December 2005 - Chimera-users - RBVI Mailing Lists

Missing tools
by Luke Kontogiannis 07 Dec '05

07 Dec '05

I had installed the current production release chimera-1.2184-linux.exe. Just now I downloaded and installed the latest snapshot release chimera-1.2186-linux.exe and this version has the multiscale tool under Tools -> Higher-order structure Luke

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chimera for linux ppc
by Alex Zelter 07 Dec '05

07 Dec '05

Hi, I was wondering if it would be possible for the developers to compile a binary version of chimer for use on linux ppc architecture seeing as it is not possible for a user to compile for themselves due to the proprietary solvent-accessible molecular surfacing library. I know this is not a common architecture, but some people do use it. Thanks in advance, Alex Zelter

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Missing tools
by Luke Kontogiannis 07 Dec '05

07 Dec '05

Hi all, I installed chimera on windows and everything works fine. However, I installed it on ubuntu linux 5.10 yesterday and there are some tools that are missing such as multiscale. Is the windows version of chimera simply more capable or have I done something wrong? I simply ran the chimeral.exe file as root and it seemed to install fine. I even tried replacing the share directory on the linux box at work with the one from the windows version but that gave errors upon launching. Any ideas? Thanks Luke

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Data reporting
by Reiner Villavicencio 05 Dec '05

05 Dec '05

Dear all, I have learned that 3D results/data from molecular dynamics or docking can be compressed to produce informative 2D diagrams for publication. Can anyone recommend such a program? Thank you and good day "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

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Add hydrogens to get -NH2 group
by Daniel Svozil 02 Dec '05

02 Dec '05

Hi all, if I use addH tool on the C-N, I would expect to get C-NH2, but I get C-NH3 instead. How should I proceed to get C-NH2 correctly? Thanks Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312

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Sequence alignment
by David G. Morgan 01 Dec '05

01 Dec '05

Hi, I'm learning to use the sequence alignment tools in chimera. I know that I can highlight sequences in the alignment window and select residues in the structure, but is it possible to do the opposite? In other words, I'd like to box or otherwise select some residue(s) in the structure and have that region highlighted or otherwise marked in the aligned sequence window. David Gene Morgan Advanced Microscopy & Proteomics Molecular & Cellular Biology University of California at Davis 530 752 2693 (lab) 530 752 3085 (FAX)

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