- Chimera-users - RBVI Mailing Lists

chimera --stereo crash
by Liu, Hao-Yang 24 Jan '05

24 Jan '05

Dear Sir/Madam, I am running chimera in IRIX, and when I am trying to run "chimera --stereo", I got this message: Unable to find hardware stereo support (Togl: couldn't get visual) and when I click ok, the program just quit. I can use the normal (mono) mode in chimera. and I think I had the hardware, because I use midas a lot, and never had problem in midas. Could you tell me how can I use the stereo mode in chimera? What am I missing? Thanks Hao-Yang Liu

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selecting
by John Nixon 18 Jan '05

18 Jan '05

Hi folks, I'm a newbie and am having trouble getting started. Sorry to be dense. Using the command line on a single protein chain O select :32-42,44-49.O or rep sphere :43:56:59:60:61:63:65:67:68:70:71:72:73:74:75:78:110:113.0 only seems to work on the last residue. Thus I'd have to write a separate command for each residue. Could you tell me what I've missed please! John

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[Chimera-users] FW: [PyMOL] Stereo-3D in a Window: Not in MacOS X Tiger?!!
by Warren DeLano 14 Jan '05

14 Jan '05

Greetings Fellow Vendors and Software Developers! Is stereo 3D graphics support on MacOS X something you would like to see soon? If so, then please take just 30 seconds to respond to the following petition. We've received more than 300 compelling responses over the past 18 hours about the importance of supporting stereo 3D graphics today -- but we will need more to convince Apple, so please consider participating. It is as easy as clicking this following link, adding a few words with your personal perspective on the issue, and then hitting send! mailto:warren@delsci.com&subject=Stereo%203D%20Matters%20to%20Me%21 Cheers, Warren -----Original Message----- From: pymol-users-admin(a)lists.sourceforge.net [mailto:pymol-users-admin@lists.sourceforge.net] On Behalf Of Warren DeLano Sent: Thursday, January 13, 2005 5:59 PM To: pymol-users(a)lists.sourceforge.net Subject: [PyMOL] Stereo-3D in a Window: Not in MacOS X Tiger?!! Fellow Visualization Software Users: My #1 gripe with MacOS X Panther has been the lack of support for industry-standard stereo-3D graphics (in a window). So far, I and others have been unable to convince Apple that this feature matters enough to their bottom line to merit implementation. Candid discussions this week at MacWorld confirmed that Tiger (OS X 10.4) will likewise ship without this essential capability at a time when the opportunity for Apple is at its peak in this market. I believe this would be a serious error, and that Apple must now hear from us on this issue. If you agree, then please reply directly to me, RIGHT NOW (mailto:warren@delsci.com) with the words: "Stereo 3D matters to me." Your response will be printed, and I will hand-deliver them to Apple management in nearby Cupertino at the end of the month. We need AS MANY responses as we can get (ideally 1,000+), so please forward this email to all of your visualization-oriented colleagues (in any sector), and ask them to submit individual emails to me as well. Here's why: Stereoscopic 3D visualization increasingly matters in science, medicine, and engineering. Though arguably the ultimate technical computing platform, the Mac remains hopelessly crippled in this key respect when compared to Sun, HP, Dell, or IBM workstations running Linux, Solaris, or even Windows. Dual-Xeon and dual-Opteron systems now ship stereo-3D-ready thanks to powerful nVidia/Quadro and ATI/FireGL graphics cards. Thus, the competition WILL OWN THIS MARKET if Apple doesn't support stereo-3D in a window on MacOS X, ASAP. The disruptive market opportunity created by the implosion of SGI and the stopgap adoption of "home brew" Linux systems is about to end. Professional-grade stereoscopic visualization is now a standard OpenGL capability, it is vendor-supported on a variety of hardware, and it is present on every platform EXCEPT THE MAC. None of those "amazing features" in Tiger matter one bit to technical users whose basic needs remain unmet. Stereo-3D inadequacy is a show-stopper for many scientists and engineers. The Mac will not have a fair shot at this market unless Apple quickly follows though on it's assumed responsibility to support all OpenGL features, including quad-buffered stereo-3D graphics in a window. Case in point: my company just spent $5k on a dual-Opteron Sun workstation instead of a dual-G5 Mac solely because stereo-3D in a window is absent from MacOS X. This pattern will surely be amplified many thousand-fold if Apple does not take immediate corrective action. Responding together, we can insure that Apple understands what this deficiency means for the future of MacOS X in scientific, medical, and technical visualization. I do not believe that Apple management has made an informed decision regarding stereo-3D, and I think this is our last best chance to change things before the issue becomes moot. Please share your concerns by responding to this email (mailto:warren@delsci.com). It will only take a second, but the benefits could last for years to come if Apple listens well and then acts decisively. Input from current Linux and Windows users is especially welcome, since Apple would love to sell you the visualization platform of your dreams if you're willing to help define it. Thank you for your time. Cheers, Warren Author of PyMOL: http://pymol.sf.net (Note that MacPyMOL is currently shown on http://apple.com/science under "The Tools" -- cool!) DeLano Scientific LLC company profile: http://delanoscientific.com/about.html PS. An alternate way to be heard is to post on the Apple SciTech or Sci-Vis mailing lists, but please CC me too to be sure that you're counted. http://lists.apple.com/mailman/listinfo/scitech http://lists.apple.com/mailman/listinfo/sci-vis -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren@delsci.com ------------------------------------------------------- The SF.Net email is sponsored by: Beat the post-holiday blues Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek. It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt _______________________________________________ PyMOL-users mailing list PyMOL-users(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users

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Re: [Chimera-users] Mol2 Trajectory Reader?
by Eric Pettersen 06 Jan '05

06 Jan '05

Hi Joshua, Given that what you really want to do is assemble a movie of your conformations rather than actually analyze them as a trajectory, what we've decided to do is write an extension that will allow you to record whatever is going on in Chimera as a series of frames (it will have a "Start" and a "Stop" button) and will assemble those frames into an mpeg. It will optionally allow you to keep the frames in case you want to assemble them into a format that is harder for us to support across all platforms (e.g. Quicktime), and may also support generating an animated GIF. A preliminary version will probably be done in a couple of weeks and we could send that to you if you want to be a guinea pig. Otherwise, it will be in the next release, which will probably be April or so. --Eric On Dec 25, 2004, at 8:15 PM, S Joshua Swamidass wrote: > Good point. > > I didn't notice the move menu. The ultimate goal of all this for me is > to literally make some movies, either with screen shots in sequence or > ideally if chimera can output an avi automatically. So i guess, > viewdock should work IF there is a way to capture all the images to > disk rather than just play them to the screen. > > S Joshua Swamidass > > > On Sat, 25 Dec 2004 09:29:55 -0800, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: >> Hi Joshua, >> Implementing the Mol2 trajectory format looks perfectly doable >> with >> the data file you provided. Before proceeding with the work, I guess >> I >> have a question as to why you want to use the molecular-dynamics Movie >> tool on the file rather than ViewDock tool. You do know that the >> ViewDock tool has a "Movie" menu >> (http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ >> viewdock/viewdock.html#movmenu) that allows you to step through docked >> conformers one by one? I guess I'm trying to determine if I should >> really be adding this fomat to the Movie tool or if we should somehow >> be improving the capabilities of ViewDock instead. >> >> --Eric

