- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] rotational/translational shift from reference structure
by Elaine Meng 15 Sep '08

15 Sep '08

On Sep 15, 2008, at 3:13 AM, julien(GWDG) wrote: > > I wanted to know if there is a way in chimera to get the same > information as the shortcut ai but for small molecule. > When I use "ai" with small molecule I get the message : "not enough > back bone atoms", which is normal because there is no back bone atom > and because the molecule is small. > But I have a rigid docking of one ligand and I would like to see > what is the rotation components (rotation matrix) between the > different pose. Of course one could just do it by a small C++ script > but if chimera has it already implemented it would be easier for us. > > Thank you for your support and your nice soft. > > many greetings > > Julien > Hi Julien, Thanks for the compliments! There are commands to do a similar thing, although not in one step. The "match" command will fit the specified atoms and give an RMSD. Unlike the ai shortcut, it moves one structure onto the other. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> Then you can use the "matrixget" command to report the transformations of the structures. However, note this reports the total transformation: all movements that have been applied, not just what happened in the fitting step. To get only the fitting transformation, you would first need to "reset" the reference structure so it is untransformed, then "match" the other structure onto it, then use "matrixget." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html> For example, using two different structures with FAD: open 1f3p open 2npx focus preset apply int 1 reset match #1:fad #0:fad matrixget - Don't move anything around by hand between "reset" and "matrixget"! The last command sends the matrix info to the Reply Log. In this case the atoms in FAD are ordered and named consistently, so I could simply use the residue name in the match command. If you only wanted to use certain atoms, or if the atoms were not ordered and named consistently, you would have to give the atom names in the match command. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] trouble installing linux i386 executable
by Eric Pettersen 15 Sep '08

15 Sep '08

Hi Blake, I've certainly had problems that "solved themselves" like that. :-) I hope further use of Chimera is less mysterious! --Eric On Sep 15, 2008, at 12:55 PM, Blake Mertz wrote: > Eric, > > Thanks much for looking into that for me -- actually, I came back to > my machine the next morning, ran the install command exactly as > specified on the website, and it ran this time. I swear I wasn't > hallucinating when I sent that message, so thanks again for taking > the time. I'm definitely looking forward to using Chimera, as a > former student in our research group had nothing but good things to > say about it. Talk to you soon. > > Blake > > On Mon, Sep 15, 2008 at 11:46 AM, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: > Hi Blake, > _Seems_ like it should work. Running from the directory with the > Chimera installer, what is the output of the following commands: > > df . > sudo pwd > sudo ls -l > sudo ls -ld . > sudo ls -ld .. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Sep 10, 2008, at 2:33 PM, Blake Mertz wrote: > >> Hi, >> >> My name is Blake, and I'm a postdoc at the U. of Arizona. I'm >> starting >> to use Chimera after using Pymol for a long time, but have had >> trouble >> getting it installed. After downloading the .exe file and changing it >> to an executable, here is the error message I get: >> >> blake@omega:~/Desktop$ ls -l chimera-1.2540-linux.exe >> -rwxr-xr-x 1 blake blake 97898302 2008-09-10 14:12 chimera-1.2540- >> linux.exe >> blake@omega:~/Desktop$ sudo ./chimera-1.2540-linux.exe >> [sudo] password for blake: >> sudo: unable to execute ./chimera-1.2540-linux.exe: No such file or >> directory >> >> There has to be something obvious I'm missing here, correct? I'm >> running Ubuntu v. 8.04, if that helps. Thanks, and talk to you soon. >> >> Blake >> >> -- >> Research Assistant >> Department of Chemistry >> University of Arizona >> >> "Life is not easy for any of us. But what of that? We must have >> perseverance and above all confidence in ourselves. We must believe >> that we are gifted for something and that this thing must be >> attained." Marie Curie >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > Research Assistant > Department of Chemistry > University of Arizona > > "Life is not easy for any of us. But what of that? We must have > perseverance and above all confidence in ourselves. We must believe > that we are gifted for something and that this thing must be > attained." Marie Curie

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trouble installing linux i386 executable
by Blake Mertz 15 Sep '08

