February 2018 - Chimera-users - RBVI Mailing Lists

Questions regarding Ribbon Structures
by Alex Yorn 05 Feb '18

05 Feb '18

UCSF Chimera, Just discovered your software and it's amazing! Thank you for making it free for academic use! I just have a quick question regarding the possibility of "filling-in" or changing the linewidth of ribbon structures. I would like to have my ribbon structures completely filled in and not hollow, so when I view them with "Side View" opition, I don't see emptiness inside. I've attached two photos. The first is a view of the ribbon structure from the outside. The second is a view of the ribbon structure view from the inside, where you can see that it's hollow. I would like to know what function or command to use to correct this so it's complete solid inside. Sincerely, Alex YornPhD Candidate Department of Molecular BiologyUniversity of Toronoto

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Combining multiple files into one PDB file
by Liyana Binti Azmi 02 Feb '18

02 Feb '18

Hello, I’m Liyana, a PhD student from University of Glasgow. I’m using Chimera to dock my low resolution cryo-EM map to my pdb file, where the EM map represents a helical oligomeric form of the pdb file. So far, I’ve made multiple copies of my pdb and fitted it against my EM map and now I’m trying to save my multiple files as one file. I’ve referred to this message on the Chimera mailing list (www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009926.html<http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009926.html>) and tried saving my files via ‘Save PDB’ and combining my files to one file. However, I couldn’t upload this on PyMOL or any other programs for subsequent analysis. Is there something wrong with my file? Attached is my file after using instruction A. I’ve also tried combining my files using the ‘combined’ feature but still get the same problem. Attached is my file after using instruction B. Could you have a look at these files, please? Thank you for your time. Best wishes, Liyana

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Chimera Color Coding Chains that are Interacting
by Andrew Cuyegkeng 01 Feb '18

01 Feb '18

Hello, I am an undergraduate researcher still learning how to use Chimera. Our lab is exploring intramolecular bonds within a complex. I am aware of the FindContact tool but was running into problems when it came to color coding these interactions. I would like to color code the different chains that are involved in these interactions and make everything that's not interacting the color black. What would the best approach to this be? Thanks, Andrew

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