December 2012 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Disulfide bonds
by Elaine Meng 06 Dec '12

06 Dec '12

On Dec 5, 2012, at 1:20 AM, Moritz Bitzhenner wrote: > Hi Elaine, > You are a lifesaver. Thank you very much, it all worked perfectly. Now I have a nice colourful ribbon structure protein with disulfide bonds. The middle of the bond is coloured in yellow, the rest of the sidechain is coloured in light grey. Can I change the colour of the grey sidechain without changing the colour of the AA in the ribbon structure? But it´s not that important. > > I also created a movie of the rotating protein. (Command line: roll). Can I decrease the speed of the rotation? > > With best regards from Germany and many thanks for your help. > Moritz Hi Moritz, Greetings to you in Germany! You can specify that coloring should apply only to atoms/bonds (not ribbons, surfaces, etc.) using the Color Actions dialog. Menu: Actions... Color... all options, and then in that dialog see the "Coloring applies to" section. The same thing can be done in the command line, for example: color goldenrod,a :cys ...means to make atoms-only of Cys residues the color named goldenrod. Each command has a manual page, which you can see with the "help" command (e.g. commands "help roll" "help color") so I recommend looking at those for more details such as how to control the speed of roll. See also the general information on making movies: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> 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 P.S. best to send to chimera-users(a)cgl.ucsf.edu so that others can benefit

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Disulfide bonds
by Moritz Bitzhenner 04 Dec '12

04 Dec '12

Dear Chimera Users I am fairly new to the program and I have a particular problem with the display of disulfide bonds. I have an amino acid sequence, I created a pdb-file with Expasys Swiss Model Workspace. I opened the pdb file with Chimera and coloured the ribbon structue (it looks amazing), I even did a movie of my rotating protein. But I cannot display the three disulfide bonds. Is my pdb file lacking the CONECT information? How can I include them? With Swiss PDB Viewer (Deepviewer) I can show the bonds, but somehow I cannot transfer the information to the pdb file and Chimera. I also tried manually bonding the closest cysteins by selecting Cystein residues and "bond" in the command line. How do I select the two single atoms that I want to connect? I read through former similar questions in the list server but nothing helped so far. If you can find any time helping my case, it would be greatly appreciated. With best regards from Germany, Moritz Here is the AA sequence: GEIDNNQCQICELLVKDIIEGLTANQSVEVIEHGLNLICDHIPLHVRVCKQFVDSNFQKIVQFIENHDDPQEICEKCGVC

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stick representation after selection / DNA helical axis
by Damien Larivière 03 Dec '12

03 Dec '12

Dear all, I used the command sel @N1 @N3 to select the N1 and N3 atoms of a nucleic acid structure (like 1bna). when I do "show only" in Actions / Atoms&Bonds, a specific representation is displayed as in the image below: sticks connect N1 atoms of one strand and N3 atoms of the other strand. May you tell me the meaning of this representation and how can I modify it (I mean, how to change the type of atoms to be connected)? In fact, I would like to visually apprehend the helical axis. Is there a way to calculate and display this axis in Chimera? Many thanks for your help Damien

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