- Chimera-users - RBVI Mailing Lists

volume viewer question
by Ben Keshet 03 Oct '08

03 Oct '08

Hi Chimera fans, Can someone please help me understand how to read and look at .nrg files (generated by Grid)? I am interested in visually exploring the electrostatic potential around a protein. Specifically, when I opened it, everything was in one color, with negatively charged regions being darker, but I would imagine that positively charged regions should have a different color. On a related note - is there a tool to calculate and view the electric field lines around a molecule / protein? Thanks for your time and help, Ben

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Poor performance with 30 molecules
by Thomas Goddard 03 Oct '08

03 Oct '08

Hi Ben, The main trick to improve efficiency in Chimera with many copies of a molecule is to use only the C-alpha coordinates. This is usually acceptable with working with EM data resolutions. You create a PDB file with only the CA atoms (can use "select @CA" command and Chimera File / Save PDB...) reducing the total number of atoms by 10x or more. Chimera is a very memory inefficient with molecules taking about 2 Kbytes per atom. This is about 10x worse than PyMol and VMD. You start feeling this at about 100,000 atoms and up and run into real trouble around 500,000 atoms if you are using 32-bit Chimera (no 64-bit available on Windows or Mac) because you run out of address space. The ability to rotate the models depends on rendering speed. Above 100,000 atoms only "wire" style will be fast and you must have a graphics driver installed (not Mesa on Linux). With a 4 year old graphics card (Radeon 9800 Pro) I get 10 frames per second with 200,000 atoms. With a newer card you should handle 500,000 atoms in wire at reasonable frame rates. Chimera session files include all the PDB atom coordinates. Chimera has no way to show 30 copies of a PDB file at different positions without having 30 independent copies of the data, except using surfaces with the multiscale tool. The multiscale tool does not interoperate easily with fitting in maps. Tom Elaine Meng wrote: > Begin forwarded message: > >> From: Benoit Zuber <bzuber(a)mrc-lmb.cam.ac.uk> >> Date: October 2, 2008 10:24:34 AM PDT >> To: Elaine Meng <meng(a)cgl.ucsf.edu> >> Subject: Re: [Chimera-users] volume viewer window >> >> Hi Elaine, >> I just aligned a tiny subtomogram to a model with a lot of different >> parameter, which generated many volumes. Then I wanted to visualize >> all the results at once. Since each volume was tiny, chimera was not >> struggling, it was fine :-) >> >> However that reminds me another issue about memory I had sometime ago. >> I have a tomogram into which I have fitted many copies (more than 30) >> of the same pdb file. There are two problems: 1) compiling the session >> file takes ages (around 10 minutes I would say). Opening the compiled >> session file takes more than 1 minute. >> 2) if I display all the copies of the pdb, everything is very slow (I >> mean if I want to move anything in space, it takes very long). If I >> display only a few copies (plus 1 or two slices through the tomogram), >> then it works fast. >> >> For the 2nd problem, there is maybe no easy solution to speed up the >> calcultations, but for the first one, since we are dealing with copies >> of a single pdb, wouldn't it be possible to make the process faster? I >> reckon that the coordinates of each atom of each copy of the pdb are >> saved. Would there be a way to save only one copy and transformation >> matrix for every copy? Would it speed up file saving-compiling-opening >> operations? >> >> Cheers, >> Ben > > Hi Ben, > I know Tom Goddard has made many recent improvements in Volume Viewer > memory usage and speed, but it sounds like your main issue is many > atomic structures rather than lots of volume data. > > If the PDB copies are identical except in transformation, there is some > capability in Multiscale Models to only store one copy of the > coordinates and show the others as low-res surfaces. However, as soon > as you try to show any more detailed display such as ribbons or atoms > and bonds, the full coordinates for that copy are loaded. If you > actually want to view ribbons/atoms/bonds for each copy, I don't know of > any mechanism to save memory. Also, to use Multiscale Models in this > way, you would have to generate an input PDB file with matrices > describing all of the transformations, which sounds difficult. Yet > another way to handle multiple coordinate sets for the same atoms is as > a trajectory. However, then you can only view one member of ensemble > (one "time step" from the trajectory) at a time, so that also would not > solve your problem. > > I CC'd Tom and Eric in case they have any ideas. > Best, > Elaine > >

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Re: [Chimera-users] [Fwd: Re: [Dock-fans] DMS replacement]
by Elaine Meng 02 Oct '08

02 Oct '08

Hi Christian, We're glad you like the "Write DMS" tool in Chimera! <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/dms.html#writedms> Note that it does not run a surface calculation, but simply converts the molecular surface already shown in Chimera into the DMS format for output. Thus it effectively uses whatever parameters you had used to calculate the molecular surface in Chimera. That is currently done with MSMS (included with Chimera), a different program than DMS with different heuristics, so even with the most similar parameters possible I don't think the dots would be in exactly the same places even though the surfaces would basically coincide. More about molecular surfaces in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces > If you used Chimera defaults for surface calculation, the probe radius is the same as the DMS default (1.4 Angstroms), but the atomic radii and dot density are different. The dms man page says the default density gives about 5 dots per square Angstrom. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/dms1.html> You could set the Chimera molecular surface vertex density to 5 (instead of the default 2) to be similar to the dms default. To change an existing surface, Ctrl-click to select it and then for "MSMS surface" in the Selection Inspector (Actions... Select) change the "vertex density" value. If you want to change the Chimera defaults so that future surfaces will be created with that density, choose Favorites... Preferences, go to the "New Surfaces" category, change the value, click Save. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surf… > Default atomic radii in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> I don't believe the old DMS default radii are necessarily better than the Chimera default atomic radii, but if you really wanted to set the radii in Chimera to these values, it can be done with the "Define Attribute" tool or the command "defattr" along with the attribute assignment file dmsrad.txt attached below (it is a very small, simple text file). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… > I personally favor having Write DMS as a separate tool from Dock Prep because I think people should display the surface, adjust which part is displayed (since there is a nice option to only write what is displayed), and possibly change the surface calculation parameters rather than clicking a single button on Dock Prep to just do everything and write the whole surface without tailoring it to the situation. Best, 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 > > From: Christian Schudoma <schudoma(a)mpimp-golm.mpg.de> > Date: October 2, 2008 5:48:57 AM PDT > To: "dock-fans(a)docking.org" <dock-fans(a)docking.org> > Subject: Re: [Dock-fans] DMS replacement > > I think WriteDMS is a very nice new feature for Chimera. Does it run > with the same default parameters as the original dms? > > Also, I wonder if it would be possible to integrate WriteDMS into the > DockPrep tool? Maybe add an option there to run surface generation and > WriteDMS automatically when DockPrepping a molecule? > > Thanks & best regards, > Christian >

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Display symmetry axis
by Thomas Goddard 02 Oct '08

02 Oct '08

Katryna Cisek asks about display of symmetry axis: Hello Tom, Thank you for your suggestion, the code below is working very well for finding the symmetry information that I need for my dimers. Is it possible to visualize the axis of symmetry and the shift? I'm trying to reproduce a reference dimer conformation/symmetry using two monomers that have been docked to each other, but have not been able to get the exact symmetry numbers as for my reference structure, Thanks, Katryna On Fri, Sep 26, 2008 at 3:26 PM, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: > > Hi Katryna, > > > > To find a dimer symmetry axis I would open two copies of the PDB model. If > > the monomers are chain A and chain B then align chain A of one copy to chain > > B of another copy using the matchmaker command. Then print the rotation axis > > of the transformation between those two models. Unfortunately there is no > > command for this last step so I've attached a Python script that will print > > that information. > > > > Tom > > > > Example use: > > > > # > > # Report the transformation mapping one model to another, including axis of > > # rotation. Written to find dimer symmetry axes. Example: > > # > > # open 1f5w > > # open 1f5w > > # mmaker #0:.a #0:.b pairing ss > > # open symaxis.py > > # > > # Reply log output: > > # > > # match 1f5w, chain A (#0) with 1f5w, chain B (#1), score = 601.8 > > # RMSD between 118 atom pairs is 0.337 angstroms > > # > > # Matrix rotation and translation > > # 0.69329933 -0.72016666 0.02638219 22.81733764 > > # -0.72021136 -0.69368986 -0.00948567 58.05835625 > > # 0.02513232 -0.01242434 -0.99960692 102.03253762 > > # Axis -0.92013562 0.39134963 -0.01399645 > > # Axis point 0.00000000 33.92575324 50.81758910 > > # Rotation angle (degrees) 179.90850597 > > # Shift along axis 0.29797742 > > # > > > > > > Katryna Cisek wrote: >> >> >> >> Hi, >> >> Is there a way of calculating symmetry for a dimer structure >> >> in chimera, e.g. axis of symmetry? >> >> Thanks, >> >> Katryna >> >> _______________________________________________ >> >> Chimera-users mailing list >> >> Chimera-users(a)cgl.ucsf.edu >> >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > > > > > > # > > # Report the transformation mapping one model to another, including axis of > > # rotation. Written to find dimer symmetry axes. Example: > > # > > # open 1f5w > > # open 1f5w > > # mmaker #0:.a #0:.b pairing ss > > # open symaxis.py > > # > > # Reply log output: > > # > > # match 1f5w, chain A (#0) with 1f5w, chain B (#1), score = 601.8 > > # RMSD between 118 atom pairs is 0.337 angstroms > > # > > # Matrix rotation and translation > > # 0.69329933 -0.72016666 0.02638219 22.81733764 > > # -0.72021136 -0.69368986 -0.00948567 58.05835625 > > # 0.02513232 -0.01242434 -0.99960692 102.03253762 > > # Axis -0.92013562 0.39134963 -0.01399645 > > # Axis point 0.00000000 33.92575324 50.81758910 > > # Rotation angle (degrees) 179.90850597 > > # Shift along axis 0.29797742 > > # > > from chimera import openModels > > from Matrix import xform_matrix > > from FitMap.gui import transformation_description > > from Accelerators.standard_accelerators import show_reply_log > > > > xf0, xf1 = [m.openState.xform for m in openModels.list()] > > xf = xf0.inverse() > > xf.multiply(xf1) > > tf = xform_matrix(xf) > > print transformation_description(tf) > > show_reply_log() > > > >

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volume viewer window
by Benoit Zuber 02 Oct '08

02 Oct '08

Hi, In the pannel threshold and color in the volume viewer window, is there a way to switch between the displayed histograms? For example I have 33 volumes open, but I can only modify the threshold for the last 8 volumes that I opened, even if I set the maximum number of displayed thresholds to more than 8. Indeed then the window is not large enough to display all the thresholds. Thanks in advance, Ben -- Benoit Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK

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cannot interpolate models: underlying C++ Atom object is missing
by Frembgen Kesner, Tamara A 01 Oct '08

01 Oct '08

Hello, Does anyone know what the error message cannot interpolate models: underlying C++ Atom object is missing means? (And what I can do about it?) I am getting this message when I attempt to create a morph between two .pdb files using minimize. Thank you.

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Re: [Chimera-users] 1HLA- how to make ribbon image?
by Elaine Meng 30 Sep '08

30 Sep '08

Hi David, To summarize for the chimera-users list: 1HLA is an alpha-carbon-only structure, which cannot be shown as a ribbon in Chimera. However, there are many other structures of this protein, several at higher resolution and including all backbone atoms, allowing them to be displayed as ribbons. This Uniprot page has a long list of structures (about 80% of the way down is a "3d structure databases" section): http://www.uniprot.org/uniprot/P01892 The best resolution looks like 1.4 Angstroms, structures 1i4f and 1oga. Both match up with the CA-trace in 1hla quite well. Since they include all backbone atoms, they can be displayed as ribbons. I suggest using 1i4f. 1oga is just as good but has two copies. 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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1HLA- how to make ribbon image?
by Edelshtein, David 30 Sep '08

30 Sep '08

Hello, I am an ITL researcher, I use chimera for making a ribbon image of 1HLA molecule, and I need to mark specific residues, (by the number/position). So far, I am unsuccessful in converting wire style to the ribbon style. Please let me know if you can help, advice or direct me to required info. David, Edelshtein SRA II UCSF ITL

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COLOURING A SUBUNIT
by Tom Goddard 30 Sep '08

30 Sep '08

skmolugu(a)miners.utep.edu wrote: > Hi, > thank you very much for your reply, > I have another question, is there a way to colour a symmetric map which has 4 subunits in to four different colours? > thank you for your time, > regards, > sudheer. > Hi Sudheer, If you have 4 monomer PDB models fit into the map, color them differently (e.g. command "rainbow chain"), then use the Color Zone tool to color the map to match the monomers. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorz… The Chimera volume guide may help with future questions: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html Tom

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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

2 1

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 ------------------------------------------------------------------- -------------------------------------------------------------------

2 1

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

2 1

(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 **********************************************

2 1

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

1 0

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

2 1

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

2 1

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

2 1

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

2 1

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

2 1

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?

2 1

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

2 1

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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Re: [Chimera-users] reading in hdf5 files in chimera
by Joshua Turner 08 Sep '08

08 Sep '08

Hi, I have created a 3D hdf5 file and am having trouble displaying it in Chimera. Is there something specific chimera looks for that it needs to read in the .h5 file, to be able to display the file? Thanks, Josh

2 1

SGI build going the way of the dodo
by Eric Pettersen 04 Sep '08

04 Sep '08

We are decommissioning our SGI machines as of September 15th, which means that the 1.2540 release was the last production release for SGI and that daily builds will stop on the 14th or 15th (those final builds will remain available on the Daily Builds page for a few months at least). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] aqua version of Chimera
by Elaine Meng 03 Sep '08

03 Sep '08

On Sep 3, 2008, at 12:08 PM, Anindito Sen wrote: > Hi Eline > The aqua version of Chimera when installed on my Macbook(memory > 4GB, proc. 2.2 Core 2 Duo) seems to come up with a strange problem > of flickering of the main display window each time I move another > window or alter the position of a crystal structure. However I have > not faced anything on the MacOSX (X windows)version. I was > wondering what possibly can be the reason and that if ony one else > in the community have faced similar problem of this type. > Best > Andy > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908 Hi Andy, This behavior in Aqua Chimera is intentional, allowing a window to become active immediately instead of requiring an extra click when you move the cursor into that window. However, if you would rather have extra clicking than the flickering, you can turn it off in recent versions of Chimera (within the last month): open Preferences (under Favorites), change to "Mouse" category, set "Window focus follows mouse" to false. This preference only appears in the Mac Aqua version. I would like to remind everybody: To ask questions, please email chimera-users(a)cgl.ucsf.edu (unless something confidential is included), and to report problems, please use "Help... Report a Bug" or email chimera-bugs(a)cgl.ucsf.edu . It is better to send to these e-mail addresses than to an individual, because that person might be on vacation or unavailable at the time and you might not get an answer. 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

1 0

Re: [Chimera-users] sulfone files
by Eric Pettersen 03 Sep '08

03 Sep '08

Hi Barb, There are two issues here. One was that though the heavy-atom positions were identical, the added hydrogens weren't positioned identically because of "steric clashes" between the two molecules when placing hydrogens (this was in some fairly newly-added code). I modified the new code to ignore clashes between sibling submodels (other analogous older code was already doing this). With the modified code and with the two PDB files merged so that the molecules open into model 0.1 and 0.2, the hydrogens get added identically. The other issue is that antechamber only determines charges to somewhere around 0.01 accuracy, even with the atoms at identical positions. Now, Chimera is supplying antechamber with identical positions, but giving them in a different order between the two residues, so that the resulting output isn't identical. I've modified the add-charge code so that it will now present the atoms in the same order as they were input -- so the result is that the charges vary only minimally now. Nonetheless, they shouldn't really be perceived as more accurate than about +/-0.01 charge units. You'd probably have to ask on the Amber mailing list why this is so and if there is anything that can be done or will be done about it. These changes will be available in tonight's daily build, which you could get tomorrow from www.cgl.ucsf.edu/chimera -- follow the "Daily Builds" link. --Eric On Sep 3, 2008, at 6:17 AM, Barb Truitt wrote: > Eric - Thank you for your help. I find the Chimera list incredibly > helpful. > I've verified that the pdb files have the same coordinates. I also > redid the DOCK PREP without any rotation of either molecule and > still have different charge assignments. Here are the four files. > The carbons that vary the most between the two are the ones in the > aromatic ring with a single methoxy group and the ones near the > chlorine. I'm also sending an Excel file where I've sorted the atoms > based on their coordinates so that I could check the assigned > charges. I've color-coded the carbons that vary significantly. > > Barb > <charge > comparison > .xls > > > < > SSR149415 > .pdb><SSR149415_SR4.pdb><SSR149415_SR_T.mol2><SSR149415_T.mol2>

1 0

problem with chimera
by Jean-Paul Armache 03 Sep '08

03 Sep '08

Hello, Due to some long needed changes, I have switched to CentOS 5.2. Everything was fine for some time, but then, when trying to run Chimera, I encountered the following error (applies to all versions of Chimera on my harddrive - 1.2470, 1.2492 and 1.2540): Traceback (most recent call last): File "/opt/chimera/chimera1.2492/share/__main__.py", line 65, in ? value = chimeraInit.init(sys.argv) File "/opt/chimera/chimera1.2492/share/chimeraInit.py", line 302, in init splash.create() File "/opt/chimera/chimera1.2492/share/chimera/splash.py", line 17, in create splash = Tk.Frame(root, background="white") File "/opt/chimera/chimera1.2492/lib/python2.4/lib-tk/Tkinter.py", line 2375, in __init__ Widget.__init__(self, master, 'frame', cnf, {}, extra) File "/opt/chimera/chimera1.2492/lib/python2.4/lib-tk/Tkinter.py", line 1862, in __init__ self.tk.call( _tkinter.TclError: unknown color name "white" I have tkinter installed, python running properly, everything functional. Except for that. Do you know what could be done to fix it? Best, Jean-Paul

2 1

v. 2540 linux - core dump (?!?!?!)
by Boaz Shaanan 02 Sep '08

02 Sep '08

Hi, After installing v. 2540 for linux I get 'floating exception' and core dump. The installation went fine as far as I can tell. It's a laptop running Mandrake 10. So far, I've had no problem running chimera on it. any clue about what might have gone wrong ? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

2 1

Chimera running un der 64 bit Vista
by Charles Letner, Ph.D. 02 Sep '08

02 Sep '08

Hello all, Does Chimera run under 64 bit Vista? Thinking about a new desktop and sure would like to go 64 bit. Cheers, Chuck Charles Letner, Ph.D. Alpharetta, GA 30004

2 1

Display
by James Fethiere 02 Sep '08

02 Sep '08

Hi, I have a sudden problem with the display in version 1.2509. I was working with a session with about 20 models opened. For whatever reason, I just can't display any on the screen anymore; even if all are selected in the model panel. Am I missing something or is this a bug? Thanks James

2 1

assignment of charges
by Barb Truitt 02 Sep '08

02 Sep '08

I have two different pdb files that differ only in how the atoms are listed in the atom name columns. In one file all of the Carbon atoms are listed simply as C. In the other file, the carbon atoms are numbered C1, C2, etc. This is true for the other atoms in the molecule, which is not a peptide chain. The mol2 files created by Chimera under the dock prep procedure have different charges assigned to the atoms, differing most in the aromatic carbons. Some of the hydrogens also have different charges assigned to them. Most of the differences are small, but some are 10%. What is the explanation for this? Barb Truitt

2 1

sulfone
by Barb Truitt 02 Sep '08

02 Sep '08

I am trying to assign charges to a compound that contains a sulfone group. The charge assignment depends upon how I name the atoms. The atom assignment for the oxygens that are part of the sulfone group and the sulfur itself vary depending upon how they are named. How should I name them so that they are handled correctly? Barb Truitt PS - I receive the Chimera list emails, but my outgoing email address apparently doesn't match the one that I used to sign up for the list. Is there a way to fix that?