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Just fixed Re: [Chimera-users] WinXP SP1 python error on File -> Open
by Li Wang 04 Jan '05

04 Jan '05

Dear all, I forgot to attach the python code in my previous email. Please let me know if there is anything wrong with the code. By the way, I am using the Chimera beta version 1, build 1917, 2004/03/08. Should I download the newer version, version 1 build 2065? Thank you so much for your help in advance. Li

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Just fixed Re: [Chimera-users] WinXP SP1 python error on File -> Open
by Li Wang 04 Jan '05

04 Jan '05

Dear Eric, I just join the Chimera-users discussion group and haven't got reply email. However I checked the archive and found your reply email related to the WinXP SP1 python error on File -> Open. I have been using Chimera to generate the colorful ribbon picture for the pdb file using command line. Now I am tring to figure out the general way of defining the bfactor range corresponding to the different colors. I found the flexible python code for making the rainbow color by bfactor and tried it out. But it ended up with the file/open error message as I didn't see any problem in the code. Attached please find the copy of the python code. I did replace bo and b1 by min and max of bfactors in the pdb file. Your help and suggestion are greatly appreciated. Li Wang Biomedical Informatics of OSU Columbus, OH (w) (614)688-3236

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Mol2 Trajectory Reader?
by S Joshua Swamidass 21 Dec '04

21 Dec '04

Hello, How hard would it be to write an extension to chimera that read a multimolecule mol2 file into chimera as a trajectory? That would be really useful for me. Please let me know if you can do it or some advice on how to procede. S Joshua Swamidass

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Chimera Guassian Cube Extension
by S Joshua Swamidass 20 Dec '04

20 Dec '04

Hello, I have a bit of code to contribute. It allows chimera to read grid files in the GUASSIAN ascii grid format described here: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html It ignores any bond information. Who should i send it to so it will be incorporated into future releases? S Joshua Swamidass

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production release
by Eric Pettersen 17 Dec '04

17 Dec '04

Hail fellow Chimerians, We just put out a production release (version 1.2065). It is basically the same as the preceding release candidate (1.2056) except for a lot of bug fixes. The only new features are support for saving scenes in X3D format [but see the release notes for caveats], and some changes in how the label/rlabel commands interact. The release notes are at: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2065.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Chimera Multiscale using VRML?
by Thomas Goddard 13 Dec '04

13 Dec '04

Hi Dong, Here is an example VRML file that contains a virus particle model. It uses a cone as the icosahedral asymmetric unit. You could change the definition of the asymmetric unit at the top of the VRML. This file will display in Chimera 1.2056. Tom ----- File icos.vrml follows: #VRML V2.0 utf8 Transform { children [ DEF asymmetric_unit Transform { translation 0 5 0 children [ Shape { geometry Cone {} } ] } Transform { rotation 0.00000000 0.00000000 1.00000000 0.00000000 children USE asymmetric_unit } Transform { rotation -0.30901699 0.80901699 -0.50000000 3.14159265 children USE asymmetric_unit } Transform { rotation 0.57735027 0.57735027 -0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation 0.93417236 -0.35682209 -0.00000000 2.09439510 children USE asymmetric_unit } Transform { rotation 0.85065081 0.00000000 -0.52573111 2.51327412 children USE asymmetric_unit } Transform { rotation 0.52573111 -0.85065081 0.00000000 2.51327412 children USE asymmetric_unit } Transform { rotation 0.30901699 0.80901699 -0.50000000 3.14159265 children USE asymmetric_unit } Transform { rotation -0.00000000 -0.52573111 0.85065081 2.51327412 children USE asymmetric_unit } Transform { rotation 0.35682209 0.00000000 -0.93417236 2.09439510 children USE asymmetric_unit } Transform { rotation 0.52573111 -0.85065081 0.00000000 1.25663706 children USE asymmetric_unit } Transform { rotation 0.57735027 -0.57735027 -0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation 0.00000000 -0.93417236 0.35682209 2.09439510 children USE asymmetric_unit } Transform { rotation -0.50000000 -0.30901699 0.80901699 3.14159265 children USE asymmetric_unit } Transform { rotation -0.35682209 0.00000000 0.93417236 2.09439510 children USE asymmetric_unit } Transform { rotation 0.00000000 -0.52573111 -0.85065081 2.51327412 children USE asymmetric_unit } Transform { rotation -0.52573111 -0.85065081 -0.00000000 1.25663706 children USE asymmetric_unit } Transform { rotation 0.00000000 -0.93417236 -0.35682209 2.09439510 children USE asymmetric_unit } Transform { rotation -0.57735027 -0.57735027 0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation -0.50000000 0.30901699 0.80901699 3.14159265 children USE asymmetric_unit } Transform { rotation -0.57735027 0.57735027 0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation 0.30901699 0.80901699 0.50000000 3.14159265 children USE asymmetric_unit } Transform { rotation -0.93417236 -0.35682209 0.00000000 2.09439510 children USE asymmetric_unit } Transform { rotation -0.52573111 -0.85065081 0.00000000 2.51327412 children USE asymmetric_unit } Transform { rotation -0.85065081 0.00000000 0.52573111 2.51327412 children USE asymmetric_unit } Transform { rotation -0.30901699 0.80901699 0.50000000 3.14159265 children USE asymmetric_unit } Transform { rotation -0.52573111 0.85065081 0.00000000 2.51327412 children USE asymmetric_unit } Transform { rotation 0.52573111 0.85065081 0.00000000 2.51327412 children USE asymmetric_unit } Transform { rotation 1.00000000 0.00000000 0.00000000 3.14159265 children USE asymmetric_unit } Transform { rotation 0.80901699 0.50000000 -0.30901699 3.14159265 children USE asymmetric_unit } Transform { rotation 0.80901699 -0.50000000 -0.30901699 3.14159265 children USE asymmetric_unit } Transform { rotation 0.00000000 1.00000000 0.00000000 3.14159265 children USE asymmetric_unit } Transform { rotation 0.85065081 -0.00000000 -0.52573111 1.25663706 children USE asymmetric_unit } Transform { rotation 0.57735027 -0.57735027 0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation -0.00000000 0.52573111 -0.85065081 2.51327412 children USE asymmetric_unit } Transform { rotation 0.50000000 -0.30901699 0.80901699 3.14159265 children USE asymmetric_unit } Transform { rotation 0.00000000 0.52573111 -0.85065081 1.25663706 children USE asymmetric_unit } Transform { rotation 0.85065081 0.00000000 0.52573111 1.25663706 children USE asymmetric_unit } Transform { rotation 0.93417236 0.35682209 0.00000000 2.09439510 children USE asymmetric_unit } Transform { rotation 0.80901699 -0.50000000 0.30901699 3.14159265 children USE asymmetric_unit } Transform { rotation 0.00000000 0.93417236 -0.35682209 2.09439510 children USE asymmetric_unit } Transform { rotation -0.57735027 0.57735027 -0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation 0.52573111 0.85065081 -0.00000000 1.25663706 children USE asymmetric_unit } Transform { rotation 0.85065081 0.00000000 0.52573111 2.51327412 children USE asymmetric_unit } Transform { rotation 0.80901699 0.50000000 0.30901699 3.14159265 children USE asymmetric_unit } Transform { rotation -0.93417236 0.35682209 -0.00000000 2.09439510 children USE asymmetric_unit } Transform { rotation 0.00000000 0.93417236 0.35682209 2.09439510 children USE asymmetric_unit } Transform { rotation -0.52573111 0.85065081 0.00000000 1.25663706 children USE asymmetric_unit } Transform { rotation 0.57735027 0.57735027 0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation -0.85065081 0.00000000 -0.52573111 2.51327412 children USE asymmetric_unit } Transform { rotation -0.57735027 -0.57735027 -0.57735027 2.09439510 children USE asymmetric_unit } Transform { rotation -0.85065081 -0.00000000 0.52573111 1.25663706 children USE asymmetric_unit } Transform { rotation 0.00000000 0.52573111 0.85065081 2.51327412 children USE asymmetric_unit } Transform { rotation -0.00000000 0.52573111 0.85065081 1.25663706 children USE asymmetric_unit } Transform { rotation 0.50000000 0.30901699 0.80901699 3.14159265 children USE asymmetric_unit } Transform { rotation -0.85065081 0.00000000 -0.52573111 1.25663706 children USE asymmetric_unit } Transform { rotation -0.00000000 -0.52573111 -0.85065081 1.25663706 children USE asymmetric_unit } Transform { rotation 0.00000000 -0.52573111 0.85065081 1.25663706 children USE asymmetric_unit } Transform { rotation 0.00000000 0.00000000 1.00000000 3.14159265 children USE asymmetric_unit } Transform { rotation 0.35682209 0.00000000 0.93417236 2.09439510 children USE asymmetric_unit } Transform { rotation -0.35682209 0.00000000 -0.93417236 2.09439510 children USE asymmetric_unit } ] }