15 Sep '08

Hi, My name is Blake, and I'm a postdoc at the U. of Arizona. I'm starting to use Chimera after using Pymol for a long time, but have had trouble getting it installed. After downloading the .exe file and changing it to an executable, here is the error message I get: blake@omega:~/Desktop$ ls -l chimera-1.2540-linux.exe -rwxr-xr-x 1 blake blake 97898302 2008-09-10 14:12 chimera-1.2540-linux.exe blake@omega:~/Desktop$ sudo ./chimera-1.2540-linux.exe [sudo] password for blake: sudo: unable to execute ./chimera-1.2540-linux.exe: No such file or directory There has to be something obvious I'm missing here, correct? I'm running Ubuntu v. 8.04, if that helps. Thanks, and talk to you soon. Blake -- Research Assistant Department of Chemistry University of Arizona "Life is not easy for any of us. But what of that? We must have perseverance and above all confidence in ourselves. We must believe that we are gifted for something and that this thing must be attained." Marie Curie

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(Thermal ellipsoids) anisotropic temperature factor ellipsoids
by David Chenoweth 15 Sep '08

15 Sep '08

Dear Chimera team, Does Chimera have the ability to display anisotropic temperature factor ellipsoids and if not can this feature be added? Thanks in advance, Dave Chenoweth ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu **********************************************

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Crash with Intel graphics on Windows fixed
by Greg Couch 12 Sep '08

12 Sep '08

We have been seeing a large number of bug reports from Windows laptops with Intel graphics (both XP and Vista, as well as desktop systems) with the lastest chimera production release, 1.2540. The symptoms include, but are not limited to, jumbled surface triangles, incorrect lighting, "unable to share data" errors, wglMakeCurrent failures, "pure virtual function called", and the inability to exit chimera. The bug has been isolated to the Intel graphics driver and a workaround has been added to chimera. The fixed version of chimera is available today in the Daily Builds section on the chimera website, <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html>. Greg Couch UCSF Computer Graphics Lab

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grid across graphic
by Barry Lever 11 Sep '08

11 Sep '08

AS a new user of Chimera, I apologize for asking what , for many of you, is probably a trivial question.... initially when using Chimera ,creating an image (using pseudobond Reader) and then saving an image file, (save image) all worked well, but in the last couple of days, every time I save an image file in whatever mode (png, tif, jpg etc), I get my image with a heavy black grid across it.(and on two different computers). I am using Chimera 1.254. Is there a simple fix- it feels like a conflict. Thanks for your help (Windows XP, SP3) a low resolution example is appended Barry -- A B P Lever Distinguished Research Professor Emeritus York University, Chemistry CB124 4700 Keele St., Ontario, Canada, M3J 1P3 Tel: 416-736-2100 x22309 Fax: 416-736-5936 http://www.chem.yorku.ca/profs/lever

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rotational/translational shift from reference structure
by KATRYNA CISEK 11 Sep '08

11 Sep '08

Dear Chimera developer, I would like to analyze a set of dimer structures based on a reference dimer structure. Unfortunately a simple RMSD calculation does not capture the translational/rotational shift that occurs. Is it possible to extract a plane of rotation and degree of rotation between two structures in chimera? Thanks, Katryna

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rmsd in nogui mode
by Ryan 10 Sep '08

10 Sep '08

Hi again, I'd like to save the rmsd values calculated by chimera's 'rmsd' command when running in 'nogui' mode. What's the best way to go about this? Thanks! -ryan

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addh question
by P. Law 10 Sep '08

10 Sep '08

Hi, I am analyzing water-water and water-protein hydrogen bonds in a dataset of high resolution crystal structures. As part of this analysis, I will need to add hydrogens to water molecules and to the protein. I was wondering how well the "addh" tool can place hydrogens on water molecules in the first shell around the protein? If addh is not the right tool for this task, are you aware of any freely available programs that can add hydrogens to 1st shell water molecules in PDB files? Thanks for your help! Sincerely, Peter Law Graduate Student Biochemistry Department University of Washington

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importing general 3D models into Chimera
by Jeff Triffo 09 Sep '08

09 Sep '08

hi users, I figure someone on this list has run across this before. I have been using a modeling/CAM tool - Rhino - to generate a 3D model that I would like to import into Chimera, if possible. Does anyone have a "best way" to go about doing this? Rhino is a NURBS modeler that will export as .dxf or .dwg (AutoCAD), .ai (Adobe Illustrator), .fbx (MotionBuilder), .obj (Wavefront), .igs/.iges (IGES), .sat (ACIS), and .stl (Stereolithography). It also saves in its native format - .3dm - but that is a NURBS (openNURBS) format and I realize that Chimera does not render NURBS. Of the export options above, having limited familiarity with Illustrator, I am unsure what the nature of "3D" is in that format. thanks for any suggestions, -Jeff

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