2 1

POV-ray ignoring surface clipping
by Monica Tello 02 Sep '08

02 Sep '08

Help! I am having trouble saving my images when they have a surface clipped to show the inside. I attach an example for clarity, where the same view was saved with/without POV ray.. If I have a surface around my ligand and is partially clipped, at the time of saving the image: - If I save it without using POV-ray, it saves the exact same view as on the screen, with the surface clipped. - If I use POV-ray, it saves it with the full surface around the ligand, ignoring the clipping I had done. I have tried modifying several POV-ray settings but nothing has worked! Have you got any suggestions? Thanks! Monica SURFACE CLIPPED WITH POV-RAY, SURFACE DOES NOT SHOW THE CLIPPING! ------------------------------------------------- Monica Tello Soto, PhD The Salk Institute for Biological Studies Chemical Biology and Proteomics 10010 North Torrey Pines Road San Diego CA92037 858 453 4100 x1946 tello(a)salk.edu ------------------------------------------------

2 1

POV-ray ignoring surface clipping
by Monica Tello 02 Sep '08

02 Sep '08

Dear all, I am trying to save a Figure that shows my ligand with its surface around partly clipped, and use POV Ray. The problem is that POV Ray modifies the output of the figure: the final picture shows the full surface around the ligand, although on the screen I designed it so that you can see the surface partially clipped. If I use transparency on the surface, POV Ray also ignores this and shows still the full surface around the ligand, and opaque. If I don´t use POV Ray, then I get the figure as seen on the screen! Why is POV Ray ignoring the surface as I want it? It ignores any kind of alteration of the surface! I was using the default POX Ray settings, although by now I have tried to change some of the ones I thought may be related to this, based on the Chimera Manual, but I haven´t had any success. Can anyone help me with this? It will be very much appreciated! I include an example of the same figure saved with and without using POV Ray. The one without using POV ray is the one that looks like what I designed on the screen. Thank you very much!! Monica ----------- ------------------------------------------------- Monica Tello Soto, PhD The Salk Institute for Biological Studies Chemical Biology and Proteomics 10010 North Torrey Pines Road San Diego CA92037 858 453 4100 x1946 tello(a)salk.edu ------------------------------------------------

2 1

Re: [Chimera-users] ESP surface, DelphiController
by Elaine Meng 02 Sep '08

02 Sep '08

On Sep 1, 2008, at 9:14 AM, James Fethiere wrote: > > Once the .dx file is loaded in Chimera, I get a nice ESP map. > However, it seems sensitive!! how? well, when I color the surface > of a transcription factor bound to DNA (1DH3) according to the dx > ESP loaded file, it's nice. But when I display the ribbons of the > bound DNA in the same model and color these ribbons, the previous > surface reverts to the default Chimera colors and I loose the ESP > from the dx file. Quite strange no? Hi James, The reason is that the surface cannot have "custom" colors (e.g. ESP coloring) and coloring to match the underlying atoms at the same time, even in different areas of the surface. If you make sure to color only ribbon and not surface, the surface should stay ESP-colored. If you are using the Actions... Color menu, make sure to check only "ribbons" as what will be colored, color the ribbons, and then change it back to the default "all of the above" coloring targets. If you are using a command, then something like color red,r :30-50 specifies coloring ribbons only (the ",r" part). The alternative is to do all the ribbon/atom coloring first, ESP-color the surface last. > > It is also not possible to select this dx ESP file in a command > file to make a movie. And if it is displayed before movie record > starts, I get a black frame movie with the avi encoding (yes I did > modify the video acceleration in media player). So I guess it will > be still pictures. Check out the session attached. > What are you trying to do with the surface in this movie (why are you trying to select or specify it?). Most command-line selections are based on specifying a set of atoms, so you would just specify the atoms associated with the molecular surface. However, I would need to know which commands you are trying to use to be more specific/ concrete, or let you know if what you want to do is possible with commands. > Thanks > > James I am unable to deal with that attached session because it is just shown as a zillion lines of text beneath the mail message. My cut- paste attempts failed. You could instead use Help... Report a Bug and attach the session to it to illustrate the black movie problem. We may or may not be able to reproduce it, but having the session (and perhaps also your movie script?) would help. It may only let you attach one thing, so I'd say attach the session and put the script (or some short version that exhibits the problem) as part of the message text. Best, 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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POV-ray ignoring surface clipping
by Monica Tello 31 Aug '08

31 Aug '08

I am having trouble saving my images when they have a surface clipped to show the inside. If I have a surface around my ligand and is partially clipped, at the time of saving the image: - If I save it without using POV-ray, it saves the exact same view as on the screen, with the surface clipped. - If I use POV-ray, it saves it with the full surface around the ligand, ignoring the clipping I had done. I have tried modifying several POV-ray settings but nothing has worked! Have you got any suggestions? Thanks! Monica ------------------------------------------------- Monica Tello Soto, PhD The Salk Institute for Biological Studies Chemical Biology and Proteomics 10010 North Torrey Pines Road San Diego CA92037 858 453 4100 x1946 tello(a)salk.edu ------------------------------------------------

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automating/scripting bond rotation
by E. Merkley 29 Aug '08

29 Aug '08

Hello chimera team, I am trying to evaluate which regions of (chi1,chi2) space for a particular tryptophan residue create steric clashes with a bound ligand. I see from the archives that findclash can be called from the command line, but I have been unable to find a way to use the "adjust torsions" feature from the command line. Is this possible? If not, any other suggestions? Thanks in advance, Eric Merkley

2 1

decommissioning SGI Irix platform
by Eric Pettersen 29 Aug '08

29 Aug '08

Hi all, We are decommissioning our SGI machines as of 9/15, which means that the 1.2540 release was the last production release for SGI Irix. Daily builds will continue to be made for SGI until 9/15, so some post-1.2450 fixes/features will be available that way. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Povray and semitransparent maps
by odonnell＠chem.fsu.edu 29 Aug '08

29 Aug '08

Hi. I'm seeking a tip or two on how to save an image of a semitransparent map with PovRay. Povray works fine, but the image of the semitransparent map it generates is much darker that it appears on the screen. Any advice would be much appreciated. -Jason ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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ESP surface, DelphiController
by Elaine Meng 28 Aug '08

28 Aug '08

Hi James, Just because it has red, white and blue blotches does not mean it is showing ESP!! I don't think the different filenames in the DelPhi log are a problem - I believe temp files are generated from the ones you specify and used in the calculation for technical reasons. However, I do not know the reason for the error and not getting any output. You could try using Help... Report a Bug in the Chimera menu - give more details, such as all the error messages obtained and what it says at the end of the DelPhi log file. The main difficulty with DelPhi and any ESP calculation program is that atom names need to match those in the DelPhi charge parameter files. If you want to use all the hydrogens, you have to either edit all the names in the DelPhi charge parameter file or write out your PDB beforehand and edit all of its atom names to match those in the DelPhi charge parameter file. I have found this to be well nigh impossible. In general many hydrogen names not match and your molecule gets a very large net negative charge. Chimera tries to name hydrogens according to current PDB standards, but these old DelPhi parameter files use a different set of names. Instead, I would just used the DelPhi parameter files "default.crg" and "default.siz" which ignore hydrogens and just plop positives on nonhydrogen atoms in Lys, Arg (maybe His and N-term, I forget) and negatives on nonhydrogen atoms in Asp, Glu (maybe C-term). It is impossible to tell what "half all red" and "half all blue" means. It depends on what levels you have specified to be displayed as red and blue. Maybe the APBS map is fine - try changing the values set to red and blue to larger magnitudes. If APBS writes some sort of log file I would look at that, see if there is a reasonable net charge. Again most of the trickiness is in getting the right charges assigned to the atoms. You could use the PDB2PQR server to get an input file for APBS (if you didn't try that already). <http://nbcr.sdsc.edu/pdb2pqr/> Another possibility is to use the webPIPSA server as mentioned in previous messages, e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/003006.html Best, 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 On Aug 27, 2008, at 7:58 PM, James Fethiere wrote: > Hi Elaine, > > Nice that you found what I did 6kkm away!!! thanks. However, I must > say that it does look artificial. I'm just desperate to get the > electrostatic look as nice as possible (just like the pictures in http://www.cgl.ucsf.edu/chimera/tutorials/maps08/exercises.html#esp) > and found that was the closest I could get. One example I'm trying > is on 1DH3 > > On this note, I did try the delphicontroller to get the true > potentials but cannot get it to work. I have installed delphi on > windows-XP and called it from within chimera with tool/ > surfaceanalysis/delphicontroller. I entered the path for the > executable and charge and radii files. When I run delphi, I get an > error with no output file generated and some strange parameters in > the log file: > > in(pdb, file="tmph4vkzc") This does not correspond to the chimera > model I have chosen > in(siz, file="tmplk_go0") same here; not the file specified > in(crg, file="tmpbg7nlz") same thing > AC = true > CS = true > PF = 60 > SC = 1.2 > PR = 1.4 > FC = true > LG = false > LP = false > PX = false > PY = false > PZ = false > BC = 4 > ID = 2 > ED = 80 > GC = 0.0 > IS = 0.0 > IR = 0.0 > NI = 0 > > P.S. I did addH before starting Delphi! Any idea of what is going > wrong? > > I also tried to run APBS and got a potential file. But when I read > it in chimera, I get strange looking surfaces with half all red and > half all blue!!! here again I could use some guidance. > > Thanks for your help. > > James > -- > James Fethiere, Ph.D. > Institut de Recherche en Immunologie et Cancerologie > Pavillon Marcelle Coutu, University de Montreal > 2900 edouard-montpetit > Montreal, Qc H3t 1J4 > Tel: 514-343-6111 ext. 0918/0919 > Fax: 514-343-5839 > james.fethiere(a)umontreal.ca

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unattended installation on Windows
by Nelson, Lisa 27 Aug '08

27 Aug '08

Hello, I am not a chimera user; I'm an IT person. I have been asked to provide this application for next semester on our walk-up Windows computers for students. I have downloaded the necessary Windows installation materials, but I cannot find any documentation about command line parameters for the installation process itself, and the installation executable does not appear to be one of the usual suspects that I'm familiar with. Specifically, I'm looking for a way to do unattended, silent installation from a batch file. Attended installation is not an option as there are thousands of computers involved. Thanks for any help anybody can provide. I am not on the chimera mailing list, so please send replies privately. (The "contact us" webpage appears to give me the option of e-mailing to this list even though I'm not a member, so since I have only this one question and no particular need to subscribe, I've done it this way.) Thanks, Lisa.

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selection
by James Fethiere 26 Aug '08

26 Aug '08

Hi, I'm trying to create a category for separate surfacing of chains in a session that has multiple models. The following command: _surfcat sh3 #7:.a, surf sh3_ returns mangled atoms specifier. This may looks trivial but I can't find the right syntax to specify both the chain and residues in the same command. Any idea? Thanks James

2 1

mrc opaque faces
by Benoit Zuber 26 Aug '08

26 Aug '08

Hello, I have problem looking at maps in mrc format calculated with IMOD. In mesh or surface style, when I move "level" towards lower value, the outer faces of the volume gradually become opaque. When I set the level to the minimum I see a smooth rectangular parallelepiped. I can then zoom in and have the camera inside the parallelepiped. With these settings, no density is visible inside the parallelepiped, only its faces are visible. In 3dmod I checked the edges of the map: they have a variable density, and they are not all black, or all white. Has anybody got a clue of what's going wrong? Thanks Ben -- Benoit Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK

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Faster volume plane display
by Thomas Goddard 25 Aug '08

25 Aug '08

Optimization for tomogram display. I optimized volume plane display making flipping through size 2048^2 data planes run at 17 frames per second instead of the 1.2 frames per second in the last Chimera production release 1.2540. This is with solid style rendering (gray-scale) and with mid-range graphics cards (tested on Radeon X1600 and Radeon 9800 Pro). The improved performance will be available in tonights Chimera daily builds. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom

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Re: [Chimera-users] density maps in chimera- question
by Tom Goddard 22 Aug '08

22 Aug '08

Hi Sarah, Chimera does not show sigma values for a crystal map in the volume dialog. It shows whatever values are actually in the map file. Here is a description of how to convert to sigma values: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html Chimera map display was primarily intended for electron microscopy, hence the deficiencies with crystal maps you are encountering. Allowing direct display of sigma values is item 153 on our requested features list: http://www.cgl.ucsf.edu/chimera/plans.html Tom Sarah Boyce wrote: > Thanks Tom. I also was wondering about the display options for the > density. How does the histogram display level correlate to the sigma > level of the map? > > Sarah

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electrostatic surface coloring
by James Fethiere 22 Aug '08

22 Aug '08

Hi, 1. is there a way to use the electrostatic surface coloring from the tools/surface menu, in a command file? It seems that it is only available through the menu? 2. I have a pqr electrostatic potential file calculated from the PCE server http://bioserv.rpbs.jussieu.fr/Help/PCE.html using MEAD. How do I get it into chimera? Thanks

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Dr. Simon Sauve is out of the office.
by Simon Sauve 21 Aug '08

21 Aug '08

I will be out of the office starting 2008-08-21 and will not return until 2008-09-03. You can reach me at simsauve(a)yahoo.ca during the ICMRBS conference. In case of an emergency, please contact Dr. Yves Aubin by e-mail or @ 613-941-6155

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emulation of threee button mouse not working
by Geeta Narlikar 21 Aug '08

21 Aug '08

Hi, I'm having problems with the three button mouse emulation feature. My OS is Mac X Leopard and I turned on the "emulate three button" mouse feature in X11. But that does not seem to work. My version of Chimera is 1.2509. Is there any other setting I should change? Thanks for your help. Geeta Narlikar

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Re: [Chimera-users] density maps in chimera- question
by Thomas Goddard 21 Aug '08

21 Aug '08

Hi Sarah, You can use the keyboard shortcut "bv" to create a new map that covers your PDB model. To enable keyboard shortcuts use Tools / General Controls / Keyboard Shortcuts and turn on "Enable keyboard shortcuts" in the dialog. Select the atoms of your PDB model. If you have more than one map open make sure the highlighted one in the volume dialog is the crystal map for the selected atoms. Then type the "bv" shortcut to create a new map covering the select atoms. This assumes that the starting map is a full unit cell. If you don't want to go to the trouble of enabling keyboard shortcuts, you can use the command "ac bv" which runs the shortcut (accelerator) bv. You can save the covering map with volume dialog File / Save Map As.... Tom Sarah Boyce wrote: > Hi Tom- I was told you might be the person to ask about the density map > features in chimera. I'm trying to display crystallographic electron > density maps and I've run into a problem aligning some of the maps to > the protein model. When I load the map and model it looks as though the > map is of the symmetry related molecule, but when viewed using Coot it > automatically centers the map on the model. So far the only tool that > I've found to do this is by hand alignment, which doesn't work at all > for an atomic level model (or at least when I've tried it it is too much > of a pain). Is there an automated tool in chimera that will > automatically center the map on the model similar to the way Coot > handles it? > > > Thanks, Sarah

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(no subject)
by charles marchand 21 Aug '08

21 Aug '08

Greetings, I was wondering if someone could tell me how to select multiple sequences in the sequence viewer. I am trying to select different regions of RNA to visualize, but Chimera has not allowed me to pick to sequences that are separate. Is there a way to do it through the sequence viewer? Thank you, Charlie

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Re: [Chimera-users] CHARMM PBEQ calculations
by Tom Goddard 21 Aug '08

21 Aug '08

Hi Fabian, The OpenDX file you sent has a small but important error. It is missing the words "data follows" at the end of the header line that says "object 3 class array..." so Chimera never reads the data. The misleading error message comes about because the last line of the file is blank and Chimera still thinks it is reading the header. The header line object 3 class array type double rank 0 items 378885 has to be object 3 class array type double rank 0 items 378885 data follows Hopefully Sunhwan can update the phi2dx.py script to include the very important "data follows". The OpenDX format is described in Appendix B of the OpenDX User's Guide: http://opendx.npaci.edu/docs/pdf/userguide.pdf Tom Fabian Glaser wrote: > Dear Elaine, > > I am afraid it's still giving the same error when I try to open the dx > file, even when the first line is removed or # starts it. Here is the > message: > > Opening /media/data/WORKSPACE/PROJECTS/DanCassel/COP/step2_pbeq.dx > Error reading file step2_pbeq.dx, format apbs > Incorrect format: blank header line. Comments must begin with # > character. > > And the dx file is attached, probably I am doing something wrong.... > > THanks a lot, > > Fabian > > > Elaine Meng said the following on 19/08/08 19:19: >> Hi Fabian, >> Well, the error message says the format is wrong. Based on the >> message, you could try removing the blank line at the top of the file >> or adding # in front of it. >> >> If that still doesn't work you could send me the file to look at, but >> it is probably just a simple fix such as the above. >> 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 >> >> >> >> >> >> On Aug 19, 2008, at 7:03 AM, Fabian Glaser wrote: >> >>> Dear Sunhwan >>> >>> Thanks a lot for your kind answer and for the script. The script run >>> fine, but when I try to upload it to chimera I get an error: >>> >>> Opening >>> /media/data/WORKSPACE/PROJECTS/HaimManor/EladEliahoo/MODELS/POMBE/CHARMM-PBEQ/charmm-gui/step2_pbeq.dx >>> >>> Error reading file step2_pbeq.dx, format apbs >>> Incorrect format: blank header line. Comments must begin with # >>> character. >>> Done opening >>> /media/data/WORKSPACE/PROJECTS/HaimManor/EladEliahoo/MODELS/POMBE/CHARMM-PBEQ/charmm-gui/step2_pbeq.dx >>> >>> >>> Which maybe perfectly chimera problem, so I am CCing this email also >>> to Elaine Meng from the CHIMERA team. >>> >>> Any help will be very appreciated, >>> >>> Thanks a lot, >>> >>> FAbian >>> >>> Sunhwan Jo said the following on 19/08/08 15:25: >>>> Dear Dr. Glaser, >>>> >>>> I'm afraid CHIMERA is not able to read CHARMM phi80 format. But simple >>>> search guided me that CHIMERA can to read dx format file, which I >>>> have a >>>> converting script. So, please find the script in the attached file. >>>> We've been >>>> using this script to read our potential data in Pymol, so I believe >>>> this should >>>> be working fine with CHIMERA as well. >>>> >>>> usage: >>>> python phi2dx.py step2_pbeq.phi80 > step2_pbeq.dx >>>> >>>> Please feel free to contact me, if you have a further problem. >>>> >>>> Thanks, >>>> Sunhwan >>>> >>>> >>>> On Tue, Aug 19, 2008 at 4:53 AM, Fabian Glaser >>>> <fglaser(a)technion.ac.il> wrote: >>>> >>>>> Dearl CHARMM team, >>>>> >>>>> have been trying to upload the electrostatic potential calculated >>>>> by CHARMM PBEQ routine to the CHIMERA viewer, since the java >>>>> viewer you use is very good but at least in my machine does not >>>>> work. But despite I have been trying to upload it to chimera there >>>>> seems to be some stubborn problem (or I am doing something wrong). >>>>> What I am trying to do is to color the pdb by the potential in >>>>> chimera so I can freely manipulate it and compare it with other >>>>> calculations. >>>>> >>>>> If you have any suggestion I'll be very grateful, >>>>> >>>>> Best regards, >>>>> >>>>> Fabian Glaser, PhD