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Chimera export surfaces as VRML questions
by Thomas Goddard 10 Dec '04

10 Dec '04

Hi Dong, I have fixed the grayed out "Open" button in Chimera 1.2056 "Export surfaces as VRML" extenstion and that fix will be in our upcoming release (a few weeks). We are working on being able to export molecules (ribbons, ball and stick, ...) as well. We have written code that exports X3D format which is a successor to VRML format. There is no Chimera user interface for writing an X3D file yet. Few programs are able to read X3D so we may need to find a way to convert the X3D to VRML. Greg Couch on the Chimera development team is working on the X3D output. I don't know if it will be available in our next release. You mention that you had to eliminate the outermost part of the VRML code that Chimera exports Transform { children [ ] } in order to get some programs to read it. The Transform node is very common. I'm surprised it is causing trouble. What program is unable to read the unedited version of the Chimera VRML output? The Transform node usually positions the enclosing model (rotating and translating). Our current VRML output doesn't specify any rotation or translation so the VRML output does not preserve the orientation you have in the Chimera graphics window. It should. So instead of removing the Transform node I think the next step will be to add the correct rotation and translation information. I'll respond to your Multiscale questions in a separate email. Tom > Dear my concern > > Thank you for the distribution of this nice program, Chimera! > > Recently I downloaded new version of Chimera for Win32, 2056 build. > > Most of all function is fine but when I tried to export surface as VRML, the > button for "save" is not activated. > > Instead of "save" there is "open" button. This button could be activated > only by clicking "present file". > > If user clicks that activated button, the original file has gone and > replaced with new content's keeping its name. > > Is there any way to export other model, like ribbon or space fill model as > VRML? > > I think it will be very helpful. > > I tried lots of program, but the other programs are not good as Chimera at > least in terms of VRML export. > > My main purpose of using this program is "Multiscale modeling" ; I am so > interested in virus capsid model. > > It is so fabulous!!. > > I have never seen this function before and I love this.. > > However is it possible to make multiscale model from other format like VRML? > > I don't know exactly how chimera makes multiscale model, but I think chimera > may use the matrix. > > If then, I can guess we can make model from any format file whatever it is. > > Would you help me how to do this work? > > > And one more thing... > > The exported surface file VRML format from chimera starts with > > #VRML V2.0 utf8 > > Transform { > > children [ > > Shape { > > .... > > And ended with ]} > > > However without > > > Transform { > > Children [ > > > > ] } > > Sentence there is no problem to view this file. > > Moreover, some program which can import VRML file does not recognize > original exported file. > > After delete above sentence they could import VRML file. > > > Thank you > > > Dong Hoon Chung

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Chimera Multiscale using VRML?
by Thomas Goddard 10 Dec '04

10 Dec '04

Hi Dong, The Chimera Multiscale extension is described in the Chimera User's Guide in the Tools section. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… It currently calculates surfaces for PDB models and positions multiple copies of those surfaces using matrices, like the BIOMT (biological unit) matrices in PDB file headers. If I understand your question correctly, you want multiscale to use your own VRML model for individual proteins instead of the surfaces it normally calculates. It won't do that, and it is not a simple change to make. If you want a VRML model of a virus and you have the positioning matrices and a VRML surface for one asymmetric unit, you could create a new VRML file in an editor using the Transform VRML node to position each of the subunits. But such a model would not be interactive like the Multiscale models -- you would not be able to change to ribbon display, look at atomic contacts, .... Tom > Dear my concern > > Thank you for the distribution of this nice program, Chimera! > > Recently I downloaded new version of Chimera for Win32, 2056 build. > > Most of all function is fine but when I tried to export surface as VRML, the > button for "save" is not activated. > > Instead of "save" there is "open" button. This button could be activated > only by clicking "present file". > > If user clicks that activated button, the original file has gone and > replaced with new content's keeping its name. > > Is there any way to export other model, like ribbon or space fill model as > VRML? > > I think it will be very helpful. > > I tried lots of program, but the other programs are not good as Chimera at > least in terms of VRML export. > > My main purpose of using this program is "Multiscale modeling" ; I am so > interested in virus capsid model. > > It is so fabulous!!. > > I have never seen this function before and I love this.. > > However is it possible to make multiscale model from other format like VRML? > > I don't know exactly how chimera makes multiscale model, but I think chimera > may use the matrix. > > If then, I can guess we can make model from any format file whatever it is. > > Would you help me how to do this work? > > > And one more thing... > > The exported surface file VRML format from chimera starts with > > #VRML V2.0 utf8 > > Transform { > > children [ > > Shape { > > .... > > And ended with ]} > > > However without > > > Transform { > > Children [ > > > > ] } > > Sentence there is no problem to view this file. > > Moreover, some program which can import VRML file does not recognize > original exported file. > > After delete above sentence they could import VRML file. > > > Thank you > > > Dong Hoon Chung

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Re: [chimera-dev] add h
by Elaine Meng 08 Dec '04

