September 2006 - Chimera-users - RBVI Mailing Lists

display multiple bonds
by Dave Roe 05 Sep '06

05 Sep '06

Is there a way to display multiple bonds so bond types (single, double, triple) can be distinguished? -- Dave Roe roex0050(a)umn.edu

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color a residue
by Xuehong Liu 05 Sep '06

05 Sep '06

Hi, I chose the target as "selected residues", then selected the residue I want to put certain color on, but only a bond color was changed when I did that. However, if I did not select a residue, then the color option will change the color for the whole helix selected. thank Xuehong Xuehong Liu, Ph.D Research Assistant Professor Department of Physiology/Pharmacology Oregon Health & Science University 3181 SW Sam Jackson Park Rd. L334 Portland, OR 97239 phone: (503) 494-3230 fax: (503) 494-4352

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PDB Coordinates
by Albion Baucom 01 Sep '06

01 Sep '06

I have docked several models into density manually using Chimera. I saved the session, reopened it, and when I write out the docked PDB files, and read them back in, they are not oriented the same way as the model I wrote them from. Is there something I have to do to "fix" their new orientation so when they are written out they retain this orientation? I am using beta version 1 build 2199 01/24/2006 on a linux platform. Thanks Albion

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how to save a copy of the reply log via command line
by Cathy Lawson 01 Sep '06

01 Sep '06

Hi, I'd like to issue a command-line command within a python script read into chimera to save a copy of the reply log. I tried googling the chimera site but didn't find the answer--what would be the command to do this? thanks, Cathy

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