- Chimera-users - RBVI Mailing Lists

Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 08 Dec '05

08 Dec '05

I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga

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Re: [Chimera-users] Moving selected atoms
by Thomas Goddard 08 Dec '05

08 Dec '05

I improved the mouse mode for moving selected atoms so if no atoms are selected it moves everything like the normal rotation and translation mouse modes -- all active models are moved. The new code is http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar For installation instructions see my previous chimera-users message. http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-December/000609.html The new behaviour makes it easy to move some atoms, then rotate the view, then move the atoms again. After moving the atoms you can clear the selection using ctrl-click on the background of the graphics window, then rotate everything to the new view point, then press the left arrow key (undo selection) to revert to the previous selection, and continue moving the atoms. Tom

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Moving selected atoms
by Thomas Goddard 07 Dec '05

07 Dec '05

I wrote a Chimera extension that allows moving just selected atoms with the mouse. This is for modifying molecular structures. Here is the code http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar that adds mouse modes to move selected atoms. The archive contains a directory called MoveSelection. Put it in your Chimera distribution in chimera/share or on Mac in Chimera.app/Contents/Resources/share Then when you start Chimera use menu entry Favorites / Preferences, and choose category "Mouse" from the preferences dialog. This shows the mouse modes table with the available modes along the top line. The last two are for shifting and rotating selected atoms. Reassign mouse buttons (say buttons 1 and 2) to these modes and you can move selected atoms. There is no undo. I'll have to make this easier to use and put it into Chimera. Tom

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Re: [Chimera-users] chimera for linux ppc
by Geoffrey H Wathen 07 Dec '05

07 Dec '05

I've used YellowDog in the past, and I think it is a good dist. I wouldn't mind seeing a PPC Linux version of Chimera, either. Geoff. On Dec 7, 2005, at 10:50 AM, A. Zelter wrote: >> I think Conrad is saying that on the x86 architecture they can >> compile for RedHat and it will run on most distributions of x86 >> Linux. He's asking if there's a similar situation on PPC Linux, >> and which distribution of PPC Linux would provide the best >> prospects for such coverage. It seems to me that this is to >> minimize the occurrence of someone saying "I see you have the >> binaries for XYZ PPC Linux, but they don't run on my distribution >> of ABC PPC Linux. Could you please compile it for ABC PPC Linux?" > > Ahhh thanks. I knew I didn't get something. Well, I'm no expert on > that kind of thing, but Fedora Core 4 has a ppc version. I think > this is a little more modern than Red Hat Linux 7.1 - it runs > kernel 2.6.11. However, RedHat did make a PPC version of their 7.1 > distro (Red Hat Linux 7.1 for pSeries). I suppose that would be > equivalent. Another good bet might be yellowdog linux. The latest > version is 4.0.1, and it uses kernel 2.6.10. Yellowdog is based on > redhat but built specifically for Macs. This is probably what I > would try using. > Alex > >

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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 04 Dec '05

04 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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