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clipping planes question
by William Jeffrey Triffo 20 Aug '08

20 Aug '08

I know of the hinder and yon clipping planes, and also the per-model clipping plane that allows individual model clipping. I have a current imaging session where I have already used per-model clipping on several models, but would like to trim off some material from the side of the entire combined model - I don't suppose there is an arbitrary clipping plane that applies to the whole scene, like hinder-yon but from any user-defined direction? For now, I was just going to crop the resulting image. But this will result in an abrupt end to the background color (I can adjust the image border clone the background in photoshop/etc, but would be nice to be able to do that within Chimera) thanks, -Jeff

2 1

saving nol2 files
by 吴超 20 Aug '08

20 Aug '08

Hi, dear folks, I have some doubt about how chimera determines the atom type when you save mol2 files from ligand pdb files. Because when I opened the saved mol2 files, I found there were some mistakes about atom type. Does Chimera use the same procedure that Sybyl uses to determine the atom type? -- Chao Wu

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MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???
by Darrell Hurt 20 Aug '08

20 Aug '08

Hi there, I¹m trying to use the command MultiScale.color_surfaces_to_match_atoms(). I want to point out a mutation on the surface of a virus. I can color the atoms correctly, but I can¹t figure out how to apply that color to the MultiScale low-resolution surface. Any hints on how to use this command? Also, how can I increase the mesh resolution on MultiScale surfaces for input for 3D printing? Thanks! Darrell -- NIH Researchers: check out our new web site <http://inside.niaid.nih.gov/topic/IT/bioinformatics/Pages/default.aspx> Darrell Hurt, Ph.D. Section Head, Biocomputing Research Consulting Bioinformatics and Scientific IT Program (BSIP) NIAID Office of Technology Information Systems (OTIS) National Institutes of Health, DHHS Contractor, Lockheed Martin 4 Memorial Drive, Room 424 Bethesda, MD 20892-0485 Mobile: (301) 758-3559 Fax: (301) 402-0366 NIAID Intranet: http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Re: [Chimera-users] Distance and Angles
by Thomas Goddard 19 Aug '08

19 Aug '08

Hi Andy, To show a distance between atoms select the two atoms and use menu entry Tools / Structure Measurements / Distances and press the Create button. You can show distances for multiple pairs of atoms. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… Not sure what you mean by the angle between two density map surfaces. The surfaces intersect in many places making different angles. You could place 3 markers with Volume tracer and measure the angle made by those 3 markers using the Angles/Torsions tab of the Structure Measurement dialog. Tom Anindito Sen wrote: > Hi Tom > > Probably this question is already answered before- > > How do I show multiple distances between different amino acids of two > molecules from two different parts of the density map. > > Also do can I determine the angle between two surfaces? > > Thanks > Andy > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908

2 1

saving maps generated with molmap - origin?
by Grigore Pintilie 19 Aug '08

19 Aug '08

Hello, I'm wondering why when I generate a density map from a pdb structure (using the molmap command) and then save it, once I reopen it it seems to have shifted with respect to the structure. I'm noticing that before saving it, the generated map has a certain origin (shown in the Coordinates pane in the Volume Viewer), and then when I reopen it the origin appears as 0 0 0. If I copy the origin shown initially and then paste it into the origin of the opened file, this shifts the map to the correct position, but why isn't the right origin saved with the file? I'm using alpha version 1 build 2509 2008/05/01, platform win32 Many thanks, Greg

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How to Create Isopotential Contours, not Surfaces, with Chimera
by Charles Letner, Ph.D. 19 Aug '08

19 Aug '08

Hello all, I have a map of electrostatic potentials. Using volume viewer I am able to display the surfaces at any potential value I would like (as well as multiple values by having multiple bars in the volume viewer histogram). Now, I would like to be able to take a slice through that potential surface and see a line associated with a given value of the potential in that slice - call that the contour. I would like to have multiple potential contours, each with a different constant value in that contour (-10 for one contour, -20 for the next, -30 for the third, and so on- call these the iso-potential contours). This would allow the contours of potential to be seen in a single plane. Seems like I am so close using planes but that just isn't working. Am I approaching this right and if so any hints would be appreciated? If I am off base with the approach, I sure would appreciate a nudge in the right direction? Cheers, Chuck

3 3

Flipping between alternate conformations (depiction/movie)
by David Chenoweth 19 Aug '08

19 Aug '08

Dear Chimera team, Is there a movie command that can easily depict the interconversion between two alternate conformations in a nucleic acid or protein residue (designated conformation a and b) within a pdb file. I am really trying to illustrate with a movie how the phosphates flip between two well defined states in an ultra-high resolution DNA crystal structure using a chimera movie. 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 **********************************************

3 4

Question about Measure Volume and Area
by Patrick Redmill 18 Aug '08

18 Aug '08

Hi all, I am using the the calculate "Area and Volume" option in Chimera to estimate the SASA and excluded volumes of a family of fullerene materials. I need to calculate the area and volume using two different probe sizes (1.4 and 2.0, to be specific). For most of my particles, you see that the volume and area are relatively insensitive to a change in probe size (which I would expect). For one particle, however, I find the results to be quite different and unintuitive. For instance: 1.4: Area: 1174 Volume: 3534 2.0: Area: 1692 Volume: 2493 My (perhaps wrong??) assumption is that the area calculator uses a Connolly algorithm. If that is the case, I can't understand why a larger probe would give a larger area (smaller probes samples more surface). Also, why would a larger probe give a larger volume? Again, I thought the volume calculator used a Voronoi algorithm, which, to me seems independent of probe size. Any idea what may be wrong about my understanding? I've attached a .pdb of the molecule in question if you'd like to take a gander. Thanks in advance! ~Patrick

4 5

stereo
by Matthew Dougherty 16 Aug '08

16 Aug '08

I have been using chimera/macAqua with sequential stereo with no problems on a CRT. I am running into problems using the depth-q stereo projector because of the way their frame buffer works. Their left and right is inverted relative to the CRT. On other packages I activate a left/right image swap to get around this. Is there something I can do to achieve this on Chimera? Matt National Center for Macromolecular Imaging

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Fwd: Question about Measure Volume and Area
by Elaine Meng 15 Aug '08

15 Aug '08

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: August 15, 2008 12:11:33 PM PDT > To: Patrick Redmill <patrickredmill(a)gmail.com> > Cc: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Question about Measure Volume and Area > > Me again, I just wanted to quickly reiterate that if you want > analytical values, just look in the Reply Log after first showing/ > creating the surface. That will report the analytical values, and > not just the totals but also the values for each component > (disconnected blob, so outer surface and inner surface are two > components), and also both SAS and SES areas even though only the > SES is actually displayed in Chimera. > > So for molecular surfaces, there isn't really any reason to use > Measure Volume and Area or Measure and Color Blobs. Those tools are > mainly needed for other, nonmolecular surfaces. I didn't present > this clearly in the previous messages, sorry. > Best > Elaine

1 0

Re: [Chimera-users] quick angles question
by Tom Goddard 15 Aug '08

15 Aug '08

Hi Jeff, Here is a Python script to report the angles made by bonds attached selected atoms. Just select the atoms, then open the script. Output will be printed to the reply log. Tested in Chimera 1.2548 but should work in much older versions. Tom Jeff Triffo wrote: > hi Tom, > > if I have a Chimera marker file full of interconnected markers, is > there a quick/easy way to report all the angles formed in the > meshwork? (screenshot attached) > > I figure the easiest way is to cycle through the markers and survey > the angles it makes with each attached marker, but I don't know how to > do that (but it sounds like something that is probably straighforward > in python) > > thanks for any input there, > > -Jeff > # ----------------------------------------------------------------------------- # Report all angles made by bonds originating from selected atoms. # from chimera import selection, angle atoms = selection.currentAtoms() print '%d atoms selected' % len(atoms) c = 0 for a in atoms: bonds = a.bonds for b1 in bonds: for b2 in bonds: if b1 < b2: a1 = b1.otherAtom(a) a2 = b2.otherAtom(a) t = angle(a1.coord(), a.coord(), a2.coord()) print ('Angle %s %s %s = %.3f degrees' % (a1.oslIdent(), a.oslIdent(), a2.oslIdent(), t)) c += 1 print '%d angles reported' % c import Accelerators.standard_accelerators as sa sa.show_reply_log()

1 0

Re: [Chimera-users] midas/6155 (Chimera error)
by Eric Pettersen 14 Aug '08

14 Aug '08

On Aug 14, 2008, at 1:23 PM, Christine Deillon wrote: > Hi Eric, > > I try to save a movie of a collagen molecule (cylinder shape) > just moving around its major axis (along the molecule) for about > 15 secondes, then I would like to play the movie in the microsoft > power point program > is it possible to do that with chimera? > > Christine Hi Christine, Yes, absolutely you can do that. There is a Chimera tutorial that covers movie-making in good detail here: Movie Making in Chimera The "Spin Movie" section of the tutorial is almost exactly what you are asking for. Issues with embedding movies into PowerPoint are at the very end of the Movie Recorder documentation page: problems in PowerPoint --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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version 1.2540 stability
by James Fethiere 14 Aug '08

14 Aug '08

Hi, I just upgraded my May version with the last version of Chimera for PC and am having stability problems. Every now an then (every 10' or so), chimera freezes and the cursor flickers for a couple of seconds; then all goes back to normal. Sometimes, it just crashes completely. Is this last version more demanding on memory? Thanks James

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Re: [Chimera-users] calculation of volume
by Elaine Meng 14 Aug '08

14 Aug '08

Hi Navnit, Sorry, I don't know of a way to calculate the van der Waals volume in Chimera. You can see the VDW volume, of course, by simply displaying the atoms in the sphere representation, but that does not give the volume value. In theory, you could get values closer to the VDW volume by calculating molecular surface with smaller and smaller probe radius. In practice, this tends to increase the number of surface calculation failures, and currently the smallest allowed probe radius value is 0.5 angstroms. Best, 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 On Aug 14, 2008, at 7:01 AM, Navnit Kumar Mishra wrote: > Hi Elaine; > > Thank you for so detailed description. I am interested in measuring > the compactness of the complex during the simulation, I think the > calculation of the ratio of molecular volume to van der waals volume > provides the compactness. I have tried the procedure as you > suggested to calculate the molecular volume, the value in replylog > file is in two digits precision, for these calculation can I get the > value in four digits precision. I am using latest chimera version > 1.2540. I can calculate the total van der waals volume using the van > der Waals radii for each atom excluding the hydrogen atoms. Is there > a way in chimera to calcualte the van der waals volume. I would be > thankful to you for any suggestions. > > with regards, > navnit

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Color zone with transparency
by Tom Goddard 14 Aug '08

14 Aug '08

Daniel Wilson wrote: > Hi Tom, > > ... > > The other thing I noticed is that you lose transparency on a whole volume when you color zone one region of it? or am I making something wrong? Is it not possible to have a single volume with two different colours and transparent? > > Thanks for you advice and kind offer, > regards > Daniel > Hi Daniel, When I make a transparent surface for a volume by pressing the volume dialog color button and making opacity 0.5 and then use color zone to color part of the surface (using a PDB model), the transparent part far from the zone remains transparent. Also works if select the volume surface and use the Actions / Surface / Transparency menu then color zone. What are the exact steps you use when it fails to preserve transparency? Tom

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Two transparent models
by Tom Goddard 14 Aug '08

14 Aug '08

On Aug 11, 2008, at 12:15 PM, Daniel Wilson wrote: > Dear Elaine, > > I realise that there have already been requests about fixing the bug > in Chimera for displaying two transparent maps at the same time, so I > guess I am just asking whether this is likely to be fixed anytime > soon? We are desperate to use this function for a figure for a paper :) > > THanks, > Daniel > > Dr. Daniel N. Wilson > > Gene Center Munich > Department of Chemistry and Biochemistry > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > 81377 Munich, Germany Hi Daniel, The incorrect transparency in Chimera when 2 or more models are transparent is very difficult to fix and will not be fixed any time soon. The trouble is that Chimera draws each model separately and it is not possible to correctly handle transparency without intermixing the drawing of parts of models (in depth order). If you use Chimera image saving in the POVray raytracing mode it will correctly show multiple transparent models. The trouble is that this takes a long time to render and adjusting the levels of transparency many times to get the right appearance may be tedious. It would be possible to make a script that combines the currently displayed map surfaces into a single model and hides all the original models so that multimodel transparency would appear correct on-screen. But the combined model would not update when you changed the transparency, color, ... settings of the separate maps. It would require rerunning the script that makes the single model. This would be tedious to use. But if you think it worth trying I can write the script and send it to you. It would not work for transparent molecular models (ribbons and atoms), just surfaces. Tom

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Hydrogens in proteins
by Walter Novak 13 Aug '08

13 Aug '08

Hi group, So I am struggling with hydrogens in proteins. I have neutron data which shows H-atom positions. Well, Deuterons, but here are the issues. If I open a pdb in Chimera with old school hydrogen names like HG1, how can I get it to write out the new ones (like HG11) without explicitly adding the hydrogens in Chimera? I don't want the atom positions to change. Also, I notice Chimera doesn't seem to handle deuterons optimally. Writing out the pdb moved the atom name column to the left one space and changed the atom type in the last column back to H. The problem is caused by Coot, which we use to perform real space refinement of atom positions, but to quote George Sheldrick, "I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle." Unfortunately, the point of my project is to see the hydrogens!!!! Thanks for any help you can offer, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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opening CASTp results
by Walter Novak 13 Aug '08

13 Aug '08

Hi all, How can I open my own CASTp results easily? The fetch command works great, but I need to submit some modified structures, and I don't see CASTp under file type in the open window. Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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calculation of volume
by Navnit Kumar Mishra 13 Aug '08

13 Aug '08

Hello all; I am trying to compute the molecular volume of a complex. Chimera first computes solvent-excluded surface area using MSMS. I see it does not compute the surface area of ligand. I am wondering if I can add the extra parameters or atom types for my ligand in some file. I would like to calculate the molecular volume from amber trajectory. Can some one suggest me how to automate the computation of surface area and molecular volume for each snapshot. If you know, please point out the article which describes the procedure for the volume calculation. with regards, Navnit

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representing 70s ribosome in ribbon
by Bong-Gyoon Han 12 Aug '08

12 Aug '08

Hi, I am tring to show the full 70S ribosome structure (PDB id: 1GIX and 1GIY) in ribbon representation with EM experimental density together. These PDB data consist of backbone atoms only (single alpha carbon for each a.a and single phosphate for each nucleotide). Ribbon option does not generate any ribbon (due to the incomplete information in the PDB?). Is there any way to show this molecule in ribbon format? I assume that backbone atoms must be enough to generate ribbons. BGHan

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IMOD model reader question
by William Jeffrey Triffo 12 Aug '08

12 Aug '08

I have an IMOD model (just a bunch of contours, representing filaments) that I tried to load into Chimera, but it threw some errors. This was odd, because it was a model I had augmented (added more contours) from a previous model that did load correctly (and I re-verified after the load error). is it helpful to forward the model file in question? best, -Jeff

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MatchMaker and Find Clash in nogui mode
by Ryan 11 Aug '08

11 Aug '08

Hi. I read in the archive (2004) that someone was looking to use MatchMaker in the nogui mode / command line, but that was not a possibility at the time. I am wondering if this ability has ever been implemented, and if so, how does one go about scripting this. Additionally, i would like to use the 'Find Clashes/Contacts' function in nogui mode. Is this possible? Thanks a lot, ryan

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protonating the protein
by Elaine Meng 11 Aug '08

11 Aug '08

Hi Francesco, > However, if you are using charges assigned in Chimera for something > (Dock Prep with AddH, Add Charge, and write Mol2 for input to DOCK > scoring grid calculations, for example), you would need to add the > protons in Chimera before assigning charges. This could be done by > selecting the carboxylate oxygens you want to get protonated (no more > than one per carboxylate group, of course) and changing their atom > types with the command: > setattr a idatmType O3 sel > prior to running AddH and Add Charge (alone or as steps in Dock > Prep). It is not necessary to rename the residues. Add Charge will > then recognize the neutral forms of ASP and GLU and use the > corresponding partial charges. I just tested this in the Chimera > production release, 1.2540 (July 9). The above is definitely true, you do not need to rename the residues in Chimera, but further tests reveal to get the correct charge distribution on the protonated carboxylic acid, the atom names also need to match the AMBER lib files: the protonated oxygen should be named OE2 (if glutamic acid) or OD2 (if aspartic acid) and the "free" oxygen should be named OE1/OD1. This will already be true sometimes, but not always. If you need to switch the atom names around before adding charges, it can be done by text-editing the PDB file or with commands. For example, you could change the name of an atom by selecting it and then using a command like: setattr a name OE2 sel After assigning charges, you can see the values as labels, for example: labelopt info charge la :6.a Again all this was tested in the production release 1.2540. Best, 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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Volume planes tool
by Elaine Meng 08 Aug '08

08 Aug '08

Hi Jeff, Here is another idea, still not exactly what you were asking for, but perhaps worth a look. You can use the Per-Model Clipping tool (under Tools... Depiction) to show a thin slab of the data, and you can interactively rotate and translate the slab any way you want relative to the data with the mouse. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/ per-model.html Just choose which model to clip, enable clipping, turn on slab mode and adjust clipping with mouse. You may also want to adjust the contour level in Volume Viewer. I tried it on emd_1274.map in the production release (1.2540). You can use it on solid, surface, or mesh volume displays. Below I attach an image of a slab surface display together with an unclipped solid display (a second copy of the same data). There is also a command to control per-model clipping in a script, mclip. It lets you specify location/orientation in the data coordinate system or the viewing coordinate system. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mclip.html Best, 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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Chimera: doubt on axes measurement
by Giovanni Cardone 07 Aug '08

07 Aug '08

Hi everybody, I have a doubt about my proper using the tool Axes for measuring angle between helices. After aligning two model and generating the axes corresponding to the helices of interest, I select them in the 'Structure Measurements' dialog windows. As you can see from a snapshot, they look properly selected. They are almost overlapping, but in the Reply Log I get the following info: col_best_001.pdb helix 10/col_best_005.pdb helix 2 crossing angle: 36.9 degrees, distance: 15.3 angstroms Beside the value of the angle seeming to me too high, shouldn't the distance between the helices be within few angs (at least according to how I interpret the documentation)? Probably I am missing something. Thanks in advance, Giovanni Cardone

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Protonating the protein
by Francesco Pietra 07 Aug '08

07 Aug '08

Hi: I am not saying anything new. I have a (for me) difficult problem of protonating a protein homology model (built with Modeller) where there are several halogen ion ligands. Actually I succeeded in getting a workable model. Chimera loads it and add hydrogens. I could even prepare the model for DOCK6, generating spheres. Now, however (and also because, before docking small ligands with DOCK6, I want to dock polypeptides, probably with DOT2) I would like to assign specific protonation states to certain carboxylic acids. That is, I want to create an overall model where certain facing carboxylic acids actually face as "carboxylate-carboxylic acid" or as "carboxylic acid-carboxylic acid", or, finally, as "carboxylate-carboxylate", the latter also with metal ligand in between or not. Question: to which extent can Chimera aid the task? And which other package (pdb2qr, H++, ...) may aid Chimera? Or no other package, but simply renaming the said residues in the pdb file and let Amber 10 (which is the package I'll use for MD, with ff99B ff for the protein) do the job of eliminating clashes? All that shows that I have no experience in selective protonation, and the halide ions (in the above said work, I have them simply under "ATOM" under the specific chain of the amino acid residues, not "HETATM", as the latter caused a lot or problems) create difficulty to protonating packages. Thanks for giving me a general guideline along with best moving. francesco pietra