08 Dec '04

On Dec 7, 2004, at 4:17 PM, Virginie Lafont wrote: > > I am a new user of chimera and I already have a question. > I have an protonated aspartic acid in my protein and I was wondering, > is it possible to add hydrogen atom to aspartic acid with chimera? > Thanks > > Virginie Hello Virginie, It is possible, with a few steps. As you already noticed, if you just use "addh" the aspartic and glutamic acid carboxylate groups will not get protonated. In the definitions of these residues, the carboxylate oxygen atoms are type O2-, which would not get protonated. You can use Define Attribute to change the types of these atoms. First you need to know the residue number of the aspartic acid you want to protonate and which of the oxygens (OD1 or OD2) you want to receive the proton. Next, create a define attribute input file in which you specify these two atoms and change type of the oxygen you want protonated to O3 and the one you don't want protonated to type O2 (example attached). There is a file description and more examples in the manual page for Define Attribute, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html In Chimera: open your PDB file of interest run addh (note the aspartic acid is not protonated in this step) Tools... Utilities... Define Attribute (open the previously prepared input file) now run addh again (note the aspartic acid will be protonated) The proton may not be pointing the direction you want, so you will probably then want to rotate the OH to the proper position, as described in http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/ structuremeas.html#adjust My define attribute example file (attached) works with the PDB file 1zik. The define attribute file tells Chimera to change the atom types of Asp residue number 7 in chain B so that the side chain will be neutralized when AddH is run. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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release candidate
by Eric Pettersen 06 Dec '04

06 Dec '04

Hi, We've put out a "release candidate" for download (version 1.2056). We're hoping people will download it and try it and report any problems they find before we make a production release version in early January. The production release candidate will be functionally identical to the production release, except that we will fix any bugs reported between then and now. There are some new features in the 1.2056 release, and if you are interested in those you should really try it out so that if you find any problems they will be fixed in the production release. Here's a synopsis of the major new features since the 1.2038 release: NEW TOOLS: Surface Area/Volume (Utilities) - calculate surface areas and Voronoi volumes with the StrucTools server at http://molbio.info.nih.gov/structbio/basic.html TOOL CHANGES: Movie - support added for MMTK/NetCDF trajectory format - RMSD maps containing all-by-all comparisons among specified frames can be calculated (for all atoms or selected atoms) Volume Viewer - support added for APBS electrostatic potential format and TOM toolbox EM density map format sequence panel (opened from Model Panel) - secondary structure shown with color NEW COMMANDS: matrixget - write the current transformation matrices to a file matrixset - read and apply the transformation matrices from a file mmaker (matchmaker) - command implementation of MatchMaker; generates a sequence alignment for two structures and then superimposes the structures accordingly BUGS FIXED: large structures without HELIX/SHEET records now much faster to open (fixed bug in secondary-structure computation) non-default ribbon scalings from pre-1.2038 versions no longer cause bombing on startup (1.2038 would die at startup for such) Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu

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Command-line MatchMaker
by Eric Pettersen 01 Dec '04

01 Dec '04

> On May 5th 2004, Eric Pettersen wrote: > As for MatchMaker, right now it is too closely tied to the GUI > dialog > to be called from nogui mode. I will work on disassociating the > underlying computation from the graphical interface so that it can > become a command-line command. The hydrogen-bond finder has recently > been given this kind of treatment and is callable from the command line > in the release we will be making later this week. I'll send mail when > the same is true for MatchMaker. The command-line version of MatchMaker will be in our upcoming release-candidate snapshot, which will be out at the end of this week. --Eric

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Labeling Residues
by Stephen P. Molnar, Ph.D. 01 Dec '04

01 Dec '04

I have to admit to being completly flumoxed [sic] by this one! How do I label an individual residue: According to help the format is: wt %(1-letter code)s%(number)s Now I have an enzyme, 1QTI.pdb in which I wish to label the SER200 label. I have tried every combination of the example on the help page that I can think of without success. What is the exact format for creating that label? Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariant http://www.geocities.com/FoundationForChemistry

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netCDF trajectories?
by John R. Frank 24 Nov '04

24 Nov '04

Tom and other users, Based on this posting, I deduce that Chimera's Movie capability cannot yet display netCDF trajectories: http://www.cgl.ucsf.edu/pipermail/chimera-users/2004-June/000171.html MMTK generates netCDF trajectories. Can you recommend any already-built tools for converting them to multi-model PDBs? Or, perhaps you can direct me to the parts of Chimera where I could help add netCDF trajectory support? John -- ___________________________ John R. Frank <jrf(a)mit.edu> Physics Graduate Student mobile: 857-928-0614

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Re: [Chimera-users] Select Function
by Elaine Meng 23 Nov '04

23 Nov '04

Dear Dr. Molnar, All chains present in structures open in Chimera should be listed. If two chains have the same ID, however, they will not have separate listings in Select/Chain. Another thing that might be confusing is that residues can be assigned to chains named "het" or "water": Any HETATM residue that does not already have a chain identifier is assigned to chain HET, unless the residue is named WAT or HOH, in which case it is assigned to chain WATER. Additional possibilities are a bug or something strange with the input files. If you have some input files that demonstrate the problem (and don't mind sharing them), you could send them to me or to chimera-bugs(a)cgl.ucsf.edu along with a short explanation of how to duplicate the problem (how files were opened, what order). Best, Elaine ------------- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Select Function
by Stephen P. Molnar, Ph.D. 23 Nov '04

23 Nov '04

I want to load two files, one for the protein and the other for the ligand. This is, of course, not a problem. The question is how do I get both files to be present as choices in Select/Chain? Some times both of them are there, but at other times only the first one that I loade. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariant http://www.geocities.com/FoundationForChemistry

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Chimera / APBS
by Thomas Goddard 23 Nov '04

23 Nov '04

Hi Miguel, Eric Pettersen passed to me your question about Chimera reading APBS electrostatic potential maps. It looks easy to add -- probably only take me a couple hours if it is the OpenDX file format described in the APBS documentation. Could you provide me an small example file? I'll be on vacation this week starting this afternoon but I can probably do it early next week and send you the Python code for use in your current version of Chimera. Tom

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orientation matrix
by Miguel Ortiz Lombardía 18 Nov '04

18 Nov '04

Hi all, Sorry, this question may be very simple, but I didn't manage to find an answer in the documentation. Is it possible to read a transformation (rotation + translation) matrix so that the molecule is displayed exactly in the orientation you wish? Thank you! Miguel -- University of York Structural Biology Lab email: mol1(a)york.ac.uk http://www.ysbl.york.ac.uk/~mol ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées

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orientation matrix
by Miguel Ortiz Lombardía 31 Oct '04

31 Oct '04

Hi all, Sorry, this question may be very simple, but I didn't manage to find an answer in the documentation. Is it possible to read a transformation (rotation + translation) matrix so that the molecule is displayed exactly in the orientation you wish? Thank you! Miguel -- University of York Structural Biology Lab email: mol1(a)york.ac.uk http://www.ysbl.york.ac.uk/~mol ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées

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Chimera production release
by Eric Pettersen 20 Oct '04

20 Oct '04

We have now made a production release, version 1.2038, that corrects a few problems in the 1.2029 snapshot and adds a tiny number of new features. The salient new features that weren't in the 1.2029 snapshot are: Actions...Label now allows much more flexible labeling of residues Per-Model Clipping now allows a model's clip plane to be aligned with the clip plane of another model, and allows a clip plane to be flipped 180 degrees. The 1.2029 bug fixes are explicitly listed in the 1.2038 release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2038.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [Chimera-users] Specifying residue color of residues with a text file
by Elaine Meng 20 Oct '04

