Hi Nir, Thanks, we'll take a look!

As for Chimera images, you may want to scan through possibilities at our Image Gallery and our Feature Highlights page: http://www.cgl.ucsf.edu/chimera/ImageGallery/ http://www.cgl.ucsf.edu/chimera/features.html

If you like one but need higher resolution than what is provided, let me know - in many cases one of us will have a saved session so it wouldn't be that hard to remake the figure. Our "citing Chimera" advice is primarily aimed at journal paper authors, but here's a link for completeness 8-) http://www.cgl.ucsf.edu/chimera/docs/credits.html

Regards, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

On Nov 27, 2008, at 7:22 AM, Nir London wrote:

Hi all, We've started a new blog on all that is related to Macromolecular Modeling http://rosettadesigngroup.com/blog/

We opened this blog in order to provide the modeling community with a helpful resource. Keep updated with what's new in the modeling world, read executive summaries of the latest literature and stay in touch with pears.

On its background there is an image of a protein-protein complex I've created using chimera, can any of you suggest a nicer figure for the background ? The best image anyone will send me will be used as background (with due credits :) please check it out and tell me what you think...

Cheers, Nir London. Rosetta Design Group http://rosettadesigngroup.com

Hi Isai,

Chimera did not save the Icosahedron Surface and parameters in sessions until today. Some others have requested this (it is item #40 on the requested features web page, http://www.cgl.ucsf.edu/chimera/plans.html) so I have added it. Tonight's Chimera daily builds will have that.

http://www.cgl.ucsf.edu/chimera/alpha-downloads.html

It won't make it into the soon-to-be released Chimera 1.3. If you save an icosahedron surface in a session in Chimera 1.4 you won't be able to open that session in older Chimera versions.

Tom

Eaazhisai Kandiah wrote:

Hello,

I created an Icosahedron surface for my EM map and color it using surface color. How do I save the Icos surface and its specifications like surface color, sphere factor, radius, etc? They didnt get saved when I saved the session.

Thanks in advance.

Isai _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Daniel, Please see the Rotamers tool. It can show all the rotamers (at least, all the ones in the rotamer library you specified) at a position: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h...

The "Structure Analysis and Comparison" tutorial includes using the Rotamer tool: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html>

Just a reminder, you can search the manual for terms such as "rotamer" with "Help... Search Documentation" in the Chimera menu.

Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

On Dec 6, 2008, at 4:57 AM, daniel.hilger@lrz.uni-muenchen.de wrote:

Hi all, I want to visualize all possible rotamers of an amino acid side chain inside a protein structure in one picture. Is this possible or does the program only supports the visualization of one rotamer per side chain ? Many thanks !!! Daniel