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Chimera 1.2540 installer options and unattended installation
by Frank Thommen 07 Aug '08

07 Aug '08

Hi chimera-users, the Chimera installer seems to know some options and modifiers, but I could not find out what they mean: # ./chimera-1.2540-linux.exe -help UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Valid options are -tfupcz and -d <exdir>; modifiers are -abjnoqCLMVX. # Does anybody know what these options and modifiers do or where I can read about them? My motivation is, that I'd like to install Chimera in a non-interactive way (batchscript) in a non-standard location. Is there a way to achieve that? Thanks in advance frank -- Frank Thommen - Structures IT Management and Support - EMBL Heidelberg structures-support(a)embl-heidelberg.de - +49 6221 387 8353

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ConSurf display in Chimera
by Elaine Meng 06 Aug '08

06 Aug '08

Hello everybody, The ConSurf Server <http://consurf.tau.ac.il/> now provides results as Chimera Web data: a single click displays the color-coded query structure and multiple sequence alignment in your locally installed copy of Chimera. For a screenshot and example Web data file, see: http://www.cgl.ucsf.edu/chimera/consurf/consurf.html More about Chimera Web data: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.ht… Special thanks to Elana Erez and the Ben-Tal and Pupko groups at Tel Aviv University, and to Fabian Glaser. Enjoy! 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] mouse selection problem
by Eric Pettersen 06 Aug '08

06 Aug '08

Meikel Diepholz wrote: > Hi, > just a small problem I hope. > When I am selecting residues with ctrl +left mouse > button, chimera is always replacing the earlier selection, > independent on the selection mode I chose (append, subtract). > > Is it possible to change this? Hi Meikel, This behavior isn't a bug per se, but rather a deliberate design decision. We decided to not have the mouse selection honor the selection mode since it is possible to emulate all the selection modes directly with the mouse (except for intersect). If you hold down the Shift key as you are making a mouse selection then everything chosen with the mouse will have it's selection state toggled (selected items become unselected and vice versa), and other items will not have their selection state changed. So you can "subtract" by shift-control clicking/dragging on selected items, and you can "append" by shift- control clicking/dragging on unselected items. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Text statistics from Matchmaker
by nettles 04 Aug '08

04 Aug '08

I have found MatchMaker in Chimera an incredibly useful alignment tool. Thank you to the UCSF team! Now, I want to do do a mutliple alignment of many structures (~100) off a single reference structure, and output a text record of the residue pairings involved in the individual alignments along with their RMSD. In this particular case, I'll be looking at only small sequence variations of the same protein (with different drugs and cofactors). Accordingly, I would also like to output the RMSD of residue pairs beyond the alignment cut for relatively easy identification of regions having maximal variations. Advise is appreciated, With regard, Jim ________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine ________________________________________________________

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copy cmd in nogui script
by James A. Cleland 01 Aug '08

01 Aug '08

I was wondering if anyone was able to run chimera 'headless' using -nogui. I would like to be able to run the program from a script and without an X server, or against Xvfb or equivalent if necessary. My command line is /var/lib/chimera/bin/chimera --nogui --silent --script <scriptname> The script that I run sets the window size, element colors, rotates the image, and then does a copy file to save a ray traced PNG file. I have run this without -nogui and accepted the POV Ray license agreement. Adding -nogui results in the following output Error while processing <scriptname>: AttributeError: '_chimera.NoGuiViewer' object has no attribute 'x3dWrite' (see reply log for Python traceback info) Parse error at line 1: no element found My chimera version is "chimera production version 1 build 2540 2008/07/09". This is running on a linux machine, 2.6 kernel. Any suggestions you have would be appreciated. Thanks! James

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problem with the volume display in version 1.2540
by Magali Cottevieille 01 Aug '08

01 Aug '08

Hi, I have just installed version 1.2540 of Chimera (I had before version 1.2470). There is a problem with MRC and SPIDER EM volumes: see attached image: left a volume in the new Chimera; right the same volume with the old Chimera. Is it a bug, or linked to my configuration?? Thanks in advance, -- Magali Cottevieille, Ph.D. Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, 630 W 168th St, P&S Black Building 2-221 New York, NY 10032 Ph: (+1) 212-305-9521 Fax: (+1) 212-305-9500 Email: mc3077(a)columbia.edu magali.cottevieille(a)gmail.com

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import GRID contour map
by Sebastian Kruggel 01 Aug '08

01 Aug '08

Hi All, I try to import a contour map generated with GRID and saved as *.grd or *.cnt file. Trying to open th e*.grd file in chimera I get the error message Opening I:\strukturen\prep_modTemp\1j1b_DRY.grd I:\strukturen\prep_modTemp\1j1b_DRY.grd: UHBD file does not contain integer value 1 at bytes 96-99 using either little or big endian byte order. Found 46146 Done opening I:\strukturen\prep_modTemp\1j1b_DRY.grd With *.cnt I get file not found, because file is supposed to be a *.bmp. Does anybody have an idea, how to open my nice GRID contour map? Greetings Sebastian -- Sebastian Kruggel Institut für Pharmazie Raum 112 Bundesstr.45 D 20146 Hamburg Tel. +49(0)40 42838 3626 Hi All, I try to import a contour map generated with GRID and saved as *.grd or *.cnt file. Trying to open th e*.grd file in chimera I get the error message Opening I:\strukturen\prep_modTemp\1j1b_DRY.grd I:\strukturen\prep_modTemp\1j1b_DRY.grd: UHBD file does not contain integer value 1 at bytes 96-99 using either little or big endian byte order. Found 46146 Done opening I:\strukturen\prep_modTemp\1j1b_DRY.grd With *.cnt I get ‘file not found’, because file is supposed to be a *.bmp. Does anybody have an idea, how to open my nice GRID contour map? Greetings Sebastian -- Sebastian Kruggel Institut für Pharmaz ie Raum 112 Bundesstr.45 D 20146 Hamburg Tel. +49(0)40 42838 3626

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Re: [Chimera-users] question posted in chimera mailing list
by Elaine Meng 01 Aug '08

01 Aug '08

Hi Sebastian, Chimera does not read maps from GRID. Here are the map formats that Chimera knows about: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume Because you used filename extensions we assigned to other formats as shown in that table, Chimera tried to read the file as those formats (which it is not, hence the errors). Also, I do not know what is happening with your chimera-users subscription - maybe try to sign up again? http://www.cgl.ucsf.edu/ mailman/listinfo/chimera-users/index.html Best, 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 On Aug 1, 2008, at 12:54 AM, Sebastian Kruggel wrote: > Dear Elaine, > > I posted a message in the mailing list – and got the answer I > wasn’t member, though I am?! > So I just send it once more, directly to you, because you answered * > very > * helpful last time ;-) > > Message was: > Hi All, > > I try to import a contour map generated with GRID and saved as > *.grd or *.cnt file. > Trying to open th e*.grd file in chimera I get the error message > > Opening I:\strukturen\prep_modTemp\1j1b_DRY.grd > I:\strukturen\prep_modTemp\1j1b_DRY.grd: UHBD file does not contain > integer value 1 at bytes 96-99 > using either little or big endian byte order. Found 46146 > Done opening I:\strukturen\prep_modTemp\1j1b_DRY.grd > > With *.cnt I get ‘file not found’, because file is > supposed to be a *.bmp. > > Does anybody have an idea, how to open my nice GRID contour map? > Greetings > Sebastian > > Thanks in advance > Sebastian > > > > -- > > Sebastian Kruggel > Institut für Pharmazie > Raum 112 > Bundesstr.45 > D 20146 Hamburg > Tel. +49(0)40 42838 3626 >

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Re: [Chimera-users] suggestion for superimposig
by Elaine Meng 01 Aug '08

01 Aug '08

On Aug 1, 2008, at 7:35 AM, Srinath Thiruneelakantan wrote: > Hi, > I am microbiologist and wanted to know the strucutre of a protein > of M. tuberculosis, whose crystal structure has not been solved, > but its homologue in Bacillus has been. So by Swiss-modeller > generated a MODEL and downloaded it in PDB format. Now I wanted to > superimpose the generated model with of bacillus and with PDB of > truncated protein of E. coli. As I am not of bioinformatic > bakground, please suggest me how to get the FINAL output in PDB > format so can have a comarison of domains between these three > proteins. > Thank you, > Srinath Hi Srinath, Just open all of the PDB files in Chimera (for example, with File... Open). You can change the display if you want, for example with Presets... Interactive 1 (ribbons). Then you can use the MatchMaker tool (under Tools... Structure Comparison) to superimpose the proteins. Choose the "reference" structure on the left and one or more structures to match onto it on the right. It usually does not matter which one you use as the "reference" - try using the first one listed. In most cases, the default settings work well, so it is very easy: turn off "Show alignment(s)..." if you don't want to see the sequence alignments, but otherwise just click "Apply" to match the structures. It will take a few seconds to compute the alignments and then match the structures. Then you can compare the structures in Chimera, or write out PDB as mentioned below. If that does not give a good enough superposition, then you can try changing parameters. For details see the MatchMaker manual page (simply clicking "Help" on the dialog will open your local copy): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ matchmaker.html These tutorials have examples of superimposing and comparing structures: "Superpositions and Alignments" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ alignments.html "Structure Analysis and Comparison" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html Additional discussions about superimposing structures: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/ morph.html#superimposing http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ images.html#matching After the proteins are superimposed, you can write out the structures as one or more PDB files with "File... Save PDB" in the Chimera menu. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb 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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Distance Lines
by hsosa＠aecom.yu.edu 31 Jul '08

31 Jul '08

Hi , I want to make a solid line (with chosen color) between two atoms. Kind of like the line that appears when measuring distances between atoms, but without the distance legend. Is there an easy way to do that ? 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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PDB morphing
by Dougherty, Matthew T. 28 Jul '08

28 Jul '08

I have a complex structure in two conformations: resting and active. Each structure consists of 24 monomers, corresponding to 24 pdb files. Each monomer file between conformations matches in terms of atom numbers, chain ID, etc. I can morph a single monomer between conformations. I am having no success morphing all the monomers simultaneously between the conformations. Any suggestions on how to organize my data to overcome this? thanks, Matt Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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Distance between helices
by Thomas Goddard 28 Jul '08

28 Jul '08

HI Tom How do I compute and show the distance between 2 regions (2 alpha helixes) of 2 crystal structures (docked in the density maps), similar portions of each is already highlighted/selected to show the DNA binding region (without showing the atoms). THanks 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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Re: [Chimera-users] BIOMT matrix in Chimera?
by Elaine Meng 28 Jul '08

28 Jul '08

On Jul 27, 2008, at 10:38 AM, Francesco Pietra wrote: > > Hi Elaine: > After a brief playing with Multiscale Models, I was considering your > last suggestion below. I modeled each chain separately, also because > the X-ray diffr data show some conformational differences. Modeling > gave very good DOPE score. Now the problem is appending Chain B to > chain A, etc (each chain opens correctly in Chimera). I have a Python > script (not tried yet) to insert the Chain identifier (which Modeller > did not print), update the Atom serial number, and then append the > files. May I ask, in view of Chimera, if the "Atom number + 1" printed > in Modeller pdb files at column 80 can be left at it is, i.e. not > updated on appending the files? I forgot about that and I have already > problems enough with the script at my minimal level with Python. I > assumed that Python identifies the columns one unity less than PDB > numbering. Finally, do you know what means "1SG" at columns 74-76 of > Modeller pdb files? Hi Francesco, I don't know what MODELLER puts in those columns after "B- factor" (61-66, which may actually contain the "modeller error profile," since a homology model doesn't really have B-factors). Maybe you could ask the modeller people. However, for Chimera purposes they could be omitted (changed to blank). According to the description of ATOM lines: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html 67-76 is supposed to be blank, 77-78 element symbol, 79-80 charge. I believe Chimera tolerates lines without the last few columns, as long as the X,Y,Z coords are still there. If your files have stuff in the later columns, it might still be OK, just try opening them in Chimera to see. My suggestion of modeling the multimer from a template multimer would still incorporate the chain differences - you would still use A as the template for A, B for B, etc. However, I don't know how to make modeller do that. > Following the "appending" plan below, is it correct to > append pdb files lacking all hydrogens (as provided by Modeller) and > then rely on Amber's LEAP to complete the multimer? > francesco I don't know what you mean by "complete the multimer" - if just adding hydrogens, you can do that with AddH in Chimera (or addh command). That does not use leap/amber. Best, Elaine

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How to print molecular structures?
by �� 28 Jul '08

28 Jul '08

Hi all, I want to print 1000 molecular structures one by one. I am wondering if it is possible to print molecular structures by Chimera. If it is not, are there some other software can do this? Please kindly advice. Any answer would be appreciated! Best regards, Yolanda Guo Northeast Normal University

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Pointers to writing extensions in chimera
by Mario J. Borgnia 25 Jul '08

25 Jul '08

Hi all, I would like to try and write an extension to chimera. Could anyone give me some pointers on where to find the tools necessary to do so. Thanks Mario -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

3 2

BIOMT matrix in Chimera?
by Francesco Pietra 25 Jul '08

25 Jul '08

>From a homotrimer pdb template I have created (with Modeler) a homology model, with very good score, using a single subunit. Is it possible with Chimera to create the homology homotrimer, as this is what I need? To this concern, the original pdb for the template includes the BIOMT transformation matrix for both crystallographic and non-crystallographic operation. That is, the pdb includes as many identical chains to open directly the homotrimer for the crystallographic pose. Is that BIOMT matrix usable by Chimera for the homology model? Or the way ti take is another one? I used much technical language, well above - however - my expertise in these affairs. That in view of any help, for which I'll be most grateful. Thanks francesco pietra

2 1

nogui vrml export?
by Paul 25 Jul '08

25 Jul '08

Hello, Is there any way to export .vrml or .wrl in the nogui mode? The idea would be to run a script that would load a .pdb file and transform it into a few different representations and then export them. I saw in previous posts that there is no support for exporting images in this mode. Thanks, Paul

2 1

superimposing active sites
by Elaine Meng 24 Jul '08

24 Jul '08

On Jul 23, 2008, at 6:18 PM, Maria wrote: > Elaine, > I have created active sites by using the zone in > chimera for 72 proteins. Is there a way I can > do structural superimposition of the active > sites using chimera? > Thanks, > Maria Hi Maria, Sure, there are many, many ways to superimpose structures in Chimera. If the structures are homologous (have the same fold, usually also some sequence similarity), probably the easiest are these two methods: (A) MatchMaker tool (or the "matchmaker" command, which acts exactly the same way) - it creates a sequence alignment and then uses those alignment columns to superimpose the structures (B) if you already have a sequence alignment, you can open that in Chimera and use it to superimpose the structures With both (A) and (B) you would use the whole structures - it is OK if you are only displaying a zone as long as the other atoms are still there (are merely hidden, not deleted). Some other approaches can be used for either homologous or nonhomologous proteins: (C) "match" command - you specifically name the atoms you want to use for fitting in the command; for example, atoms from a few active site residues and/or from the ligand (D) interactive fitting "by hand" Links to more detailed information... Discussion and examples of more than one method: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#s… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#com… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/images.html#match… MatchMaker man page: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma… "matchmaker" command man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html "match" command man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Using a pre-existing sequence alignment: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/fr… (see "Structural Superposition" section) Best, 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

1 0

making MD movie
by bala 24 Jul '08

24 Jul '08

Hello freinds, While recording a MD movie or saving an image, chimera considers full screen ares. Is there any way that i can select a particular area in the screen and ouput the image or the MD movie accordingly. Thanks, Bala

2 1

Movie recording does not stop
by Tom Goddard 23 Jul '08

23 Jul '08

Hi Jean-Paul, The script you sent works for me with Mac X11 Chimera 1.2540 on Mac OS 10.4.11. I open two maps and the resulting movie is correct. You don't have any motion going on like a "roll" do you? Because the first line of this script "wait" with no frame count means that subsequent lines of the script will not be executed until all motion ceases. Likewise you have wait command with no frame count on the first two transparency setting lines. Tom Jean-Paul Armache wrote: > Thank you for the reply. It seems that I have today a lot of questions. > There is one more: > I have a script. When not in movie recording mode, it works fine. > However, if I input movie record and at the end movie stop and encode, > then at some point the script stops. Once it stopped with the labels, > so at the end I removed the labels. Now I have one map visible and I want > it to slowly get transparent to a point when it is no longer visible. > And here lies the problem. The script is fairly easy: > > wait; > movie record directory /Users/jean-paularmache/tmp-chimera; > > volume #1 transparency 0.0; wait; > volume #0 transparency 0.0; wait; > > > volume #0 transparency 0.05; wait 3; > volume #0 transparency 0.1; wait 3; > volume #0 transparency 0.15; wait 3; > volume #0 transparency 0.2; wait 3; > volume #0 transparency 0.25; wait 3; > volume #0 transparency 0.3; wait 3; > volume #0 transparency 0.35; wait 3; > volume #0 transparency 0.4; wait 3; > volume #0 transparency 0.45; wait 3; > volume #0 transparency 0.5; wait 3; > volume #0 transparency 0.55; wait 3; > volume #0 transparency 0.6; wait 3; > volume #0 transparency 0.65; wait 3; > volume #0 transparency 0.7; wait 3; > volume #0 transparency 0.75; wait 3; > volume #0 transparency 0.8; wait 3; > volume #0 transparency 0.85; wait 3; > volume #0 transparency 0.9; wait 3; > volume #0 transparency 0.95; wait 3; > volume #0 transparency 1.0; wait 3; > > > #movie finished > movie stop; > movie encode bitrate 12000 mformat avi output > /Users/jean-paularmache/Desktop/firstmovie.avi > > > > Ok, what happens is that Chimera generates endless amount of images. > Really, without cease. Now, if I do "movie stop;" from the command > line, it generates the avi file. However, the whole avi file consists > of one frame movie (meaning that even though it has the right amount of > frames, all are just one frame). > What is more surprising is that with other scripts this transparency > works. It is just right here that it doesn't want to cooperate. Could you > think of any reasons it might be behaving like that? > > > Best regards, > > Jean-Paul Armache