20 Oct '04

Hi David, You can specify residues and corresponding R,G,B values using Define Attribute, which is included in our newer releases (snapshot 1.2029 and production release 1.2038, of which I recommend the latter). Basically, this tool reads a file that specifies the residues and the associated values. The manual page for Define Attribute can be viewed at: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… including three examples near the end: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin… There are two general approaches you may want to consider: (1) the direct approach that you described. Just reassign R,G,B values to the existing attribute of atom color and/or residue ribbonColor. This is most like the third example, except that you would use residue specifications by number (e.g., :12.A) instead of name, and the color specifications would be in the form of R G B (e.g., 1.0 0.2 1.0) instead of color names. (2) a less direct approach but one that provides more flexibility in how you show the data. Create your own new attribute (as in the first example). Then, you can use Render by Attribute (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html) to show these values with colors, atom radii, and/or "worm" radii. The data will show as a histogram, and the mapping to colors and radii can be controlled with markers you place on the histogram. This may be a lot to digest, so please feel free to contact us with any further questions/issues. Thanks, Elaine ------------------- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu 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-users] Specifying residue color of residues with a text file
by David Piper 20 Oct '04

20 Oct '04

Chimera, Is it possible to provide a color input file that would include a residue number and an [R,G,B] value to color each residue in a structure? Or does one simply have to select each residue seperately within the program and specify an [R,G,B] value? For example, I would like to map some experimentally measured, functional data onto a model structure by coding it into a color. Would be much easier to use a lookup table of values than click and set each one. Thanks, David

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new Chimera snapshot release
by Eric Pettersen 19 Oct '04

19 Oct '04

Hi all, A new Chimera snapshot release (version 1.2029) is now available for download. I've summarized the major changes since the last release (1.1951) below. A list of _all_ the changes since the last release is in the release notes: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2029.html Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu General changes --------------- The "web fetch" part of the "File...Open" dialog has been split off into its own "Fetch by ID" dialog. The Fetch dialog now supports fetching NDB IDs. Labels are now offset in the viewing coordinate system (rather than the model coordinate system), making them much less likely to be obscured. Moved C3' off of ribbon backbone so that the sugar ring isn't distorted. New Tools --------- Nucleotides (Graphics): create various nucleotide-specific depictions, such as stylized representations of base pairings or filled sugar rings Define Attribute (Utilities, Programming): assign values to new or existing attributes of atoms, residues, or models. Particularly useful in conjunction with the Render by Attribute tool. Tool Changes ------------ AddH improved to avoid steric clashes (and appears in model panel) Match -> Align can handle circular permutations in multiple alignments [formerly only in pairwise] Movie can read PSF/DCD files from CHARMM, NAMD, and X-PLOR; can read PDB-format trajectories (single concatenated file or one file per frame) Multalign Viewer can save a subset of an alignment to a file Multiscale Models includes the zone-selection options Near and Contacts PipesAndPlanks now connects the secondary structure elements with loops Web Data preference category renamed to Web Access and includes HTTP proxy options Render by Attribute implements Radii section (atom radius scales with attribute value) and Worms section ("worm" ribbon radius scales with attribute value) Ribbon Style Editor scalings are now treated similarly to cross sections (per-residue, no startup default except in New Molecules preferences); new "residue class" tab allows specification of which atoms should guide the ribbon, this generalizing ribbons to polymers other than standard peptides and nucleic acids ViewDock includes new interface for choosing compounds by descriptor values New Commands ------------ addaa: add amino acids to the C-terminus of a peptide/protein addh: add hydrogens (command implementation of AddH) bond/~bond: create and delete bonds chirality: report the R/S configuration of a chiral center (see User's Guide for caveats) defattr: define a new attribute and/or assign attribute values (command implementation of Define Attribute) rangecolor: color over a range according to attribute values rmsd: evaluate the RMSD between specified sets of atoms (without matching) Command Changes --------------- atom specification operators added for union (|) and negation (~) [previously just intersection (&) and operators for combining attributes] hbonds has "tilde version" (~hbonds) which removes the pseudobonds showing hydrogen bonds labelopt info has "res" or "residue" keyword indicating that only residue name and number should be shown (not atom name) rainbow can color by model (previously only by residue or chain); likewise for Rainbow tool select has "up" or "down" arguments which behave like up-arrow and down-arrow to broaden and narrow a pre-existing selection

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Help, chimera keeps crashing on startup
by Ann Mullin 19 Oct '04

19 Oct '04

Hi, I run Chimera on MacOS 10.3 with X11. Today I started having problems with Chimera crashing on startup. I deleted the programs and downloaded them again. No help. I reinstalled X11. Again no help. Thanks for all help. Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amullin(a)tulane.edu

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by Dr .Julio Ortiz 13 Oct '04

13 Oct '04

Dear Srs: I am a new user of Chimera, and I really like it! I would like to know if some of the developers could include a new format for density maps amongs those that are readable in Chimera: EM format. That would increase its use in our group, because now we need convert our density maps to mrc each time that we want to use Chimera. With my actual skills in programming, to write a plugin will take me like a year, and I think that should be relative easy for someone with experience. As attachment I am sending a text file with a procedure wrote in matlab to read EM format files. The syntax should not be so different from python. I could also provide you with test data. Thank you very much for your help, Dr. Julio Ortiz -- Max-Planck Institut für Biochemie Abteilung Molekulare Strukturbiologie Am Klopferspitz 18 D-82152 Martinsried Germany Tel: +49 (89) 8578 2034 fax: +49 (89) 8578 2641 --------------------------------------------------------------------- This message was sent using https://webmail.biochem.mpg.de If you encounter any problems please report to rz-linux(a)biochem.mpg.de

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[Chimera-users] Re: streaks in Chimera image of virus electron density map
by Thomas Goddard 12 Oct '04

12 Oct '04

Hi Lu, The streaks on your Chimera density map display are very likely a driver bug specific to the Mac ATI Radeon 9600 Pro (RV350, 64 Mb). You don't see the streaks on a Mac with Radeon 9600 XT graphics (RV360, 128 Mb), and I don't see them with your data set on my Mac Radeon 9800 Pro (R350, 128 Mb). Setting the transparency to a non-zero value makes the streaks go away. When you use transparency Chimera does not use OpenGL display lists. This suggests that the graphics driver bug is related to display lists. OpenGL is an industry standard 3D graphics library that Chimera uses. We have had alot of graphics driver problems with Apple. We submit bug reports to them and sometimes visit them in Cupertino, but it is unlikely we could get this fixed since it appears to be limited to a graphics card they no longer sell. If the streaks do not bother you on-screen too much, a reasonable work-around might be to set transparency to 0.001 just when saving an image. This setting will substantially slow down rotation of the model so it is best to leave the transparency at 0 until you get the right orientation for image saving. Thanks for reporting the problem. Tom > Date: Tue, 12 Oct 2004 14:23:37 -0700 > From: Lu <lugan(a)scripps.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: streaks in Chimera image of virus electron density map > > Hi Tom, > I see definitely see streaks in the Chimera display, and they appear to be > parallel to the one of the crystal lattices. They remain even if I rotate > the particle. When I loaded a .pdb with axis coordinates, they appear > parallel with the Y-axis. Another phenotype is that if I make the > transparency non-zero, the streaks go away. > The graphics card is an ATI Radeon 9600 Pro, 64mb. We don't notice this > problem on our other G5, which has an ATI RV360 chip with 128MB of RAM. So > there's a possibility that either our video card is bad, or that specific > ATI model has some issues. > I've attached an example map (which is a low resolution crystal structure > by the way) of our virus particle. It's dsn6/omap formatted. > I hope the problem is just isolated to our video card. > Thanks. > > -Lu > > On Tue, 12 Oct 2004, Thomas Goddard wrote: > > > Hi Lu, > > > > I took a look at the virus EM map image you sent to Eric Pettersen. > > I haven't seen this bug in Chimera. Do you see the streaks in the > > Chimera graphics window? Or do they only appear in the saved image? > > If they appear in the graphics window are they features that persist > > when the model is rotated? Also are the streaks parallel the data set > > x, y, or z axis? You could see this by displaying the outline box > > around the map with volume viewer / options / show outline box. > > > > I have the same Mac as you only my RV350 has 128 Mb. Do you happen > > to know what model graphics card you have, for example, mine is Radeon > > 9800 Pro? I don't think you can find this out from Mac OS -- you just > > have to know from when the machine was purchased. > > > > I suspect our latest Chimera snapshot release 2029 that just came > > out will exhibit the same problem. But it might be worth trying it. > > > > Can you reproduce the streaks with any small data set that I could > > get from you (by web, ftp, or email)? > > > > Hopefully we'll be able to figure this out quickly. > > > > Tom > >

