- Chimera-users - RBVI Mailing Lists

Creating and visualizing a plane
by James Nettles 23 Sep '08

23 Sep '08

I'm not sure if this is a function available in Chimera. I have a protein system with three residues which define a plane, or floor, relative to an active site. I would like to display a translucent plane passing through the alpha carbon of these three residues to shoot an image. Further, I would like to quantify deviation of mobile regions relative to this plane. Thanks, Jim ________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine ________________________________________________________

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Scale_bar Gradient Color
by Anindito Sen 22 Sep '08

22 Sep '08

Hi All A simple question- How do I color the scale bar (in a gradient form). Also Has anyone experienced the problem of scale bar giving an incorrect measurement when a density map in .dat format is displayed in Chimera? Best Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Show position in volume
by Magnus Gedda 22 Sep '08

22 Sep '08

Hello, I'm quite new to Chimera and have a small but annoying problem. I can place a marker in the volume and move it around, but I cannot find a way to see the xyz coordinate of the marker. How do I do this? Is there any other way to find out the xyz coordinates of a position in the volume? Best regards, Magnus

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VRML scene
by Eduardo Sanz García 19 Sep '08

19 Sep '08

Is it possible to export a VRML scene of only what it is been displayed in the window instead of the whole model? I wasn't able to open in chimera X3D files exported with chimera itself. Does chimera only writes but not read X3D files? Thank you.

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Colouring surfaces from EM density maps
by David Bhella 19 Sep '08

19 Sep '08

I am looking at some rather noisy cryo-tomography data and I would like to create something akin to icosahedral and spherical sections, using different shapes (cylinders, ellipses etc). I have found spherical and icosahedral sectioning to be a valuable way to represent density and would like to use this in other types of structure. Is it possible to colour the surface of an imported VRML object in the same way as spheres and icosahedra are in the tools>volume data>surface colour dialogue? In my current chimera installation, VRML objects are not listed in this window.... The sort of effect I want to achieve is similar to that described here: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icossu… except that I want to use custom geometries.... Many thanks, Dave Dr David Bhella MRC Virology Unit Church Street Glasgow G11 5JR Telephone: 0141-330-3685 Graphics lab: 0141-330-2989 Mobile: 07717-202439 Virus Structure Web Site: http://www.mrcvu.gla.ac.uk/research/bhellad/virus_structure.htm Molecular Machines - Images from Virus Research (Art Exhibition): http://www.molecularmachines.org.uk Departmental Web Site: http://www.mrcvu.gla.ac.uk/staff/bhellad.html

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code 5 error
by steve field 18 Sep '08

18 Sep '08

Hello' I am trying to render a surface depiction on various fluorescent protein molecules. The program seems to work with some but not others. A code 5 error message displays. Any insight into what is causing this? PyMol is able to depict the surface from the same PDB file and Chimera works with other molecules, but not the one I need. Any thoughts would be appreciated. Thank you, steve field _________________________________________________________________ Want to do more with Windows Live? Learn “10 hidden secrets” from Jamie. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!5…

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Re: [Chimera-users] [chimera-dev] Hydrophobicity
by Elaine Meng 18 Sep '08

18 Sep '08

On Sep 18, 2008, at 9:54 AM, Leo O'Young wrote: > Hi Elaine, > > Thanks for such a quick and detailed response. > I am looking to get the Hydrophobicity-Surface model so > the it will look smoother...the edges not so rough. > I am not very technical, hopefully I am making some sense. > I have attached a file. > > Thanks again, > Leo Hi Leo, In that case, I think you want to change the "vertex density" surface parameter mentioned in the previous message. That uses a greater number of points and thus triangles in the surface, leading to a smoother appearance. However, be aware that doing this may decrease the interactivity (slow down responses to movements with the mouse) depending on your computer, so you may need to experiment a little to find a happy medium. Actually the picture you sent is of a rather small molecule, so I don't think there will be any slowdown. If you were showing a huge protein or several proteins it would be more likely. Best, Elaine

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Re: [Chimera-users] [chimera-dev] Hydrophobicity
by Elaine Meng 18 Sep '08

18 Sep '08

On Sep 17, 2008, at 10:14 PM, Leo O'Young wrote: > > I am new to the list, I am wondering if it is possible to increase > the geometry > of the Hydrophobicity-Surface models. > > Thanks, > Leo Hi Leo, Welcome! The "hydrophobicity" in the preset is just a coloring scheme, so I will set that aside and discuss molecular surfaces. I am not sure what you mean by "increase the geometry." There are several ways you can adjust molecular surfaces in Chimera: change vertex density, probe radius, and also the radii of the underlying atoms. It is a molecular surface by the Richards definition, also known as the solvent-excluded surface, made of probe contact and re- entrant patches; it shows the VDW surface of the structure except with crevices smoothed. Currently Chimera does not show the solvent- accessible surface, which is where the probe center goes. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces > If you mean you want to make the surface "bigger" to enclose a greater volume, that can be done by increasing the VDW radii of the atoms, and to a lesser extent, increasing the probe radius, which will smooth the crevices more. One way to increase VDW radii is with a command; this would increase all radii by 0.7 A, for example: vdwdefine +0.7 (the command ~vdwdefine changes the radii back to defaults). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html#changing > To change probe radius or other parameters of an existing molecular surface: - Ctrl-click the surface to select it - open the Selection Inspector (click the greenish button on the lower right corner of the Chimera window or choose Actions... Inspect from the menu) - in that dialog, Inspect "MSMS surface", and then edit the various parameters as desired <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html#msmsprop > You can also set preferences to use different parameters for surfaces created in the future, so you don't have to change each one after you create it. To do that, choose Favorites... Preferences, go to the New Surfaces category, change parameters as desired and click Save. That only pertains to surface parameters, not VDW radii of atoms, however. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surf… > 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 _______________________________________________ Chimera-dev mailing list Chimera-dev(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Protonating ASP and GLU
by Francesco Pietra 18 Sep '08