4 6

StrucMeasure and distance
by Jean Didier Pie Marechal 23 Jul '08

23 Jul '08

Dear all, a small question. I know how to calculate the distance between two atoms calling the "distance" command and I generally use it embedded in the scripts I write. However, this time, I'd like to have access through my script only to the values of the distances (nothing related to the display) in order to stock them. I thought I would find my way through by using the StructMeasure module, but I am not able to do so. How could I just have a return of the distances between two atoms in the shell? Thanks a lot, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Agost 8, 2007 9:00 pm Assumpte: Chimera-users Digest, Vol 52, Issue 6 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. writing translation/rotation (Thomas C. Marlovits) > 2. Re: writing translation/rotation (Elaine Meng) > 3. Re: writing translation/rotation (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 8 Aug 2007 14:19:43 +0200 > From: "Thomas C. Marlovits" <marlovits(a)imp.univie.ac.at> > Subject: [Chimera-users] writing translation/rotation > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <BAFCFCAA-D911-4E0C-8F5E-B41430E8E1B6(a)imp.univie.ac.at> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > am looking for an analysis tool in Chimera that would write out - > let's say a matrix for translation/rotation of a pdb-file in > respect > to another one. > > Usage: would like to align chain A and chain B present in a pdb- > file > and want to know which translation/rotation matrix has to be > applied > in order to convert the non-aligned pdb-coordinates of chain B to > the 'new" aligned pdb-coordinates. > > Thanx for your help, > -Thomas > > > > -------------------------------------------------------------------- > ---- > ------- > > Thomas C. Marlovits, PhD, M.A.S. > > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences > (IMBA) > > Dr. Bohr-Gasse 3 > Room IMBA/6.02 > A-1030 Vienna > Austria, Europe > > fone: (++43-1) 79044-4630 > fax: (++43-1) 79044-4401 > email: marlovits(a)imp.univie.ac.at > > > >

3 2

Making a spin movie
by Tom Goddard 23 Jul '08

23 Jul '08

Hi Andy, Here is a Chimera command script to make a movie that rotates the displayed models 360 degrees in 3 degree increments (120 frames) and writes the movie in Quicktime format (*.mov). movie record turn y 3 120 wait 120 movie stop movie encode output /tmp/movie.mov mformat mov bitrate 6000 Put this in a file with suffix *.cmd (e.g. spin.cmd) and open it with Chimera File / Open... or the open command to create the movie. Tom Anindito Sen wrote: > Hi Tom > Thanks for the reply. > > in the crystal structure- the region of interest (selected and > highlighted) lies in the interior. The idea is to make a movie of the > crystal structure rotating around the Y axis and one can visualize the > region of interest in a better manner. > > Therefore how can I generate a movie of this kind. > > Thanks > Andy

1 0

Electron density map around selected residues
by Miles Pufall 23 Jul '08

23 Jul '08

Hello - I have a couple of structures depicting a complex where the function of a loop appears to be important, depending on conditions. An overlay of structures solved under these two conditions shows subtle differences, but an examination of omit maps for this loop overlap where the model is built, but show quite different extra density, suggesting different alternate conformations. I am trying to make a figure of this loop with the 2fofc and omit maps overlaid on this loop under the two conditions. The figure, with a model and two electron density maps, can get messy. I would like to show just the electron density surrounding just the loop. Can you recommend a way to do this in chimera? Thanks - Miles Miles Pufall UC San Francisco

3 2

vista chimera 1.2540 R6025-pure virtual function call error when opening pdb or mrc file
by Nils Woetzel 22 Jul '08

22 Jul '08

Hi, I have problems with chimera 1.2540 win32 and 1.2539 win32. it is working in version: 1.2524 win32 I installed it an windows vista business sp1. I have also installed visual studio 2008 (9.0). When I try to open either pdb or an mrc file I get the same error window: Title: Microsoft visual c++ runtime library text: Runtimje Error! Program: C:\Program Files\chimera\bin\pythonw.exe R6025-pure virtual function call. the debug command line option just brings: initializing graphics create application loading Tix loading Pmw creating main window creating menus creating toolbar creating lenses initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: 255 Press return or enter to to exit i try to open the pdb file (different files) before the return code: 255 I am not sure if the error actually comes from python.exe - but i could not find anything when searching for it. http://support.microsoft.com/kb/125749 explains the error, but i am not sure how to debug python code Is there a problem with that version of python or chimera with a visual studio installation or this runtime library error appearing independently of having visual studio installed or not. But the older release is working just fine: 1.2524 win32 so some new feature in chimera probably causes the error and might only show up in my environment?! Thanks Nils Woetzel Vanderbilt University

3 2

surface rendering
by Peter Lewis 22 Jul '08

22 Jul '08

Dear Chimera-Users I've recently changed my computer to a quad core system which runs Red Hat and virtual Windows. I've installed chimera (32 bit) on both linux and windows. I have tried using chimera downloads posted in both June and July this year but cannot get surface rendering to work for either operating system. Is this a bug with recent versions of chimera, and if so, how do I fix it, or is it a bug with my new system? Any help gratefully appreciated. Peter A/Prof Peter Lewis Molecular Microbiology Group School of Environmental and Life Sciences University of Newcastle Callaghan NSW 2308 Australia Ph: +612 4921 5701 Fx: +612 4921 5472

2 1

Movie contains overlapping windows
by Tom Goddard 21 Jul '08

21 Jul '08

Hi Jean-Paul, Yes movie recording will include windows that overlap the Chimera graphics window. This is an unfortunate limitation of the Chimera image saving caused by it capturing images directly from the screen. On some platforms an overlapped window may not appear because the contents of the graphics window are saved even when another window overlaps. But that is not the case on most platforms. So in most cases the machine cannot be used for other purposes when a movie rendering is in progress. We have been interested in eliminating this limitation for some years but Greg Couch who handles image capture has not had time to get to it, If you use raytracing for the movie capture then it does not matter if the Chimera window is covered. But raytracing takes much longer to render. Tom Jean-Paul Armache wrote: > Hello again, > > I re-checked the spider loading, and now it seems to work. I don't > know why it did not previously. > > I have another question though. I have two versions of Chimera on my > computer now. I am using Chimera X Window to generate movies, > because in respect to the Aqua version, if I start another application > (like Keynote, web browser etc), the movie does not contain any parts of > the screen on top of it. > If I use the Aqua version (and on Linux is the same), it includes the > currently on-top graphics into the movie. Is there a way to not do so in > Aqua? > > Best regards, > > Jean-Paul Armache >

1 0

10.5 mac Chimera hangs on resize
by Eric Pettersen 21 Jul '08

21 Jul '08

On Jul 21, 2008, at 4:32 PM, Jean-Paul Armache wrote: > Submitter Name: Jean-Paul Armache > Platform: (X11) Darwin 9.4.0 i386 > Chimera Version: production version 1 build 2540 2008/07/09 > Description > well, the X window tends to hang just after manually resizing the > window. Hi Jean-Paul, I was able to reproduce this and was able to come up with two solutions. One is to resize carefully. In particular, do not release the mouse button until you have stopped the mouse. I find that this always avoids the hang. The other solution is to upgrade your X11.app to the 2.3.0 version (as a prerequisite you need to be at OS X 10.5.4. or later). You can download 2.3.0 from here: http://xquartz.macosforge.org/trac/wiki/X112.3.0 --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Problems saving eps files on Windows
by Julianne Chung 21 Jul '08

21 Jul '08

Hi, I am having trouble saving images in Chimera and was hoping that you may be able to help me out. I am running the latest version of Chimera on Windows. I have a molecule that I want to save as an eps file. I got to File --> Save Image --> Save As -->change the file type to eps and click Save, but no eps file appears in the directory I specified. Jpeg, png and tiff all work fine, but I can't get eps and ps to work. I've installed Ghostscript too, but that doesn't seem to help. Any suggestions are appreciated, Thanks, Julianne Chung Emory University

2 1

Re: [Chimera-users] Possible image saving bug
by Walter Novak 21 Jul '08

21 Jul '08

Hi Elaine, I agree that some colors are shinier than others. Also, my brightness was not zero, but was the default of 1. I think however, I have tracked the issue down to the position of my lights. I had them pretty straight on and resetting this position gives the pov-ray shininess I was expecting. Thank you, Wally On Jul 17, 2008, at 9:29 PM, Elaine Meng wrote: > Hi Wally, > on to problem #2. > > I was unable to reproduce this problem. Are you sure that the > "brightness" is >0? If brightness is zero, there are no > highlights. Below are two images, the top with shininess 128 and > brightness 10, the bottom with shininess 128 and brightness 0. > Actually now that I look at it carefully, the bottom one confuses me > because the cyan things are still shiny, so I'm cc-ing the others > (Greg, any explanation??). The other colors in the bottom image are > non-shiny as expected, however! > > Best, > Elaine > > <imagebright10.png> > > > <imagebright0.png> > > > Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

2 1

<< two questions about Chimera >>
by Hatuey Hack 21 Jul '08

21 Jul '08

Hi all, I have to questions about Chimera: 1st.- Is it possible to search the mailing list to avoid doing questions that were already answered? 2nd.- As I do not know the answer to the first question, I would like to know how I can visualize double and triple bound as well as aromatic rings explicitly within Chimera. Regards, Hatuey

3 2

Morphing aligned maps
by Tom Goddard 21 Jul '08

21 Jul '08

Hi Haixin, The morph map tool just linearly interpolates the two volume 3-d arrays at each grid point. So it does not work correctly if you have moved one map relative to the other since it ignores their relative positioning. To use it in this case you need both maps to use the same grid so you have to "resample" one map. That is you recompute that map on the same grid as the other map using interpolation. The command to do that is "vop", for example, vop #1 resample onGrid #0 modelId #2 Now use morph map between model #0 and the resampled volume #2. Morph map doesn't provide a way to morph between more than 2 maps. That would be useful. You can use it to morph the separate pairs of maps 0 -> 1, then 1 -> 2. You can almost record a movie of this using the following trick. First record 0 -> 1 but when it asks you to save the movie leave that dialog alone (don't cancel since that will erase the saved image frames). Then record 1 -> 2 and then save the movie. Frames from both morphs will be included in the movie. The problem is that each morph plays both forward and backward so you get 0 ->1 -> 0 jumps to 1 -> 2 -> 1. You could avoid the looping with a small modification to the Morph Map code. You would edit chimera/share/MorphMap/gui.py adding a few lines in the next_frame_cb() routine. if next_f >= fmax: next_f = fmax self.step_direction = -1 would become if next_f >= fmax: next_f = fmax self.step_direction = -1 if self.recording: self.finish_recording() Keep indentation as shown since that is important in Chimera. Tom Haixin Sui wrote: > Hi, Tom > > ... > I have a map morphing question. I manually aligned two maps in Chimera > in order to do a map morphing for my presentation. However, the map > morphing does not happen at the aligned positions but shifted the > second map back to the position before the alignment. I wonder how > should I get arroudn this problem. Saving the second maps relatie to > the first and read it in again? > > Meanwhile, I have several maps I want to do map morphing and show > changing in between them. It will be great if chimera can work with > more than one maps and show the changed from map#1 to map#2, and then > #3 ... This feature can be helpful when people want to show several > conformational changes. > > Haixin

1 0

selection of a specific region from different chains
by Tom Goddard 21 Jul '08

21 Jul '08

Hi Andy, Use a command like "select :100-200 to select residues 100 through 200 in all chains. Tom Anindito Sen wrote: > HI Tom > I have a 5 separate chains (of the same crystal structure) docked > along my filament reconstruction. How do I select and highlight a > certain length of amino acids from each and every chain. Problem > happens when I try to select a region of the second or 3rd chain, > which "deselects" the pervious selection. > > Best Andy

2 1

3 volume histograms
by Tom Goddard 18 Jul '08

18 Jul '08

Hi Haixin, Chimera can display any number of volume data sets. But it only shows 3 histograms in the volume dialog, the 3 whose settings were most recently changed. You can use the Data menu on the volume dialog to show the histogram for a different volume (replacing the least recently used of the current 3 histograms). If you want a different maximum number of histograms (like 1 or 5) there is a setting in the volume dialog Data Display Options panel for "Maximum number of histograms". To make this new value the default use the Features menu Save Default Dialog Settings. Tom > >> *From: *Haixin Sui >> *Date: *July 17, 2008 6:12:29 PM PDT >> >> Installed the newest version and found a problem. This version can >> only work with at most three density maps. When you have four or more >> density maps read in, the volume viewer window will only display the >> control for the last three maps. >>

1 0

Distance between atoms using Python
by Tom Goddard 18 Jul '08

18 Jul '08

Hi Ed, Attached is some Python code for controlling ligand display based on distance between two atoms. Tom Edward Brignole wrote: > > Tom, > > Thanks again for your help with that atom display. Got another > MDtrajectory issue for you. I've got a ligand in each of 10 domains > in the structure and I only want to display the ligands in the frames > that have less than a certain distance between a particular atom in > the ligand and a particular atom in a neighboring domain. > > The distance command won't work for me because all it does is add a > distance to the distance dialog when I need it as a variable in the > script to evaluate with "if distance < 10: display atomspecs" > > Sorry to keep bugging you with these things but I assure you it isn't > without trying for several hours to no avail before finally resorting > to asking. > > Ed > def atom_distance(spec1, spec2): from chimera.specifier import evalSpec atom1 = evalSpec(spec1).atoms()[0] atom2 = evalSpec(spec2).atoms()[0] d = atom1.xformCoord().distance(atom2.xformCoord()) return d from chimera import runCommand if atom_distance('#0:15.B@C4', '#0:7.A@N3') >= 10: runCommand('display #0:SPM') else: runCommand('~display #0:SPM')

1 0

center of mass for multiple models.
by Jean Didier Pie Marechal 18 Jul '08

18 Jul '08

Hi everyone, I am stuck with a script and my mistake seems to come from my poor understanding on how to treat atom coordinates with multiple models. I join to this e-mail a chimera file with a simple system to illustrate my problem. In the file, I have two indentique phenyl moleculer each of them in different models and I would like to stock the center of mass of both molecules in a list. I wrote this very simple script using the way of calcuting the center of mass you provided me recently. import chimera import BuildStructure from chimera import runCommand as run from chimera import selection, Vector from chimera import openModels, Molecule, Point #Stock the two fragments in the list FRAG run("select") frag=[] for i in chimera.selection.currentResidues(): frag.append(i) #Calculate center of mass of both entities #stocked in the list MAS mas=[] for i in range(len(frag)): sum=0 center = Vector(0, 0, 0) for a in frag[i].atoms: sum += a.element.mass center += a.element.mass * Vector(*a.coord().data()) mas.append(Point(center[0]/sum,center[1]/sum,center[2]/sum)) print i,mas[i] The results I have are 0 20.0465 70.3735 23.9063 1 20.0465 70.3735 23.9064 Basically, the coordinates of the center of mass are the same? What did I do wrong in the way I treated this problem? Thanks a lot for any answer, All the best JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dijous, Juliol 17, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 63, Issue 17 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Possible image saving bug (Greg Couch) > 2. Possible image saving bug (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 17 Jul 2008 10:35:26 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Possible image saving bug > To: Walter Novak <wnovak(a)brandeis.edu> > Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.OSF.4.63.0807171001010.1939086(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Thu, 17 Jul 2008, Walter Novak wrote: > > > Hi All, > > > > I submitted a bug report on this, but the behavior is both odd > and > > reproducible for me. Using the latest production release and > trying to save > > an image using supersampling, the image is not stitched back > together > > appropriately. It is odd, because it always happens for a certain > session > > file I have. It doesn't seem to happen if I open a new molecule > and make a > > picture. I can provide the session file if needed. First image is > using 3x3 > > and second is 6x6. > > I see from the bug report that you're using Mac OS X 10.5. We are > having > "issues" with the new X11 application in 10.5. And we have seen > that > slightly different X11 applications are installed on otherwise > identical > Macs and that reinstalling from the Mac OS X Install Disk fixed a > non-chimera bug. > > Also, I have read on the web that if you install the 10.4 X11 > application > on 10.5, then OpenGL applications will work better. Since that is > not an > option for everyone, we are spending more time to improve the Aqua > version > that is available as a Snapshot release on the chimera download > page. It > has different bugs, but the graphics is better. So you should try > it out > and see how well it works for you. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jul 2008 10:40:13 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: [Chimera-users] Possible image saving bug > To: wnovak(a)brandeis.edu > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <B15630DD-299C-4B48-A8B4-469FA8995872(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Wally, > I also had this tiling problem. We think it may be something about > > X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not > been > observed with 10.4/X11. > > Two workarounds that were successful in my case (I don't know if > they > will fix all instances of the problem): > > (A) simply show the Command Line before saving the image. I tried > hiding it again after that, but then the problem reoccurred, albeit > in > a more subtle fashion. > > (B) save the session, restore it in the aqua version of Chimera > (still > on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) > is > easier, but I didn't discover that one until this morning, after > receiving your mail. > > I hope these solutions are general! Sorry about the inconvenience, > 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 > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 63, Issue 17 > ********************************************* >

2 1

center of mass for multiple models
by Jean Didier Pie Marechal 18 Jul '08

18 Jul '08

Hi everyone, I am stuck with a script and my mistake seems to come from my poor understanding on how to treat atom coordinates with multiple models. I join to this e-mail a chimera file with a simple system to illustrate my problem. In the file, I have two indentique phenyl moleculer each of them in different models and I would like to stock the center of mass of both molecules in a list. I wrote this very simple script using the way of calcuting the center of mass you provided me recently. import chimera import BuildStructure from chimera import runCommand as run from chimera import selection, Vector from chimera import openModels, Molecule, Point #Stock the two fragments in the list FRAG run("select") frag=[] for i in chimera.selection.currentResidues(): frag.append(i) #Calculate center of mass of both entities #stocked in the list MAS mas=[] for i in range(len(frag)): sum=0 center = Vector(0, 0, 0) for a in frag[i].atoms: sum += a.element.mass center += a.element.mass * Vector(*a.coord().data()) mas.append(Point(center[0]/sum,center[1]/sum,center[2]/sum)) print i,mas[i] The results I have are 0 20.0465 70.3735 23.9063 1 20.0465 70.3735 23.9064 Basically, the coordinates of the center of mass are the same? What did I do wrong in the way I treated this problem? Thanks a lot for any answer, All the best JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dijous, Juliol 17, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 63, Issue 17 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Possible image saving bug (Greg Couch) > 2. Possible image saving bug (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 17 Jul 2008 10:35:26 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Possible image saving bug > To: Walter Novak <wnovak(a)brandeis.edu> > Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.OSF.4.63.0807171001010.1939086(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > On Thu, 17 Jul 2008, Walter Novak wrote: > > > Hi All, > > > > I submitted a bug report on this, but the behavior is both odd > and > > reproducible for me. Using the latest production release and > trying to save > > an image using supersampling, the image is not stitched back > together > > appropriately. It is odd, because it always happens for a certain > session > > file I have. It doesn't seem to happen if I open a new molecule > and make a > > picture. I can provide the session file if needed. First image is > using 3x3 > > and second is 6x6. > > I see from the bug report that you're using Mac OS X 10.5. We are > having > "issues" with the new X11 application in 10.5. And we have seen > that > slightly different X11 applications are installed on otherwise > identical > Macs and that reinstalling from the Mac OS X Install Disk fixed a > non-chimera bug. > > Also, I have read on the web that if you install the 10.4 X11 > application > on 10.5, then OpenGL applications will work better. Since that is > not an > option for everyone, we are spending more time to improve the Aqua > version > that is available as a Snapshot release on the chimera download > page. It > has different bugs, but the graphics is better. So you should try > it out > and see how well it works for you. > > Greg Couch > UCSF Computer Graphics Lab > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Jul 2008 10:40:13 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: [Chimera-users] Possible image saving bug > To: wnovak(a)brandeis.edu > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <B15630DD-299C-4B48-A8B4-469FA8995872(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Wally, > I also had this tiling problem. We think it may be something about > > X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not > been > observed with 10.4/X11. > > Two workarounds that were successful in my case (I don't know if > they > will fix all instances of the problem): > > (A) simply show the Command Line before saving the image. I tried > hiding it again after that, but then the problem reoccurred, albeit > in > a more subtle fashion. > > (B) save the session, restore it in the aqua version of Chimera > (still > on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) > is > easier, but I didn't discover that one until this morning, after > receiving your mail. > > I hope these solutions are general! Sorry about the inconvenience, > 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 > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 63, Issue 17 > ********************************************* >

