- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] SEPARATING A SUBUNIT
by skmolugu＠miners.utep.edu 29 Sep '08

29 Sep '08

Hi, I have a CryoEM density map with 14 subunits with seven fold symmetry. Is there a way in chimera to separate only one subunit from the entire map. thanks, sudheer

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Calculating RMSD for ligand
by 吴超 27 Sep '08

27 Sep '08

Hi, dear folks, I want to evaluate the docking performance by calculating the RMSD of heavy atoms between ligand crystal conformation and docked conformation. I use the following command: rmsd #0:1.het & ~element.H #1:1.het & ~element.H But Chimera seems to forget the correct order and give a pairwise alignment not the way I want . I wonder if there is a way that I can get the correct selection order so as to calculate RMSD. Best -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206

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calculating symmetry for a dimer structure
by Katryna Cisek 26 Sep '08

26 Sep '08

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna

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calculating symmetry for a dimer structure
by Katryna Cisek 26 Sep '08

26 Sep '08

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna

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error in vista
by Mugnaioli, Enrico 25 Sep '08

25 Sep '08

Dear Chimera Users, I installed Chimera in my new PC, working under Vista. Apparently, the installation was fine, but when I started the program I got this error. What can I do? Best regards, Enrico Mugnaioli

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adding H
by Barbara Truitt 25 Sep '08

25 Sep '08

I have a compound which has an imidazole ring. When I Add Hydrogens, no hydrogens are added to the nitrogen atoms when I use the build from 9/21/08. The build from 9/4/08 adds the hydrogens, but some of the charge assignments in the resulting mol2 file don't make sense. Barb Truitt

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Re: [Chimera-users] Creating and visualizing a plane
by Elaine Meng 24 Sep '08

24 Sep '08

On Sep 24, 2008, at 12:29 PM, Monica Tello wrote: > I found this very useful, thanks! > I have been trying to do a similar thing but creating a sphere to > put it surrounding the residues in the active site. I tried to > create a big water molecule, and this made the trick until I was > stuck because I can't change its transparency. Then I thought about > creating a marker such as you described for the plane, but I am not > familiar with creating these marker files and I am probably missing > commands in the .cmm file, because Chimera can't open the file and > is giving an error with the info written in it. > Could you help me out with it? Hi Monica, A marker is really just an atom, so that wouldn't make a difference. Normally you would use "Volume Tracer" (under Tools... Volume Data) to create the marker interactively with the mouse and then save it as a file from that tool instead of creating the file with a text-editor. I only edited the file in my example so I could specify the coordinates exactly. In fact, I created 3 markers interactively, saved the marker file from Volume Tracer, and then just edited the x,y,z coordinate values. You can make an atom/marker transparent by creating a transparent color and then using it (for example, choosing Tools... Utilities... Color Editor, clicking Opacity to include a transparency slider, creating the color, and using "colorpanel" as the color name in a command or "Actions... Color... from editor" in the menu). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html> You can also create and name transparent colors with the "colordef" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html> Show the atom in the sphere representation; you can change its radius, for example by selecting the atom and using a command something like: vdwdef 5.0 sel <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> In fact, the "Volume Eraser" tool (under Tools... Volume Data) just makes a big transparent marker and its dialog has convenient controls for changing its color, radius, and position, so you might want to try that instead: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/volerase… > Yet another possibility is to make a spherical surface instead of an atom/marker. This can be done with the command "shape": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> You can move that spherical surface relative to your structure and change its color just as described for the planar surface in my earlier message to Jim. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab 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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Unable to turn reset multisampling. Graphics hardware supports request, but can not switch while maintaining display data.
by Andy LiWang 24 Sep '08

24 Sep '08

Dear Chimera, I just installed Chimera on my Dell XPS 1210 laptop (Windows Vista; Mobile Intel(R) 945GM Express Chipset Family). I get the following error everytime I start Chimera: Unable to turn reset multisampling. Graphics hardware supports request, but can not switch while maintaining display data. Molecules are not properly rendered and does not hide objects rotated behind other objects. I.e., some object appear in front regardless of rotation. This is a new problem. Chimera used to work fine on this computer. However, recently, I had Windows Vista reinstalled. Since the reinstallation, Chimera has these new problems. Any ideas? Thanks, Andy -- Associate Professor School of Natural Sciences UC Merced Atwater, CA 95301 Tel: (209) 228-4617 Fax: (209) 724-4356

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Re: [Chimera-users] Generating random helix
by skmolugu＠miners.utep.edu 24 Sep '08

24 Sep '08

Dear Chimera team, Is there any option in chimera that builds helix in a map at a position that is assumed to be a helix. thanks, sudheer

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Out of topic for Elaine
by Francesco Pietra 24 Sep '08

24 Sep '08

Hi Elaine: Although out of topic, as the author of the program "grid" you could be in the best position to give me general advice. Selecting spheres for only a portion of the protein failed to execute "grid" (at 0.3A grid_spacing) in a reasonable time. I choose this route in the hope to be able to examine docking (DOCK6) for the various parts of the molecule, in order to have the whole. I believe to have good reasons to do that. Is that what one should expect or does it mean that I did something wrongly? Thanks francesco pietra

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Movie recording
by Ibrahim Moustafa 24 Sep '08

24 Sep '08

Dear Chimera team, I have a problem with making a movie of morphed conformations in chimera (only for chimera 1.2548 installed on my laptop running XP). After doing the ³morph² when trying to record the movie I got the following error message: ³Error stopping/encoding movie: MidasError: Keyword and¹ does not match any known keywords² I don¹t understand the error message and what does it mean by ³keyword and²? I¹m not running a script. I don¹t have this problem with the Mac version of Chimera. The funny thing is that I was able to create a movie on the windows version a week ago. I¹m not sure if this problem has relation with XP and perhaps some new updates! Any idea how to solve this problem? many thanks for your great help. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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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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