, after 40+ years doing wet work I had to leave the bench, medical reasons, and so although my students continue doing work at the bench I have decide to go the route of proteimics and informatic for myself. The informatics is fine. How do I get started on the proteimics? Does the tutorial help? Any thing some one can suggest I read first? Thank, Burt
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-----Original Message-----
From: "Marek Maly" <marek.maly at ujep.cz>
Sender: chimera-users-bounces at cgl.ucsf.edu
Date: Sat, 01 Jun 2013 17:18:53 
To: chimera-users at cgl.ucsf.edu<chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] How to force Chimera to properly analyze and
 visualize in each MD movie frame the ribon representation of the protein
 structure ?

Dear all,
I just found that if one loads several frames from the simulation
(Amber prmtop + inpcrd, *.rst files) chimera calculate/set the character
of ribons (random colil, beta sheet, alpha helix) just using the first
loaded frame and even if structure of the protein is changing in the
next frames (e.g. forming beta sheet structure from the originally random  
the visual ribon representation is not changed.

I found this, when I loaded just the isolated frame from the simulation and
saw nice forming of the local beta sheet which was nicely highlighted by
proper ribon representation (wide arrow) in the palce where was originally  
(in the initial frame) just random coil. But when I loaded both (initial  
frame and that after some MD simulation),
chimera keep to use random coil representation for both frames.

I did also reverse experiment i.e. first loaded later frame from MD  
simulation and
then the initial frame and this time chimera fixed for both frames beta  
sheet representation
in that protein area. Please is there any possibility to prevent such  
unwanted behavior and
to force Chimera that analyses properly protein configuration at each  
loaded frame and eventually
changes properly the ribon representation ?

     Thank you in advance for any useful advices !

         Best wishes,


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