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Possible image saving bug
by Elaine Meng 17 Jul '08

17 Jul '08

Hi Wally, I also had this tiling problem. We think it may be something about X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not been observed with 10.4/X11. Two workarounds that were successful in my case (I don't know if they will fix all instances of the problem): (A) simply show the Command Line before saving the image. I tried hiding it again after that, but then the problem reoccurred, albeit in a more subtle fashion. (B) save the session, restore it in the aqua version of Chimera (still on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) is easier, but I didn't discover that one until this morning, after receiving your mail. I hope these solutions are general! Sorry about the inconvenience, 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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Possible image saving bug
by Walter Novak 17 Jul '08

17 Jul '08

Hi All, I submitted a bug report on this, but the behavior is both odd and reproducible for me. Using the latest production release and trying to save an image using supersampling, the image is not stitched back together appropriately. It is odd, because it always happens for a certain session file I have. It doesn't seem to happen if I open a new molecule and make a picture. I can provide the session file if needed. First image is using 3x3 and second is 6x6. Also, when using pov-ray, the balls are completely devoid of shininess, regardless of my shininess settings (I set it to 128). That is the last image. Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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Coloring a binding site
by Tom Goddard 16 Jul '08

16 Jul '08

Hi Andy, To color a binding site I would select the ligand (DNA in your case) then select all the nearby atoms using Select / Zone..., then use Actions / Color to color those atoms. Tom Anindito Sen wrote: > Another question - I need to color a portion of the crystal structure > differently (ribbon diagram) in order to indicate the binding sites of > the DNA with the protein molecule and how do I do that. > > Thanks and Best Wishes > Andy

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possible bug
by Ben Keshet 16 Jul '08

16 Jul '08

Hi, when I un-select atoms, I had some weird long lines crossing my structures across (picture attached). I restarted the program how ever the same exact thing happened again. The two files that were opened worked perfectly in the past and before I un-selected the atom (ctrl+left click in the "air"). Other wise - great software. Thank you. Ben

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Re: [Chimera-users] History feature for command line between sessions
by Eric Pettersen 15 Jul '08

15 Jul '08

> On Apr 17, 2008, at 8:52 AM, Boaz Shaanan wrote: > > > The history of commands in the command line mode is retained > > within a session and is very convenient but I was wondering whether > > there is a feature that will allow you to recall commands from > > previous sessions (such as in O for example - it generates an .o- > > history file which is being constantly updated and is very > > convenient). If not, is it possible to request the addition of such > > a feature ? There are many ways to implement this of course and I'm > > sure you'll find the best way, if it's not already there lurking in > > Chimera. > > Hi Boaz, > Good idea -- and shouldn't be too hard to implement. I was thinking > of remembering the last 100 commands. Will that be enough you think? > > --Eric This is implemented now. It should show up in the next daily build that works. Only remembers 60 by default, but that number is changeable in Preferences. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Can't type in Chimera
by Thomas Goddard 15 Jul '08

15 Jul '08

Hi Andy, I don't know how Chimera could get in a state where it will not accept any typed input. Do you recall the last thing you did in Chimera before it stopped accepting key input? If I were stuck in this situation and could not type a file name to save the Chimera session I would create an empty file with the session file name I wanted using a text editor. Then choose that file with the mouse in the Chimera session saving dialog. Desperate measures. If you can reproduce the problem please tell me how and I will fix Chimera. Tom Anindito Sen wrote: > HI Tom > > I have installed the latest version of Chimera on my LINUX box Fedora > Core 6.0. I faced a strange problem- while carrying out a docking of a > crystal structure in a density map I was using the command line for the > differnt movements and controls. After some time I am unable to type > anything on the command line. Infact I am even unable to save the > session as I cannot type the "NAME" of the session. I checked my keyboad > and typed on the terminal and on text editiors and it worked normally. > > Waiting for your response. > > Best Wishes > 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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Re: [Chimera-users] reg. ribbon reprsentation
by Elaine Meng 15 Jul '08

15 Jul '08

>> >> Greetings. I have already posted a similar question on the forum >> previously and hence i am writing to your email. My problem is when >> i open a protein pdb, i get wonderful ribbon representation when i >> opt for it. But when i give a protein pdb with only a CA atoms/ >> CA,C,N atoms, i dnt get the ribbon representation. I understand >> that ribbon is constructed by considering CA,C,N,O and OXT atoms. >> What i did was that i simply removed O and OXT atoms by going >> through Tools--> Depiction --> Ribbon style Editor. It may be a >> wrong idea to do that. But i would appreciate if you could write me >> some way to draw the ribbon for protein having only CA or CA,C,N >> atoms IF POSSIBLE. >> >> Regards, >> Bala >> Hi Bala, If you have N-CA-C atoms, it actually works pretty well if you open Ribbon Style Editor, go to the "Residue Class" tab, choose "amino acid" but then change the "Orientation atom" to C instead of O, and Apply. (You still need to show ribbon if you didn't already do that.) You can save and name the new residue class for re-use in some later Chimera session if you want. The resulting ribbon looks the same to me as the standard ribbon made from N,CA,C,O (I tested this by writing a PDB of only the N,CA,C atoms from a complete structure, reading it back in, and experimenting with Ribbon Style Editor). http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon… If you have CA atoms only, then there is no way to figure out the plane of the ribbon - it does not work to set both the "Guide atom" and "Orientation atom" to CA. Unfortunately this prevents you from displaying "licorice" ribbons even though they don't use an orientation plane. My only solution in this case is to use some program to build the additional atoms from the CA trace, for example this web server: http://www.ebi.ac.uk/Tools/maxsprout/index.html 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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Re: [Chimera-users] email address
by Khanei Mkumeni 14 Jul '08

14 Jul '08

khmlukundo(a)gmail.com

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SpaceNavigator with Linux
by D. Greening 14 Jul '08

14 Jul '08

Hi, I just downloaded Chimera 1.2540 and was pleased to see that the SpaceNavigator 3-D mouse is now supported for Windows and Mac. Will those of us who use Linux be able to use our SpaceNavigators with Chimera any time soon? Thanks. D. Greening Memorial University of Newfoundland

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drawing molecules
by Kathleen.Zocher＠ernaehrung.uni-giessen.de 14 Jul '08

14 Jul '08

Dear Sir or Madam, I`ve just one question concerning some special tools of Chimera. Is it possible to draw small molecules (ligands) within chimera? I can not find some information for this problem in the manual. For further docking experiments I just need a 3D-structure which is minimized (in a mol2 file). Many thanks in advance! Sincerely yours Kathleen Zocher ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Question about bond length modification
by Benjamin G.S. Horsman 14 Jul '08

14 Jul '08

Hello, I have what appears to be simple problem but is I can't find the solution in previous mailing list queries. My problem is that I am unable to modify the lengths of any bonds in a PDB molecule. I am rather frustrated with myself over such a stupid problem, having tried dozens of times over dozens molecules to get it right but to no avail. Any possible solutions from the community? I am using MacpyMol to generate PDB structures and Chimera v1 build 1470. Thanks for any help, Ben

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Re: [Chimera-users] [Chimera-announce] Chimera production release
by Elaine Meng 13 Jul '08

13 Jul '08

Hello Yao, Don't worry, the new versions still include the ability to fit map in map. It is simply that two tools were combined into a new tool with a slightly different name. Changes in this production release relative to the previous one include: "Fit Model in Map" and "Fit Map in Map" (Volume Data) — * merged into new "Fit in Map" tool * can update fit values continuously * can simulate map from atomic coordinates, report map-map correlation current documentation: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/ fitmaps/fitmaps.html Best, 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 On Jul 12, 2008, at 11:49 PM, Yao Cong wrote: > Hello Chimera developer, > > Appreciate your great efforts to make Chimera an perfect tool for > Cryo-EM study. > > I and many of my colleges notice that in your latest versions, you > omit the "fit map into map" module, which is very convenient in > many cases. Is there a specific reason for that? And we all > consider it will be very helpful if you could add this function > back in your next version, maybe daily release? Otherwise, we still > keep the old version to have that function and meanwhile install > your newer version to enjoy the newer functions. > > Thanks, > Yao > ----------------------- > Yao Cong, Ph.D. >

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Creating abridged multimer
by Francesco Pietra 12 Jul '08

12 Jul '08

I am posting again after having once again subscribed In order to create an abridged multimer made of non covalently bound subunits (from available pdb of subunit) which is the preferable route? (1) Load the monomer, delete substructures, and then assemble an abridged multimer? Are the headers furnished with the monomer OK for the abridged subunit? (2) Build the unabridged multimer and proceed to simplify each subunit the same way? Thanks francesco pietra

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distance measurements on surfaces
by Daniel Hautzinger 10 Jul '08

10 Jul '08

Dear all, from the Volume Visualization Tour, I discovered the topography command that now allows me to dsiplay atomic force microscopy data (basically bitmap images with grey scales representing height). In that way I got some very nice images. I also found out how to scale the voxel size, so the scale of the structures should be correct. To test this, and to be able to add some length markers, I wanted to measure distances on the surface generated by the topography command. But while that seems possible for volume data (by setting markers), I had no success with the surface representation of my data nor the original image (which is handled as kind of a volume, but a single slice) when it came to setting markers or measuring distances in another way. Did I miss anything, or is that just not possible? I am using build number 2509, because of the topography feature. Setting markers is described as working by setting the marker in the first maximum in the line of sight at the click position. For surfaces, you could just take the position of the visible pixel clicked. Or maybe it is possible to convert surfaces to volumes? Thank you for your help Daniel Hautzinger

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changing selection color
by Michael DiMattia 10 Jul '08

10 Jul '08

Hi all, I have a quick question regarding a figure I am trying to make. I have a multi-chain protein loaded with each subunit surface-rendered individually. We wanted to find a way to highlight the outline of one of the subunits in the 3d surface rendering and selecting the surface of the chain works really well for this in Chimera. The familiar green outline highlights the subunit well, even though I realize this is probably not the primary purpose for such highlighting. I imagine it is just to let the user know what is selected. But if i were to use the selection highlighting to show such an outline in a figure, i was wondering if it is possible to change the color of the selection outline from green to any other color or if it is possible to change the width of the outline. I realize it's a long shot, but thought I'd ask anyway in case anyone has tried this before. Many thanks Mike DiMattia

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Chimera production release
by Elaine Meng 10 Jul '08

10 Jul '08

Hi everybody, A new production release, version 1.2540, is now available from: http://www.cgl.ucsf.edu/chimera/download.html#production Many improvements and new features have been added since the previous production release (Nov 2007), as detailed in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html For the time-challenged, here are just a few of the reasons you may want to use the new version: 1) new fetch types: - comparative models from ModBase - protein pocket data from CASTp database - small molecule structures from Pub3D - small molecule structures built from SMILES strings 2) surface improvements: - increased reliability - surface areas automatically calculated - Actions menu, other tools work on more types of surfaces 3) appearance: - default lighting changed to improve POV-Ray results - larger default scale - helix ribbon insides can be colored separately - 2D labels can include Greek letters and other symbols 4) new tools: Axes, EnsembleCluster, Solvate, Structure Diagram 5) new commands: export, mclip, molmap, perframe, ribinsidecolor, shape, solvate, topography, vop See the release notes for details. The production release includes versions for Windows, Mac/X11, Linux, SGI IRIX, and HP Tru64. The Mac Aqua version has been improved significantly, but for now remains a snapshot download: http://www.cgl.ucsf.edu/chimera/download.html#snapshots Enjoy! The Chimera Team

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Multiscale models and surface coloring
by David Sept 09 Jul '08

09 Jul '08

I need to create a series of images of large protein complexes, and since it is tedious to do this through the menus, I am trying to script this for Chimera. I want to create low-res, EM looking surfaces and color the individual protein chains different colors. So far, I can read in multiple structures and create the surfaces, but I can't figure out how to change the coloring. Here's what I have: ---- test.py ------- from chimera import openModels m = openModels.open('model-1.pdb')[0] import MultiScale d = MultiScale.show_multiscale_model_dialog() d.make_multimers([m]) chimera.viewer.viewAll() ---- test.py ------- The above python script work and makes very nice blobs. I can color the entire structure (say red) by adding something like: d.select_all_chains_cb() d.change_color_cb((1, 0, 0, 1)) but I can't figure out how to select individual chains and color them (not sure how to use select_chains). This also gets more complicated when I load in two structures at the same time and they have common chain letters. Since I found a way to get this (almost) working in python, I've been sticking with it, but if this can easily be done directly using a chimera command file, I'm happy to do that. Any help is appreciated. Thanks, Dave ---------------------------------------------------- David Sept, Ph.D. Associate Professor Biomedical Engineering and Center for Computational Biology Washington University, Campus Box 1097, St. Louis, MO 63130 Phone: (314) 935-8837 Fax: (314) 935-7448 dsept(a)biomed.wustl.edu http://habanero.ibme.wustl.edu

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Coloring different set of marker with different radius
by Bui Khanh Huy 08 Jul '08

08 Jul '08

Hi, I tried to color my EM electron density and thought that if I can color different maker sets with different radii, that would make thing much easierMy idea is to color one set using radius a, then select another set, color with radius b. But then the color from the first set disappeared. . Is there any way to do that? Best regards, Huy

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Mac Chimera in-window menu bars
by Thomas Goddard 07 Jul '08

07 Jul '08

Hi Kevin, The Chimera Aqua version has a menu bar at the top of the screen as normal Mac applications do and also at the top of the graphics window. I agree there should be a preference setting to eliminate the in-window menu bar. Here's the reason for this weirdness. There are 13 Chimera dialogs that have their own menu bars and menus. Use of these involves switching between actions in the main window and the dialog repeatedly. With menus for the active window only shown at the top of the screen this interaction becomes very tedious. For this reason I added menu bars within each Chimera window that has its own set of menus. Those in-window menus don't work very well. If you post one menu then put the pointer over an adjacent menu it will not pop up. An even worse atrocity in Aqua Chimera is that it implements "focus follows mouse". As the pointer is moved over the various Chimera windows the one underneath becomes active. This again was added because common Chimera usage involves switching frequently between windows and the normal Mac "click to focus" behavior is inconvenient for this. We would like instead to use "click through" where the first mouse click on a window both activates that window and presses the button or activates the entry field that was clicked on. I have not been able to do this in Aqua Tk, the windowing toolkit we use. The problem we're facing is that the Chimera user interface with its many windows and frequent switching between windows is poorly suited to the Mac GUI conventions. The in-window menus and focus-follows-mouse mode are a first stab at a compromise solution -- still much to be desired. Tom Kevin Walzer wrote: The latest build of Chimera from 7/3/08 on OS X/Aqua (10.5.4) includes menubars at the top of the screen (the standard OS X behavior) *and* on the main toplevel window itself, as on Windows and X11. This behavior is simply weird--two menus? It can only b e regarded as a bug, not a feature. What purpose does it serve? The correct Mac behavior can be restored by commenting out lines 1470-1476 of tkgui.py. If some of your Mac users are requesting this kind of behavior in menubars, at the very least the non- standard window-based menubar should be a preferences item that can be toggled off.

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Tile Structure default view
by Eduardo Sanz Garcia 07 Jul '08

07 Jul '08

I would like to request an extra feature for chimera, if it is not there already. I normally open multiple structures in chimera and then I use the "Tile Structure" button to visualize them in an array. This is nice, for example, to visualize the evolution of a cryo-EM 3D reconstruction. I would like that chimera could open multiple structures in an array view by default. Could a "Default view" button be added to the Tile Structure window, so that the "Border scale" value setting is saved and then the next time I open several structures they would be displayed in array view? Thank you very much.

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renumbering pdb
by bustik＠gmx.net 05 Jul '08

05 Jul '08

dear chimera-users, i am just starting to use chimera, so this will be a really simple question to you (although i didn't find anything about this in the manual...): is there a simple command to change residue numbers in a pdb file (i built up a homology model and want to elevate all residue numbers in the model the same amount)? thanks in advance sebastian -- Sebastian Kruggel Eppendorfer Weg 17d D 20259 Hamburg fon: +49 (0)40 4192 9579 mobil: +49 (0)151 1789 2232 e-mail: bustik(a)gmx.net

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graphics performance: amira v. chimera
by Matthew Dougherty 02 Jul '08

02 Jul '08

I loaded a MRC file, isosurfaced it, gave it a transparency around 0.48, and generated a vrml in chimera. I loaded the vrml into amira. initial comparison: I reloaded the vrml into chimera, I turned off the fog on chimera, moving the object around the refresh rate seems to be around 8 fps. On amira it seems to be around 24fps. results: The graphics on Chimera seems to be better during the rotation of transparent objects: full rotation in chimera is flawless, full rotation in amira results in flipping of the object (vertices in back quantum-ly jump to the front, front vertices go to back, looks like a z buffer error) periodically at 180 degrees, making it useless for many camera positions. Any comments or suggestions?