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Re: [Chimera-users] display vectors
by Eric Pettersen 11 Oct '04

11 Oct '04

On Oct 11, 2004, at 6:50 AM, Mingfeng Yang wrote: > I want to show motions of some atoms. Is it possible to draw vectors > origin from each atoms in Chimera? Specifically, I like to draw an > arrow, originning from each atom, with direction and length to > describe the motion. The answer is yes, though the process is a little involved. Can I ask you in what context you are doing this? Is it related to an MD trajectory? Perhaps in future releases we could make this easier if we know specifically what you want to do and what data you are working from. Anyway, there are two methods I can suggest: VRML and pseudobonds. You can show exactly what you want with VRML, but it may be more effort. Pseudobonds may be easier, but you can’t have arrowheads. For VRML, you just compose a VRML file using a cylinder and cone for each arrow. The cone is the “arrowhead” and you have the cylinder go from the atom to the base of the cone, and have the cone point in the right direction. If you don’t know how to use VRML, this page has a spec and examples: http://www.web3d.org/x3d/specifications/vrml/ISO_IEC_14772-All/ index.html For pseudobonds, you would make up a fake molecule where the “atoms” are at the ends of the vectors you want to show. If you make a PDB file, start it with a TER card and use HETATM records for each atom, with a different residue number for each. This will ensure that Chimera won’t connect any of the atoms in the fake molecule. You can then use the PBReader tool (in the Utilities category) to read in the pseudobonds to display (including colors and optional labels). You can use the pseudobond panel (under inspectors) to control if the pseudobonds are wires or sticks, if they are dashed [wire only], and so forth. Let me know if you need any more help getting started with this. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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[Chimera-users] streaks in Chimera image of virus electron density map
by Lu 11 Oct '04

11 Oct '04

Hello, I've been using Chimera to generate beautiful images of entire virus particle from an O-style map file. However, most of the images that I capture have a few black streaks in the image. The streaks appear as thin, parallel lines, like someone dragged a pen across a painting before it dried. Does anyone know how I can remove these streaks without having to resort to Photoshop? I can provide sample images too. Thanks in advance! -Lu Gan

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Problems in Windows XP
by Jutta J Roth 28 Sep '04

28 Sep '04

To whom it may concern: We have been trying to run chimera in Windows XP and unfortunately are not able to do so. The program runs great on the Mac machines though. The only problem obvious for us is, that the collaboratoryHub shortcut does not show up. We can start the program, but when we try to open a file the sequence window starts flickering and the structure does not load. We really like the program a lot and would like to cite it in a paper we are currently working on, but in order to do that we need to get it to work on the PCs. Therefore every advice would be highly appreciated. Thanks! Sincerely, Jutta Roth ''''''''''''''''''''''''''''''''''''''''''''''' Jutta Johanna Roth Department of Ecology and Evolutionary Biology Yale University 165 Prospect Street New Haven, CT 06511 Tel.: 203.432.9741 (w) 203.776.2364 (h) Fax: 203.432.3870

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display of single letter AA code?
by Mark Daniels 28 Sep '04

28 Sep '04

Hello Chimera administrator(s)- I was wondering if there is any way fior Chimera to display amino acid residue names in single-letter format, rather than the three-letter format one gets when selecting Actions-->Label-->residue-->name ? I have looked over all the documentation I can but have not found anything to answer this question. Thanks in advance- Mark Mark J Daniels Department of Cell Biology The Scripps Research Institute La Jolla, CA 92037

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Request info
by Negi, Surendra S. 22 Sep '04

22 Sep '04

Hi, How can i save some region of an EM data in Chimera. I can corp the region of my interest in EM map using chimera but I am unable to save the data in mrc format. How can i save this region of EM data in mrc file. Thanks for your help. Best, surnedra

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Fwd: [Chimera-users] Chimera, Python, WindowsXP or AMD64 conflict?
by David Piper 17 Sep '04

17 Sep '04

Unfortunately, there is not a suitable graphics driver update for the ATI Radeon card for the notebook I am using. David

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Just fixed Re: [Chimera-users] WinXP SP1 python error on File -> Open
by Pattanayek, Sabuj 17 Sep '04

17 Sep '04

Hi, I just tried this and it fixed the problem: Delete these directories: C:\Documents and Settings\All Users\Application Data\chimera C:\Documents and Settings\sabuj\Application Data\chimera (whatever your username may be) Then uninstall and reinstall chimera and file->open works again. Thanks, ...Sabuj Quoting "Pattanayek, Sabuj" <sabuj.pattanayek(a)vanderbilt.edu>: > Hi, > > I'm getting a strange error when I start chimera and do file->open. This is > the > reply log: > > ValueError: list.index(x): x not in list > (see reply log for Python traceback info) > Traceback (most recent call last): > File "C:\Program Files\Chimera\share\__main__.py", line 56, in ? > value = chimeraInit.init(sys.argv) > File "C:\Program Files\Chimera\share\chimeraInit.py", line 301, in init > tkgui.eventLoop() > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2891, in > eventLoop > app.mainloop() > File "C:\Program Files\Chimera\bin\lib\lib-tk\Tkinter.py", line 965, in > mainloop > self.tk.mainloop(n) > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1751, > in > __call__ > _reporterror(self.func, args) > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1814, > in > _reporterror > displayerror(msg) > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1377, > in > displayerror > _errorReportFile.write(text + '\n') > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, > in > __call__ > return apply(self.func, args) > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 272, in > _importModel > clientSticky='ew') > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 178, in > __init__ > OpenModeless.__init__(self, **kw) > File "C:\Program Files\Chimera\share\OpenSave\__init__.py", line 185, in > __init__ > ModelessBase.__init__(self, **self.dialogKw) > File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 378, in > __init__ > BaseDialog.__init__(self, master, *args, **kw) > File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 220, in > __init__ > self.fillInUI(self.__top) > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 181, in > fillInUI > OpenModeless.fillInUI(self, parent) > File "C:\Program Files\Chimera\share\OpenSave\__init__.py", line 92, in > fillInUI > self.millerBrowser = MillerBrowser(parent, **self.millerKw) > File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 184, in > __init__ > self.makeMainColumn(initialdir, firstTime=1) > File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 509, in > makeMainColumn > titleMode=None, firstTime=firstTime) > File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 823, in > __init__ > index = normItems.index( > ValueError: list.index(x): x not in list > > I have also posted the screenshot here > http://linegli.mc.vanderbilt.edu/~sabuj/chimeraOpenError.jpg > > Also if I do "c:\Program Files\Chimera\bin\chimera.exe" file.pdb from the > command line, then do file -> open, it works again. I've tried running it > with > and without precompiling modules after installation, but get the same > result. > > I've downloaded the binary installation several times, done uninstall, then > install, but I'm still getting the same error. I have not been able to > re-create > the error on another winxp sp1 machine. > > Any help would be appreciated, > Thanks, > Sabuj Pattanayek > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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WinXP SP1 python error on File -> Open
by Pattanayek, Sabuj 17 Sep '04

