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 Sent via BlackBerry from T-Mobile -----Original Message----- From: "Marek Maly" <marek.maly@ujep.cz> Sender: chimera-users-bounces@cgl.ucsf.edu Date: Sat, 01 Jun 2013 17:18:53 To: chimera-users@cgl.ucsf.edu<chimera-users@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 coil), 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, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Marek, Yes, we recommend that for ribbon display of protein trajectories, you re-evaluate the secondary structure at each frame. This can be done fairly easily in MD Movie with a per-frame Chimera command script. In the MD Movie menu, choose Per-Frame... Define Script, use Chimera commands (as opposed to Python), and enter the script, which could just be: ksdssp OK/Apply will start running that script at each frame. MD Movie documentation: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> The need to re-evaluate secondary structure is mentioned in the "viewing frames" section, and there is also a section about per-frame scripts. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#viewing> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame> 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 Jun 1, 2013, at 8:18 AM, Marek Maly wrote:

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 coil), 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,

Marek