18 Sep '08

Is there any special reason why, in the AddH option, side chains are only considered for HIS (with full options)? Why similar options are not given to protonate GLU and/or ASP at the carboxylate? The general option to consider H-bonding does not work in my case for such residues close to one another in space with Chimera (the two O atoms of two ASP residues are at 2.56A from one another). Even Reduce, supposed to protonate close lying carboxylates, failed in my case. This is why I would consider to add that option in future versions of Chimera. Thanks francesco pietra

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heavy black awful nuisance grid
by Barry Lever 16 Sep '08

16 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. I attach one of the images Thanks for your help (Windows XP, SP3) Barry -- A. B. P. Lever Distinguished Research Professor Emeritus Chemistry, CB124, York University 4700 Keele St., Toronto, Ont., Canada M3J 1P3 Tel:416-736-2100 x22309 Fax: 416-736-5936 http://www.chem.yorku.ca/profs/lever

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solaris version
by o.h.weiergraeber＠fz-juelich.de 16 Sep '08

16 Sep '08

A question to the chimera developers: Having used chimera for several years on IRIX and Linux machines, we can say it is maybe the most useful tool available for molecular visualization and related purposes. However, most important (freeware) packages in the field of x-ray crystallography have also become available as Solaris(x86) versions over the past few years. In my opinion it is quite an attractive platform mainly because it avoids all the confusions and incompatibilities arising from the multitude of distributions in the Linux world. Thanks to the overall conceptual similarity to Linux compilation should (in principle) not run into tremendous problems. I would try myself, but the source code available is not complete afaik :( So, are there plans for a Solaris version of chimera in the near future? In previous discussions on this mailing list I found there are even some Solaris-related comments in the source code ;) Greetings Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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Pyrazine problem
by Francesco Pietra 15 Sep '08

15 Sep '08

Hi: I am dealing with pyrazine compunds in view of docking with DOCK6. The two nitrogens proved problematic for Chimera so that, to simplify, I tried with pyrazine itself, getting the same problems. I used for getting the pdb the MM package I am familiar with: 1. draw benzene, 2. replace two para carbons with N, 3. replace the H on N with a lone pair. The two nitrogens are now indicated of MM3 (or MMX) type 37 (-N=C-/PYR (DELOCALIZED). The charge on the nitrogens is 0.15, on the lone pairs -0.21, on carbon 0.14, on H 0.04. Save as pdb, load to Chimera, then Tools, Structure editing .. Add charge, it results total charge -2. In fact, commanding addH adds a hydrogen to each nitrogen and the resulting molecule is neutral, while it should be +2. If in Chimera I save the loaded pdb as mol2, the two nitrogens result of Tripos type N.pl3, i.e., trigonal planar nitrogen, which is the wrong type. Naively, I replaced N.pl3 with N.ar (aromatic nitrogen) in the mol2.file, getting the same results on reloading the mol2. So the two packages, MM and Chimera are internally consistent but (for the first time in my experience with both packages) they are not mutually consistent. I tried to build pyrazine atom-by-atom, getting the same results. Attached is the pdb and the mol2. When opening the pdb, Chimera says: "Ignored bad pdb record found on line 26"; actually there are fewer than 26 lines. Thanks for help francesco pietra

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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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surface capping command
by Gabriel Lander 09 Sep '08

09 Sep '08

Is there a way to turn on surface capping from the Chimera command line?

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saving images -- wire representation at higher dpi
by Ryan 09 Sep '08

09 Sep '08

Hi, I am trying to save higher resolution images that contain some residues with a wire width of 2. I have noticed that when i increase the dpi of the images, the saved images look different than what is displayed in the viewer -- nodes appear at each atom of the residues that are displayed as wires. As i increase the dpi of the saved images, the nodes become increasingly exaggerated (of a thicker radius than the wire bonds). Is this what should be happening? If so, is there a way to have both the atoms and bonds save with the same radius? Thanks a lot, ryan

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Models or chain
by hsosa＠aecom.yu.edu 09 Sep '08

09 Sep '08

I have created a model from several PDB files and saved it using the save PDB utility in chimera. The resulting PDB file had the different molecules separated in the PDB file with the lines MODEL 1 . . . MODEL 2 . . . MODEL 3 . . . and so on. Is it possible instead to save the PDB file as one model but using different chain names for the different molecules ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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