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OS X Chimera
by Christopher Vavricka 02 Jul '08

02 Jul '08

I have OS X 10.4.11 and I am trying to run Chimera. When I start Chimera.app it tells me to start X windowing system (Apple X server). X11 is not located in my applications/utlilties folder. How do I get this application? Is it on my installation disc for OS X? Regards, Chris Vavricka

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(no subject)
by Levy, Hazel C. 02 Jul '08

02 Jul '08

Hi, I am a postdoctoral researcher and an enthusiastic Chimera user. We are trying to finish up a manuscript to submit tomorrow to JSB and we have been frantically trying to figure out how to convert from Chimera's "contour level" to the more conventional "sigma level" for density map viewing at different noise levels. We understand that the higher the contour level the smaller the map volume displayed (less noisy), but we are not quit sure how to report this as a sigma level. Each map that we are comparing has a different contour range assigned, I am wondering if sigma level corresponds to some proportion of the maximum volume. Please let us know how to do this conversion or please point us in the direction toward the person that can help us. Thanks you so much...this information will settle a long-standing mystery for us. Hazel Levy

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Mutate by D- res...
by Yasser Almeida Hernández 30 Jun '08

30 Jun '08

Can Chimera mutate by D-residues? If this is possible, how i can do it? Thanks... -- Yasser Almeida Hernández Estudiante, 4to Año Bioquímica Facultad de Biología Universidad de la Habana

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Dummy atoms
by Jean Didier Pie Marechal 30 Jun '08

30 Jun '08

Dear all, I think the question was already posted but I can't find it. I would like to make an atom I placed as an helium to a Dummy: What is the corresponding atom type in Chimera? All the best JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimarts, Juny 24, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 21 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: how could u know the order of atoms? (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 23 Jun 2008 14:22:31 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] how could u know the order of atoms? > To: Kamal Al Nasr <k_alnasr(a)yahoo.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <8901DE4E-D117-4B18-968B-D3095AD735D4(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Jun 19, 2008, at 10:08 AM, Kamal Al Nasr wrote: > > > Dear Sir/Madam, > > > > I am using Chimera viewer..and it is a great viewer ever... > > Thanks! I'm glad you like it. > > > I kindly have a question... how could you know (from PDB file) > the > > coorect bonding between atoms? I mean that how could you know > that > > this atom is connected with CA not N nor C.....do u have all > these > > bonds stored already in a database? or you use atom positions to > > determine that? > > For standard amino and nucleic acids, Chimera has templates > containing the correct connectivity. For non-standard residues it > bases the connectivity on inter-atomic distances, with a few added > heuristics (e.g. hydrogens can only have one bond). > > The templates are accessible in the Python layer with the > chimera.restmplFindResidue() function. You can look in the > Rotamers > extension for examples of its use. The distance-based connectivity > > function is also available for an entire molecule as > chimera.connectMolecule(). It takes the molecule as its only > argument and adds bonds to it. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >

2 1

"Floating exception" error message
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

3 3

"Floating exception" error message
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

2 1

(no subject)
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

1 0

hydrophobic pocket
by bala 27 Jun '08

27 Jun '08

Dear Chimerian's, How do i detect hydrophobic pockets in a protein using chimera ?. Thanks in advance, Bala

3 2

Re: [Chimera-users] Question about avi files in chimera
by Tom Goddard 27 Jun '08

27 Jun '08

Hi Jaap, The AVI files produced by Chimera movie recorder use the MSMPEG-4v2 (Microsoft MPEG4 version 2) video codec and the encoding is done by the open source ffmpeg program. The file size depends on the movie recorder "bit rate" setting (default 2000 Kbits/sec = 250 Kbytes/sec = 15 Mbytes/min). Changing this setting allows you to trade off file size versus image quality. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.… Tom Jaap Brink wrote: > > Hi Tom, > > > > I was wondering given the size difference in avi files that chimera > generates versus other program (Video Edit Magic for instance), which > video codec is being used? I searched the list of embedded software > packages in chimera and found the library of libavcodecs. > > > > Thanks in advance, > > > > Jaap >

1 0

upcoming production release
by Greg Couch 26 Jun '08

26 Jun '08

Hello, We are currently getting ready to put out another chimera production release. At this point, we consider the daily builds to be release candidates, so please download one and try it out. Not all of the daily builds will be production releases, in particular, the Mac OS X Aqua version is not quite ready, and will be a snapshot release. And the Linux off-screen OpenGL version is experimental and will probably stay as a daily build. Greg Couch UCSF Computer Graphics Lab Daily builds: <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html> New features: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html>

1 0

Re: [Chimera-users] how to draw lines in Chimera
by Elaine Meng 24 Jun '08

24 Jun '08

On Jun 24, 2008, at 4:24 PM, Qing Xie wrote: > Hi, > I'm trying to draw a bunch of axes from center (0,0,0). I could do > this > in 'O' by calling this macro: > > begin_object symax > colour blue > stick_xyz 139.05, -0.00, -16.25, -139.05, 0.00, 16.25, 0.25 > stick_xyz -111.40, 43.12, 73.02, 111.40, -43.12, -73.02, 0.25 > stick_xyz -107.48, 80.74, 39.10, 107.48, -80.74, -39.10, 0.25 > stick_xyz -66.72, 119.11, -31.00, 66.72, -119.11, 31.00, 0.25 > stick_xyz 50.41, 73.78, -107.77, -50.41, -73.78, 107.77, 0.25 > stick_xyz 100.65, 0.20, -97.31, -100.65, -0.20, 97.31, 0.25 > stick_xyz -68.88, 113.16, 45.26, 68.88, -113.16, -45.26, 0.25 > stick_xyz -39.02, 80.98, -107.34, 39.02, -80.98, 107.34, 0.25 > stick_xyz 10.15, 0.20, -139.64, -10.15, -0.20, 139.64, 0.25 > stick_xyz 50.47, -73.42, -108.00, -50.47, 73.42, 108.00, 0.25 > end_object symax > > Since I had to use some features in Chimera, do you know what > commands I > should combine to do similar things above? > Thank you! > Sincerely, > Qing Hi Qing, You can make a BILD file defining the objects, for example containing the following: .color medium blue .cylinder 139.05 -0.00 -16.25 -139.05 0.00 16.25 1 .cylinder -111.40 43.12 73.02 111.40 -43.12 -73.02 1 .cylinder -107.48 80.74 39.10 107.48 -80.74 -39.10 1 .cylinder -66.72 119.11 -31.00 66.72 -119.11 31.00 1 .cylinder 50.41 73.78 -107.77 -50.41 -73.78 107.77 1 .cylinder 100.65 0.20 -97.31 -100.65 -0.20 97.31 1 .cylinder -68.88 113.16 45.26 68.88 -113.16 -45.26 1 .cylinder -39.02 80.98 -107.34 39.02 -80.98 107.34 1 .cylinder 10.15 0.20 -139.64 -10.15 -0.20 139.64 1 .cylinder 50.47 -73.42 -108.00 -50.47 73.42 108.00 1 and open it in Chimera to create the objects. I also attached this below as the file sticks.bild to be opened directly in Chimera. I didn't think 0.25 looked that good, but you can edit the file to whatever radius (and color, etc.) that you want. The BILD language also includes many other objects: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Best, 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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Re: [Chimera-users] find levels and morph conformations
by Thomas Goddard 24 Jun '08

24 Jun '08

Hi Ed, The Morph Conformations tool works with submodels. It will not work between two models or submodels that have different numbers of chains. The error message you get means that you are giving it models with different numbers of chains. Tom Edward Brignole wrote: > Tom, > > ... I'd like to use morph conformations between two pdbs each > composed of the same submodels/chains. I've tried to do this through the > dialog but it displays an error telling me "cannot interpolate the > models have different numbers of chains". The only way I can see to do > this is to write the pdb as a mol2 so that all atoms are in a single > model without submodels, open the mol2, and run morph conformations. > Is there another method or is this the simplest? > > Thanks, > Ed

3 2

selecting/displaying zones
by Elaine Meng 24 Jun '08

24 Jun '08

On Jun 24, 2008, at 11:56 AM, Thomas C. Marlovits wrote: > > Am using Chimera and would like to do the following: > - would first like to focus on specific side chain residues (for > example lysines) > - at a specific atom of either one or all lysines present in my > sample, I would like to draw a region of interest (which should be > a sphere with a given distance ... then make it rather transparent > like soap bobbles ...) ... the idea of this is to highlight areas > within a given distance away from this atom > - then I would like to read out all other side chains that are > within such an area ( in a table or so) ... and eventually > highlight them with specific colors ... > > Elaine, is there an easy way to do this ? > Tx, > -Thomas > ---------------------------------------------------------------------- > --------- > > Thomas C. Marlovits, PhD, M.A.S. > IMP-IMBA Research Center > - Research Institute of Molecular Pathology (IMP) > - Institute of Molecular Biotechnology, Austrian Academy of > Sciences (IMBA) Hi Thomas, You can definitely (1) select the atoms or residues within a specified cutoff of some other atoms and write a list of what is selected to the Reply Log or to a file. Slightly trickier is (2) displaying a "bubble." (1) The following command selects all atoms within 4.5 angstroms of atom NZ in lysine 92, chain A (example structure 2gbp): select :92.a@nz za<4.5 to select the whole residues with any atom in the zone, use "z" or "zr" instead of "za", and to use all the atoms of that lysine, just omit "@nz" from the command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#zones This selection process can also be done by Ctrl-clicking to select the atom and then using Select... Zone. You can write out a list of the selection with Actions... Write List (click Log if you want to send it to the Reply Log instead). The default is a list of all the atoms individually, but you can set it to "residues" instead to just get one line of output per residue. The command to do that same thing is "writesel" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/writesel.html (2) The "bubble." I imagine something like Volume Eraser would be nice (check it out: Tools... Volume Data... Volume Eraser). However, that does not let you specify particular coordinates for the center. You have to move it around by hand. Volume Eraser really just makes a big atom and gives it a transparent color. You could add an atom in Build Structure (under Tools... Structure Editing), color it a transparent color, and change its radius with "vdwdefine" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ editing.html#build http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html It doesn't let you enter specific coordinates for the atom. However, if you add the atom as a "new model" you can match it to different locations on the first. For example, if the new atom is model 1 and the structure of interest (say 2gbp) is model 0: rep sphere #1 colordef tpink 1 .6 .6 .6 color tpink #1 vdwdef 3.0 #1 vdwdef +1 #1 vdwdef +1 #1 match #1 #0:147.a@nz select #1 za<5 & #0 [... etc. ...] The radius would just be for display purposes. You'd still have to specify the zone distance when selecting. A couple of failed ideas: (a) You can make a spherical surface of specified radius with the command "shape" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html but you cannot directly specify coordinates for the center or easily modify radius after it has been created. (b) Create a spherical object in BILD format. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Disadvantages are inability to make it transparent and having to delete/recreate the object just to change its radius. Best, 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 > >

1 0

how could u know the order of atoms?
by Kamal Al Nasr 23 Jun '08

23 Jun '08

Dear Sir/Madam, I am using Chimera viewer..and it is a great viewer ever... I kindly have a question... how could you know (from PDB file) the coorect bonding between atoms? I mean that how could you know that this atom is connected with CA not N nor C.....do u have all these bonds stored already in a database? or you use atom positions to determine that? I appreciate your time.... Kamal

2 1

connectivity
by Jean Didier Pie Marechal 18 Jun '08

18 Jun '08

Dear all, I would like to use chimera to generate inputs for gaussian QM/MM calculations (ONIOM). One of the element I need is the connectivity of the atoms. I looked around the programmer's guide but couldn't find the right module that takes this in charge. what is the way to have access the connectivity of a given molecule? All the best, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Juny 18, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 18 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Find contour level to enclose a specified volume (Thomas > Goddard) 2. Re: Find contour level to enclose a specified volume > (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 17 Jun 2008 15:44:57 -0700 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: [Chimera-users] Find contour level to enclose a specified > volume > To: "'Chimera BB'" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <48583E69.5090608(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Ed Brignole asked about setting a volume contouring level so that > the > resulting surface encloses a desired volume (cubic Angstroms). > Attached > is a Python script that does this in two ways. The first way is > fast > but approximate finding the level such that the number of enclosed > grid > points times the voxel volume equals the requested volume. > Estimating > the enclosed volume of the surface this way can give a much > different > result than actually computing analytically the volume within the > surface. The second approach computes surfaces at different > contour > levels and calculates analytically the volume. It uses bisection > to > find the correct contour level. This approach can be slow, about > 30 > seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface > triangles. Most of that time (80%) is actually computing the > enclosed > volume. That should be very fast but the code is checking for > holes in > the surface in a rather slow way. Both methods use the step size > (subsampling) set in the volume dialog. > > Tom >

2 1

Find contour level to enclose a specified volume
by Thomas Goddard 18 Jun '08

18 Jun '08

Ed Brignole asked about setting a volume contouring level so that the resulting surface encloses a desired volume (cubic Angstroms). Attached is a Python script that does this in two ways. The first way is fast but approximate finding the level such that the number of enclosed grid points times the voxel volume equals the requested volume. Estimating the enclosed volume of the surface this way can give a much different result than actually computing analytically the volume within the surface. The second approach computes surfaces at different contour levels and calculates analytically the volume. It uses bisection to find the correct contour level. This approach can be slow, about 30 seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface triangles. Most of that time (80%) is actually computing the enclosed volume. That should be very fast but the code is checking for holes in the surface in a rather slow way. Both methods use the step size (subsampling) set in the volume dialog. Tom # ----------------------------------------------------------------------------- # Find threshold level so that a contour surface encloses a specified volume. # # Method: Estimates how many grid points should lie within # surface then finds the level having that many grid points with higher values. # This method can produce a level where the enclosed volume is very # different from the requested volume. # def level_enclosing_grid_points(v, vol): (x0,y0,z0), (x1,y1,z1) = v.xyz_bounds() tvol = (x1-x0)*(y1-y0)*(z1-z0) r = 1.0 - vol/tvol s = v.matrix_value_statistics() level = s.rank_data_value(r) return level # ----------------------------------------------------------------------------- # Find threshold level so that a contour surface encloses a specified volume. # # Method: Computes surfaces for different levels and resulting volumes # using bisection to determine the correct level. # def level_by_bisection(v, vol, iterations = 10): m = v.matrix() l0, l1 = m.min(), m.max() ijk_step = v.region[2] from numpy import product voxel_volume = product(ijk_step) * product(v.data.step) mvol = vol / voxel_volume return find_level(m, l0, l1, mvol, iterations) # ----------------------------------------------------------------------------- # def find_level(m, l0, l1, mvol, iterations): l = 0.5*(l0+l1) if iterations <= 1: return l from _contour import surface varray, tarray = surface(m, l, cap_faces = True) from _surface import enclosed_volume vl, hole_count = enclosed_volume(varray, tarray) varray = tarray = None if vl == mvol: return l if vl > mvol: l0 = l else: l1 = l return find_level(m, l0, l1, mvol, iterations - 1) # ----------------------------------------------------------------------------- # vol = 3.227e6 # sfv.mrc, threshold level 1000. from chimera import openModels from VolumeViewer import volume_list for v in volume_list(): level1 = level_enclosing_grid_points(v, vol) level2 = level_by_bisection(v, vol) print v.name, level1, level2

2 1

3D surfaces from MacMolPlt or Gamess
by David Chenoweth 13 Jun '08

13 Jun '08

Dear Chimera team, I am having a bit of trouble reading a file into Chimera. Currently I am using Gamess to run DFT calculations and I can open these files in MacMolPlt which allows me to display orbitals or plot electrostatic potential surfaces. I can export the 3D surface data however I can't get Chimera to read the 3D grid files. Can you help me? I attached the file format info below and I can send you example files if you need. I am really trying to use Chimera for all my graphics needs wether it be viewing surfaces or orbitals from DFT calculations or looking at electron density maps from crystal structure data. If I could convert the 3D surface data files below into ccp4 or cns formated files that should also work for Chimera I just haven't found a way to do this yet. Thanks in advance, Dave ********************************************** 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 ********************************************** File format data info: http://www.scl.ameslab.gov/~brett/MacMolPlt 2D and 3D Surfaces (Import and Export) MacMolPlt implements a simple format for importing and exporting 2D and 3D surface data. To export a surface first create a surface and make sure that the surface is updated so that the grid data is available for export. Then choose the Export menu command and the Surface export format. MacMolPlt will then export the surface grid data to the file you specify (this is useful to check the input format as well). To import a 2D or 3D surface create a new General 2D or 3D surface. From the surface dialog you can then choose the file containing the grid data. The format for the 2D and 3D files are similar but there are a couple of differences. Floating point numbers may be given in a variety of formats and the grid data may contain any number of values per line. The units for the coordinate system should normally be angstroms. For 2D planes the format is: 1Line Label 30 # grid points -4.165882 -4.306789 0.839681 //Origin of the 2D grid 0.297019 0.000000 0.000000 //X inc vector 0.000000 0.297019 0.000000 //Y inc vector -0.000018 -0.000021... (# of grid points squared grid values) For 3D surfaces: 1 Line label 35 12 41 //nx ny nz -4.687880 -1.587537 -5.059790 //Origin of the 3D grid 0.280144 0.288642 0.275207 //x increment, y inc, z inc/ grid(x(y(z))) 0.000000 0.000000... (nx*ny*nz grid values)

2 2

3D surfaces from MacMolPlt or Gamess
by David Chenoweth 12 Jun '08

12 Jun '08

Dear Chimera team, I am having a bit of trouble reading a file into Chimera. Currently I am using Gamess to run DFT calculations and I can open these files in MacMolPlt which allows me to display orbitals or plot electrostatic potential surfaces. I can export the 3D surface data however I can't get Chimera to read the 3D grid files. Can you help me? I attached the file format info below with an exported density file and electrostatic potential map. I am really trying to use Chimera for all my graphics needs wether it be viewing surfaces or orbitals from DFT calculations or looking at electron density maps from crystal structure data. If I could convert the 3D surface data files below into ccp4 or cns formated files that should also work for Chimera I just haven't found a way to do this yet. Thanks in advance, Dave ********************************************** 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 ********************************************** File format data info: http://www.scl.ameslab.gov/~brett/MacMolPlt 2D and 3D Surfaces (Import and Export) MacMolPlt implements a simple format for importing and exporting 2D and 3D surface data. To export a surface first create a surface and make sure that the surface is updated so that the grid data is available for export. Then choose the Export menu command and the Surface export format. MacMolPlt will then export the surface grid data to the file you specify (this is useful to check the input format as well). To import a 2D or 3D surface create a new General 2D or 3D surface. From the surface dialog you can then choose the file containing the grid data. The format for the 2D and 3D files are similar but there are a couple of differences. Floating point numbers may be given in a variety of formats and the grid data may contain any number of values per line. The units for the coordinate system should normally be angstroms. For 2D planes the format is: 1Line Label 30 # grid points -4.165882 -4.306789 0.839681 //Origin of the 2D grid 0.297019 0.000000 0.000000 //X inc vector 0.000000 0.297019 0.000000 //Y inc vector -0.000018 -0.000021... (# of grid points squared grid values) For 3D surfaces: 1 Line label 35 12 41 //nx ny nz -4.687880 -1.587537 -5.059790 //Origin of the 3D grid 0.280144 0.288642 0.275207 //x increment, y inc, z inc/ grid(x(y(z))) 0.000000 0.000000... (nx*ny*nz grid values)

1 0

Swapaa from Java Runtime.exec
by ProtEUS 11 Jun '08

11 Jun '08

Hello all! I am sorry if this is a dump question, but is it possible for swapaa to run fromJava server with Runtime.exec()? Thank you very much!! Andreas, Greece.