17 Sep '04

Hi, I'm getting a strange error when I start chimera and do file->open. This is the reply log: ValueError: list.index(x): x not in list (see reply log for Python traceback info) Traceback (most recent call last): File "C:\Program Files\Chimera\share\__main__.py", line 56, in ? value = chimeraInit.init(sys.argv) File "C:\Program Files\Chimera\share\chimeraInit.py", line 301, in init tkgui.eventLoop() File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2891, in eventLoop app.mainloop() File "C:\Program Files\Chimera\bin\lib\lib-tk\Tkinter.py", line 965, in mainloop self.tk.mainloop(n) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1751, in __call__ _reporterror(self.func, args) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1814, in _reporterror displayerror(msg) File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1377, in displayerror _errorReportFile.write(text + '\n') File "C:\Program Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 272, in _importModel clientSticky='ew') File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 178, in __init__ OpenModeless.__init__(self, **kw) File "C:\Program Files\Chimera\share\OpenSave\__init__.py", line 185, in __init__ ModelessBase.__init__(self, **self.dialogKw) File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 378, in __init__ BaseDialog.__init__(self, master, *args, **kw) File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 220, in __init__ self.fillInUI(self.__top) File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 181, in fillInUI OpenModeless.fillInUI(self, parent) File "C:\Program Files\Chimera\share\OpenSave\__init__.py", line 92, in fillInUI self.millerBrowser = MillerBrowser(parent, **self.millerKw) File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 184, in __init__ self.makeMainColumn(initialdir, firstTime=1) File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 509, in makeMainColumn titleMode=None, firstTime=firstTime) File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 823, in __init__ index = normItems.index( ValueError: list.index(x): x not in list I have also posted the screenshot here http://linegli.mc.vanderbilt.edu/~sabuj/chimeraOpenError.jpg Also if I do "c:\Program Files\Chimera\bin\chimera.exe" file.pdb from the command line, then do file -> open, it works again. I've tried running it with and without precompiling modules after installation, but get the same result. I've downloaded the binary installation several times, done uninstall, then install, but I'm still getting the same error. I have not been able to re-create the error on another winxp sp1 machine. Any help would be appreciated, Thanks, Sabuj Pattanayek

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Chimera, Python, WindowsXP or AMD64 conflict?
by David Piper 16 Sep '04

16 Sep '04

Chimera, Wonderful software package!!! I am running successfully on my desktop (Intel P4 2.8 GHz; Windows XP Professional) at the lab. On my eMachines M6807 notebook (Mobile AMD Athlon 64 3000+, 800 MHz, Windows XP home edition) although I can start Chimera and open a PDB file, as soon as I try to do anything (say rotate the molecule) I get an error message: Assertion failed! Program: C:\Program Files\Chimera\pythonw.exe File: togl.c Line: 960 Expression: res == TRUE && "Togl_MakeCurrent: failed" I did not see anything on your website addressing such a conflict, but hoped you might have a suggestion for me. Thanks, David Piper

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3D viewing?
by Steven J Kolodziej 15 Sep '04

15 Sep '04

Hi; I was wondering if Chimera had an option for viewing files in 3D from a PC using glasses and if so what hardware is needed. Steve Kolodziej steven.j.kolodziej(a)uth.tmc.edu

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chimera in fink
by Ersatz Sophist 15 Sep '04

15 Sep '04

Hi, Have you considered distributing chimera through fink? Payam ------ "...who search the reason of things Are those who bring the most sorrow on themselves." --Euripides, The Medea ------ "...who search the reason of things Are those who bring the most sorrow on themselves." --Euripides, The Medea

3 3

by Sheetal Patil 07 Sep '04

07 Sep '04

Hello, Iam trying to configure Phantom desktop with Chimera. I get the following error: "Couldnot load Chimers_phantomcursor library.Can you please tell me where I can find this piece of software? Thanks, Sheetal +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ " The future belongs to those, who believe in the beauty of their dreams "

2 1

ribbons of nucleic acids
by Ann Mullin 01 Sep '04

01 Sep '04

Hello, I am wondering how to adjust the ribbons of nucleic acids so that they follow the path of the phosphates or the sugars, anything but the averaged path they have now. I want to show the backbone as a ribbon with bases projecting out, but now some bases float about the backbone. Thanks for any help. Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amullin(a)tulane.edu

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Chimera and building molecules
by Elaine Meng 31 Aug '04

31 Aug '04

Dear Ben, We definitely agree that molecule-building would be a very useful addition to Chimera. Toward this functionality, Chimera includes hydrogen addition; also, the "bond" command has been implemented (and will be available in the next release). Chimera also includes the "swapaa" and "swapna" commands which "mutate" one sidechain or base to another, although they are not very sophisticated. I am not certain what you are referring to in MIDAS, which only had very rudimentary building capabilities and no ability to add hydrogens. The "addgrp" command did allow definition of new amino acid sidechains, but was quite unwieldy and not usable for building in general. Similarly, "addaa" could append one of the standard amino acids to the end of a peptide but was not generalizable to other types of molecules. If you could clarify how you were applying these tools, we might be able to prioritize developments accordingly. Thank you, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu 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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building molecules
by Ben Schuler 31 Aug '04

31 Aug '04

Dear Chimera developers, It seems to me that the manual formation of bonds and building of any type of molecules (not only proteins and nucleic acids), which was a strength of MIDAS, is not supported by Chimera. I would very much welcome an implementation of these features to make Chimera a real replacement for MIDAS. Ben __________________________________________________ Prof. Ben Schuler, PhD Biochemisches Institut, Universität Zürich Winterthurerstr. 190, CH-8057 Zürich Tel: +41 44 635 5535, Fax: +41 44 635 5907 Web: www.biochem.unizh.ch/schuler Email: schuler(a)bioc.unizh.ch

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chimera --send with multiple Chimeras
by Thomas Goddard 22 Jul '04

22 Jul '04

Hi Sandeep, If you have more than one Chimera running on a machine then "chimera --send" sends the file to the most recent one that is accepting connections. Each time you change the Favorites/Preferences/Web Data option to accept connections, that Chimera becomes the most recent. The way this works is there is a list of running Chimera instances that are accepting connections in file (on unix /tmp/chim_webinfo-<username> where <username> is your login name). This file lists the Chimera process id and port number it is listening on. The last line indicates the most recent Chimera that is accepting connections. I wouldn't recommend relying on info in this file since the implementation may change in the future. Tom