2 3

translation + rotation of a whole scene
by Nils Becker 11 Jun '08

11 Jun '08

Hi list, I have a question about rotating and translating a bunch of models together while preserving their spatial relations. In particular, I would like to apply a matrix almost as in the matrixset command. THe difference is that I do not want to apply it individually to each model, but to one chosen models, while having the rest move together with the chosen model. Is that feasible in chimera? cheers, Nils

3 4

saving 2 maps for difference
by Gabriel Lander 09 Jun '08

09 Jun '08

I have 2 density maps, and use the "fit in map" function to best align the 2 of them. I'd like to use this fitting to create a difference map, but the original maps are not the same size. Does anyone know how to save both maps to the same grid in Chimera? For now I've been using the "subregion selection" tool in combination with "resampling voxel size", but if someone has a more direct method it'd be much appreciated. Thanks, -gabe

2 1

<< Plotting Gaussian MO >>
by Hatuey Hack 09 Jun '08

09 Jun '08

Hi all, I have a cube file with the Molecular Orbitals calculated with Gaussian. When I load the cub file into Chimera, I am only seen half of the orbital surface. I would like to know what should I do to get the whole molecular orbital surface colored (as usually) with only to colors (each on for one half). Regards, Hatuey

3 3

gaussian orbitals, Chimera-users Digest, Vol 62, Issue 11
by Jonathan Hilmer 09 Jun '08

09 Jun '08

Hatuey, If I remember correctly, you need to open the density map twice, then contour at the same level for both maps: one at the positive value and the other negative. Each map is colored independently, so they can be depicted however you want. Jonathan On Mon, Jun 9, 2008 at 1:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. << Plotting Gaussian MO >> (Hatuey Hack) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Jun 2008 10:24:29 -0300 > From: "Hatuey Hack" <hatuey.hack(a)gmail.com> > Subject: [Chimera-users] << Plotting Gaussian MO >> > To: chimera-users(a)cgl.ucsf.edu > Message-ID: > <612c95fa0806090624l5395ab11k6c9b235379e1a4fe(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > I have a cube file with the Molecular Orbitals calculated with Gaussian. > > When I load the cub file into Chimera, I am only seen half of the > orbital surface. > > I would like to know what should I do to get the whole molecular > orbital surface colored (as usually) with only to colors (each on for > one half). > > Regards, > > Hatuey > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 62, Issue 11 > ********************************************* >

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Molecular voodoo
by Tom Goddard 06 Jun '08

06 Jun '08

While debugging a bit of Chimera code I stumbled upon molecular voodoo. Stick pins in any evil molecule. Ask your doctor if this treatment may be right for you. A snake toxin (PDB 1a0m) has been fully cursed in the attached image. I attach the voodoo doll Chimera script for your amusement. You open voodoodoll.py in Chimera and then ctrl-right-mouse-button lets you place pins. Works in Chimera production release 1.2470 and newer. Tom def mouse_down_cb(viewer, event): from VolumeViewer import slice xyz_in, xyz_out = slice.clip_plane_points(event.x, event.y) from chimera import selection selection.clearCurrent() from VolumePath import place_marker place_marker(xyz_in) place_marker(xyz_out) from chimera import mousemodes as m m.addFunction('hide triangle', (mouse_down_cb, None, None)) m.setButtonFunction('3', ['Ctrl'], 'hide triangle')

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smoothening the edge of molecular surface
by Maurice Ho 06 Jun '08

06 Jun '08

Is there any way to smoothen the edge of molecular surface when only part of it would be displayed? It's quite often that a couple of triangles sticking out from the edges which makes the image a bit absurd. Please kindly advice. rgds, Maurice Ho

3 2

Installing Chimera in Ubunty Hardy
by David 05 Jun '08

05 Jun '08

Hi, Im a long time user of Chimera, but now I changed XP for Ubuntu for 6 gb of ram that couldn't be used in XP 32 bits. I need help installing Linux version of Chimera, I have read and goggled web for instructions, and none of them seems to work, I run .exe in terminal (knowing linux doesn't use .exe i find this confusing) and nothing happens, I try that Chmod command and running again and nothing too... Im a really beginner here in linux, also browsed Ubuntu forums for help and at least till today have got no answer. All help would be greatly appreciated. sincerely, David Bulnes Abundis

2 1

Chimera - quantitative possibilities using surfnet?
by mgochin＠touro.edu 05 Jun '08

05 Jun '08

I am wondering if it is possible to get numerical values for areas / volumes of molecular cavities and indentations drawn by surfnet in either the Interface or Selected Atoms mode. Any help is appreciated. - Miriam Gochin

3 2

coloring residues according to electrostatic force
by Maurice Ho 05 Jun '08

05 Jun '08

How to color residues of a protein according to the electrostatic potential map generated by APBS? I could only color the molecular surface by loading the potential map. Please kindly advice. Thanks and regards, Maurice Ho

2 1

OS X aqua version
by Glenn Millhauser 03 Jun '08

03 Jun '08

Hi Folks, I just saw the mac aqua version at the download site and decided to give it a try. Layout looks terrific. However, it seems to move molecules much more slowly than the X windows version. I'm running on a macbook (intel) with inherent limited graphics capabilities, so perhaps that's the problem. Any comments? thanks, g Glenn Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 459 2935 fax 831 566 3337 cell glennm(a)chemistry.ucsc.edu http://chemistry.ucsc.edu/~glennm

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making a plane through the atoms of a ring and Distance measurements
by David Chenoweth 03 Jun '08

03 Jun '08

Dear Chimera team, I would like to make a plane through the atoms of an aromatic ring and then measure a distance from an atom to the ring centroid. I would also like to measure the angle between the normal to the ring plane and the line joining the centroid and the atom I am measuring from. It would also be nice if I could specify the dimensions, color, and transparency of the plane. In addition it would be great to be able to make multiple planes through atoms, select and color them separately, and measure the angles at the intersection of the planes. Just wondering if there is a way to do this with Chimera. Thanks in advance, Dave ********************************************** 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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fit correlation
by Elena Orlova 03 Jun '08

03 Jun '08

Dear Chimera team, I have some troubles in getting numbers of the quality of the atomic structure fit into EM map. I wonder if you can give me directions where I can find the quantitative assessment of such fit? Do you have something like Cross Correlation Coeficient or R factor, or any other statistical test ? many thanks in advance. Elena -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Elena Orlova Dept. of Crystallography Tel: (+44) (0)20 7631 6845 Birkbeck College Fax: (+44) (0)20 7631 6803 University of London Malet Street London WC1E 7HX UK e-mail: e.orlova(a)mail.cryst.bbk.ac.uk

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Re: [Chimera-users] Chimera-users Digest, Vol 61, Issue 29
by Ibrahim Moustafa 02 Jun '08

02 Jun '08

Dear Chimera developers, Many many thanks for your great help. The script provided by Eric Peterson did the job very easily. Many thanks, Ibrahim On 5/31/08 12:54 PM, "chimera-users-request(a)cgl.ucsf.edu" <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Plotting modes from PCA onto the structure (Eric Pettersen) > 2. Re: add atom type in MMTK (Elaine Meng) > 3. Import error with chimera-1.2509-osx_x11.dmg, May 01, 2008 > (Bruce D. Ray) > 4. Re: Import error with chimera-1.2509-osx_x11.dmg, May 01, > 2008 (Randy Heiland) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 May 2008 15:15:02 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Plotting modes from PCA onto the > structure > To: Ibrahim Moustafa <I.moustafa(a)psu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <476E9F7A-2FDD-4558-8053-5345D9995A02(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Ibrahim, > As Bala pointed out, IED in VMD may well be the way to go for now. > Also, the "porcupine needles" can be accomplished with BILD, as > Elaine mentioned. I've attached a script that reads a file of > displacements and applies them to the CAs of a structure. Obviously, > there should be as many lines in the file as there are CAs in the > structure. Each line should consist of 3 numbers, the X, Y, and Z > displacements. Since the script only modifies the CAs, you should > probably only be displaying the CAs -- the rest of the structure will > be out of position. You may need to edit the script to put in the > name of the file with the displacements, otherwise it will use a file > named "displacements" in the same directory as the script. You run > the script by simply opening it with File...Open or the "open" command. > We are working on closer coordination between Amber and Chimera, > with the help of Wei Zhang. He has already contributed one tool, > Solvate, which uses sleap to solvate a system. Solvate is available > in daily builds. In the short term he hopes to write tools to add > ions and write parmtop files. Longer term goals are to include the > minimization and MD functionality of NAB, and ptraj trajectory analysis. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > ? > On May 29, 2008, at 10:08 AM, Ibrahim Moustafa wrote: > >> Dear Chimera support, >> >> I hope Chimera (with supporting scripts) can be used to make the >> figures described below: >> >> I want to make a figure to display the different modes >> obtained from PCA analysis (on MD trajectory obtained from AMBER) >> as different snapshots of the structure under study. >> >> To explain it more, I have a file containing the displacement in >> X, Y, Z for each C-alpha in a column format. Is there a simple >> script that can add the displacement vectors to the x, y, z >> coordinates of the original structure? So the new structure with >> modified C-alpha can be plotted representing a particular mode in >> Chimera. >> >> Also, related to the same point, is it possible to represent the >> vectors at each C-alpha as arrows/porcupine needle in Chimera? >> >> P.S. It would be great if Chimera can add features to represent >> these kind of figures from PTRAJ output or similar analysis >> programs used in MD simulation. Especially, Chimera support >> analysis of AMBER trajectory. >> >> Thanks in advance for your great support, >> 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 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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How to define a center of rotation when applying a symmetry
by Giovanni Cardone 02 Jun '08

02 Jun '08

Hi, I would like to apply a rotation to a pdb model, in order to place copies of it in equivalent symmetry points (icosahedral symmetry). I am not sure I understand all the different coordinate systems in chimera, but digging into the program code, I was able to write the following script. I am not sure it is the best way to do it, and obviously at the moment it does not work properly, because I am not specifying the center of rotation. With respect to the coordinates of the pdb model, I know the center of symmetry, let's say (161,161,161), but I don't know how to impose it. I tried to assign these coordinates to the parameter 'cofr', but the result does not change. Does anyone know how to apply, inside a script, a rotation matrix around a given point? Any other feedback on the correctness of the script is very welcome. Thank you. Giovanni ############################################### from chimera import openModels, Point from PDBmatrices import chimera_xform from Icosahedron import icosahedral_symmetry_matrices icomats = icosahedral_symmetry_matrices(orientation = '222r') for rmat in icomats: xf = chimera_xform(rmat) m, = openModels.open('/dummy/dummy.pdb') # open a copy of the model m.openState.xform = xf # set rotation ############################################### ============================================= Giovanni Cardone Laboratory of Structural Biology Research National Institutes of Health 50 South Drive (Building 50), Room 1511 Bethesda, MD 20892-8025 USA Tel: (301) 451-8247 FAX: (301) 480-7629 Giovanni_Cardone(a)nih.gov =============================================

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rotation matrices around a given center (Chimera-users Digest, Vol 62, Issue 3)
by Jonathan Hilmer 02 Jun '08

02 Jun '08

I haven't tried it out, but it looks like all you have to do is apply a transformation to your model before you apply the set of rotations. You could create a set of matrices to do it all in one step, but that's more trouble than it's worth. Something like this should work: Jonathan ############################################### from chimera import openModels from PDBmatrices import chimera_xform from Icosahedron import icosahedral_symmetry_matrices icomats = icosahedral_symmetry_matrices(orientation = '222r') centerRot = (161.,161.,161.) tMat = ((1.0,0.0,0.0,-centerRot[0]), (0.0,1.0,0.0,-centerRot[1]), (0.0,0.0,1.0,-centerRot[2])) for rmat in icomats: m, = openModels.open('/dummy/dummy.pdb') # open a copy of the model m.openState.xform = chimera_xform(tMat) # set translation to for center of rotation offset m.openState.xform = chimera_xform(rmat) # set rotation ############################################### On Mon, Jun 2, 2008 at 1:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > 1. How to define a center of rotation when applying a symmetry > (Giovanni Cardone) > 2. Re: Volume viewer negative isosurface (Elaine Meng) > 3. problem with opengl glx kubuntu (Fabian Glaser) > 4. Re: OS X aqua version (Thomas Goddard) > 5. Re: OS X aqua version (Eric Pettersen) > 6. Re: problem with opengl glx kubuntu (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 Jun 2008 12:18:25 -0400 > From: Giovanni Cardone <cardoneg(a)mail.nih.gov> > Subject: [Chimera-users] How to define a center of rotation when > applying a symmetry > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <919BC0E8-98BD-4F1A-97DD-13F048B71C13(a)mail.nih.gov> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I would like to apply a rotation to a pdb model, in order to place > copies of it in equivalent symmetry points (icosahedral symmetry). > I am not sure I understand all the different coordinate systems in > chimera, but digging into the program code, I was able to write the > following script. > I am not sure it is the best way to do it, and obviously at the > moment it does not work properly, because I am not specifying the > center of rotation. > With respect to the coordinates of the pdb model, I know the center > of symmetry, let's say (161,161,161), but I don't know how to impose it. > I tried to assign these coordinates to the parameter 'cofr', but the > result does not change. > Does anyone know how to apply, inside a script, a rotation matrix > around a given point? > Any other feedback on the correctness of the script is very welcome. > > Thank you. > > Giovanni > > > > ############################################### > > from chimera import openModels, Point > > from PDBmatrices import chimera_xform > > from Icosahedron import icosahedral_symmetry_matrices > > > icomats = icosahedral_symmetry_matrices(orientation = '222r') > > > for rmat in icomats: > > xf = chimera_xform(rmat) > > m, = openModels.open('/dummy/dummy.pdb') # open a copy of the > model > > m.openState.xform = xf # set rotation > > ############################################### > > > > > ============================================= > Giovanni Cardone > Laboratory of Structural Biology Research > National Institutes of Health > 50 South Drive (Building 50), Room 1511 > Bethesda, MD 20892-8025 USA > > Tel: (301) 451-8247 > FAX: (301) 480-7629 > Giovanni_Cardone(a)nih.gov > =============================================

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problem with opengl glx kubuntu
by Fabian Glaser 02 Jun '08

02 Jun '08

Hi, I installed a new version of chimera in kubuntu,and after a while, I started to get the following error when I click chimera: "Missing opengl windowing protocol (glx)" I am using kubuntu version: Linux 2.6.24-16-generic #1 SMP UTC 2008 i686 GNU/Linux nvidia and nvidia-glx are updated and installed. Any help will be highly appreciated. Best, Fabian -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

2 1

Volume viewer negative isosurface
by Miguel Ortiz-Lombardía 02 Jun '08

02 Jun '08

Hi, I'm using Chimera 1.2509 for X11 on a G4 iBook running OSX.4.11 I have a problem with Volume Viewer to visualize an electrostatic potential map calculated with APBS. The same potential map can be used without trouble to color a molecular surface. The problem is that when I try to set a negative isosurface to a negative value, the box that contains map also gets colored, making the scene unclear. I'm attaching a picture to illustrate this effect. I have tried to change several settings but so far unsuccessfully... Thanking you in advance for your help, Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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Import error with chimera-1.2509-osx_x11.dmg, May 01, 2008
by Bruce D. Ray 31 May '08

31 May '08

I have a Mac G4 PPC running OS X 10.3.9 on which previous versions of chimera have run without incident. I installed chimera-1.2509 of May 01, 2008 after removing the chimera-1.2492 of Feb 11, 2008 I had been using. However, when I attempted to run chimera-1.2509 it did not start and the following error messages were written to the console.log file accessible by console.app rather than to the X-terminal: Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 279, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 15, in <module> from _chimera import * ImportError: dynamic module does not define init function (init_chimera) This appears to be specific to the Mac OS X version as the Windows version of chimera-1.2509 works. Obviously, I removed chimera-1.2509 from the Mac and reinstalled chimera-1.2492 of Feb 11, 2008 which does work on this Mac. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273

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add atom type in MMTK
by Lionel Nauton 30 May '08

30 May '08

hello everybody this is my first question since I use chimera, more than 3 years ago, and I would like to know if is it possible to add atom type in the MMTK basis set ? I actually work on a molecule containing platinium, and I can't run mopac because there is no description. I'm looking for some description files , and I found this : /antechamber/dat/antechamber/*****.DAT which is the good one and which is the way to modify it ? thank's for your answer and excuse me for my english..... best regards -- ================================================= NAUTON Lionel Ingénieur d'études. Laboratoire de Synthèse Et Etude de Systèmes à Intérêt Biologique UMR6504 : université Blaise Pascal – CNRS 24, avenue des Landais – Campus des Cézeaux 63177 AUBIERE Cedex France Tel : 04 73 40 55 06 mèl : lionel.nauton(a)univ-bpclermont.fr <mailto:lionel.nauton@univ-bpclermont.fr> site web : http://seesib.univ-bpclermont.fr/site_web/pageaccueil.htm <http://seesib.univ-bpclermont.fr/site_web/pageaccueil.html> =================================================

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Plotting modes from PCA onto the structure
by Ibrahim Moustafa 30 May '08

30 May '08

Dear Chimera support, I hope Chimera (with supporting scripts) can be used to make the figures described below: I want to make a figure to display the different modes obtained from PCA analysis (on MD trajectory obtained from AMBER) as different snapshots of the structure under study. To explain it more, I have a file containing the displacement in X, Y, Z for each C-alpha in a column format. Is there a simple script that can add the displacement vectors to the x, y, z coordinates of the original structure? So the new structure with modified C-alpha can be plotted representing a particular mode in Chimera. Also, related to the same point, is it possible to represent the vectors at each C-alpha as arrows/porcupine needle in Chimera? P.S. It would be great if Chimera can add features to represent these kind of figures from PTRAJ output or similar analysis programs used in MD simulation. Especially, Chimera support analysis of AMBER trajectory. Thanks in advance for your great support, 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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Re: [Chimera-users] Chimera-users Digest, Vol 61, Issue 27
by bala 30 May '08

30 May '08

Dear Ibrahim, Try to use IED Plugin in VMD to analyze your PCA output. In fact there is a server that can produce the arrows (you want) that can show the direction and magnitude of the displacement along a Eigen vector. But i guess the server works on gromacs output only. A month ago, i posted the same query to Chimera (Analyzing PCA with chimera). I thank Elaine for his support. I would surely send some samples files of PCA analysis done with PTRAJ. I think addition of this analysis facility in Chimera is surely going to help all chimeran's a lot. Bala -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu on behalf of chimera-users-request(a)cgl.ucsf.edu Sent: Fri 5/30/2008 12:30 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 61, Issue 27 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Plotting modes from PCA onto the structure (Ibrahim Moustafa) 2. Re: Plotting modes from PCA onto the structure (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Thu, 29 May 2008 13:08:01 -0400 From: Ibrahim Moustafa <I.moustafa(a)psu.edu> Subject: [Chimera-users] Plotting modes from PCA onto the structure To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Message-ID: <C4645B32.132A%I.moustafa(a)psu.edu> Content-Type: text/plain; charset="us-ascii" Dear Chimera support, I hope Chimera (with supporting scripts) can be used to make the figures described below: I want to make a figure to display the different modes obtained from PCA analysis (on MD trajectory obtained from AMBER) as different snapshots of the structure under study. To explain it more, I have a file containing the displacement in X, Y, Z for each C-alpha in a column format. Is there a simple script that can add the displacement vectors to the x, y, z coordinates of the original structure? So the new structure with modified C-alpha can be plotted representing a particular mode in Chimera. Also, related to the same point, is it possible to represent the vectors at each C-alpha as arrows/porcupine needle in Chimera? P.S. It would be great if Chimera can add features to represent these kind of figures from PTRAJ output or similar analysis programs used in MD simulation. Especially, Chimera support analysis of AMBER trajectory. Thanks in advance for your great support, 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

1 0

Help Installing Chimera in Ubunty Hardy already read and google a lot.
by A00775435＠itesm.mx 30 May '08

30 May '08

Hi, Im a long time user of Chimera, but now I changed XP for Ubuntu for 6 gb of ram that couldn't be used in XP 32 bits. I need help installing Linux version of Chimera, I have read and goggled web for instructions, and none of them seems to work, I run .exe in terminal (knowing linux doesn't use .exe i find this confusing) and nothing happens, I try that Chmod command and running again and nothing too... Im a really beginner here in linux, also browsed Ubuntu forums for help and at least till today have got no answer. All help would be greatly appreciated. sincerely, David Bulnes Abundis

2 1

Re: [Chimera-users] preferences - povray - keep input files doesn't
by Eric Pettersen 27 May '08

27 May '08

> We're thinking of adding some generic per-frame hook as a command so > that you don't have to use Movie Recorder at all to generate a series > of POVray files that you want to post-process before rendering (you > would use the not-yet-documented "export" command to generate them). > > --Eric This hook, a command named "perframe", is now in there. It will be available in tomorrow's build if that works. There is documentation here: http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/midas/perframe.html > > On Mar 17, 2008, at 11:00 AM, Thomas Goddard wrote: > > > Hi Klaas, > > > > You can make the Chimera movie recorder use your preference for > > keeping POVray files by editing file > > > > chimera/share/MovieRecorder/RecorderHandler.py > > > > changing line 120 from > > > > raytraceKeepInput = False, > > > > to > > > > # raytraceKeepInput = False, > > > > Then restart Chimera. > > > > Perhaps we should change the Chimera default for the "keep POVray > > input files" to false and have movie recorder respect the preference > > setting. > > > > Tom > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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