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suggest OBJ export option
by Steven McQuinn 19 Jul '04

19 Jul '04

I'm really happy with Chimera, but vexed that every attempt to export a high resolution mesh via the VRML utility ends in a python failure. Have not tried exporting molecular models, only isosurfaces with 250,000+ polygons. What I use instead for export is VMD, which has an .stl export option, providing smaller file sizes than VRML. VMD is buggy on my XP system, requiring several attempts to export correctly. I use Chimera to get my isosurface settings right, then plug these values into VMD. SUGGESTION: If you provided an OBJ mesh export option, nearly every 3d application could utilize the product. The Wavefront OBJ format is the defacto universal exchange format, fairly small file sizes, retaining textures. Should be easy for you geniuses to program. Also, the stereo camera option never "takes." The walleye and crosseye cameras work OK but not the straight stereo pair, which I have to compose from the right and left images. Would like to send the development team some work samples. How do I do that? Please reply to my email address, as I don't read the list. Steven McQuinn _________________________________________________________________ MSN Toolbar provides one-click access to Hotmail from any Web page FREE download! http://toolbar.msn.click-url.com/go/onm00200413ave/direct/01/

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Re: [Chimera-users] PDB-file trajectories
by Eric Pettersen 16 Jul '04

16 Jul '04

I have PDB-file trajectory support working in Movie now. It's only in our internal development version, but I could make a custom snapshot release for anyone who wants to use it immediately. Otherwise, it will be in the next regular release, which will probably be in a month or two. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu > On Thursday, January 8, 2004, at 06:52 AM, amutha ramaswamy wrote: > >> It is possible to make movies with PDB structurers in chimera. this >> would really be helpfull in visualing the conformatinal changes. I >> know chimera has the option for movie with trajectory files. but i >> wish to kow the option with PDB files only. > > Hi Amutha, > I assume you're talking about the situation where you have one PDB > file for each "frame" of a trajectory (or a multi-MODEL PDB file of > the trajectory), rather than a starting and ending PDB file that you > want to "morph" between. Either way, unfortunately, we don't currently > support what you want. However, now that you have pointed out the > usefulness for plain-PDB support in Movie, I can probably add it in > the not-too-distant future. But given my other priorities (including > support for attribute coloring that you mentioned earlier!) the > "not-too-distant future" might still be a couple of months. I'll send > mail when there is at least a preliminary version available.

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How to send files to Chimera
by Thomas Goddard 02 Jul '04

02 Jul '04

Hi Sandeep, To open files in an already running Chimera from your program you can use the chimera --send option. For example, chimera --send myfile.mrc You need to tell Chimera to accept "web data" for this to work. You do this using Chimera menu entry Favorites/Preferences, category Web Data, set "Accept web data" to true. Press the Save button if you want this setting to apply to all future Chimera sessions (saved in ~/.chimera/preferences). If you don't set this preference, the --send command-line option will just start another copy of Chimera. This is described in the Chimera manual where command-line options are described: http://www.cgl.ucsf.edu/chimera/1.1951/docs/UsersGuide/options.html You can do fancier things, like send Python code (*.py files) or Chimera commands (*.cmd or *.com files) to Chimera to show your data in a certain way. You would still use the --send option to send the Python file. These remote control features were added to Chimera so that a web browser link can cause commands and files to be sent to Chimera and this is described in the Chimera manual: http://www.cgl.ucsf.edu/chimera/1.1951/docs/ContributedSoftware/webdata/chi… The hard part here is that volume data display options like threshold levels do not have simple Chimera commands to set them. Instead you have to dig around in the VolumeViewer Python code (in the share directory) in order to see what Python functions set these things. This is not easy to figure out. I can help you if you have specific questions about the Python functions for volume data display. Tom > Date: Fri, 2 Jul 2004 10:01:40 -0600 > From: Sandeep N Seshadri <sandeep(a)nmsu.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Re: [chimera-dev] regd error when opening a .mrc file > > Hi Tom, > sorry for being very confusing . i am trying to open up files generated from my > program . as of now all i do is chimera test1.mrc > > and next time i generate another file i would open it as chimera test2.mrc > > so it would open a new chimera window and show the next .mrc file . what i would > like to do is when i open the second file test2.mrc i would like to see it open > in the already opened chimera window for test1.mrc. > > do you think i can do this ? Please let me know > > Sandeep Seshadri

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[Chimera-users] Re: [chimera-dev] regd error when opening a .mrc file
by Thomas Goddard 01 Jul '04

01 Jul '04

Hi Sandeep, This error indicates that the mrc file data values are all zero. The error occured when making the histogram that is shown in the Volume Viewer dialog, when it was trying to scale it to fit the width of the dialog. Of course, our code should not generate an error in this case. I will fix it for the next release. If you will be opening mrc files that may be all zero you can change chimera/share/VolumeViewer/histogram.py line 26 hscale = float(cheight) / max_height to if max_height == 0: hscale = 1 else: hscale = float(cheight) / max_height Then you will not get any error and the histogram will display correctly. Thanks for pointing out this problem. I am not familiar with pdb2mrc so I do not know why it is generating a volume consisting of all zeros. Tom > Date: Wed, 30 Jun 2004 21:33:12 -0600 > From: Sandeep N Seshadri <sandeep(a)nmsu.edu> > To: chimera-dev(a)cgl.ucsf.edu > Subject: [chimera-dev] regd error when opening a .mrc file > > i am getting the following error when i try to open a .mrc file . i generated a > .pdb file and use a pdb2mrc to generate a .mrc file . i tried opening the .pdb > file it works fine but when i try to open the .mrc file it gives the error. > > if anyone has any idea on why this error occurs please let me know > > thanks > sandeep > > > Error while processing test-helix.mrc: > ZeroDivisionError: float division > (see reply log for Python traceback info) > Traceback (most recent call last): > File "/home/sandeep/chimera/share/__main__.py", line 56, in ? > value = chimeraInit.init(sys.argv) > File "/home/sandeep/chimera/share/chimeraInit.py", line 275, in init > prefixableType=1) > File "/home/sandeep/chimera/share/chimera/__init__.py", line 886, in open > models = func(filename, *args, **kw) > File "/home/sandeep/chimera/share/VolumeViewer/ChimeraExtension.py", line 30, > in open_cb > d.add_data_sets([g]) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 175, in > add_data_sets > self.redisplay_cb() > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 459, in > redisplay_cb > self.show_using_dialog_settings(self.focus_region) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 380, in > show_using_dialog_settings > tp.update_histograms(data_region) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 1142, in > update_histograms > cw.update_histogram(data_region, read_matrix, self.dialog.message) > File "/home/sandeep/chimera/share/VolumeViewer/__init__.py", line 1465, in > update_histogram > h.show_data(Numeric.log(s.counts + 1)) > File "/home/sandeep/chimera/share/VolumeViewer/histogram.py", line 26, in > show_data > hscale = float(cheight) / max_height > ZeroDivisionError: float division

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Is it possible to undo an action?
by Lesheng Kong 30 Jun '04

30 Jun '04

Hi, Is it possible to undo an action in Chimera? I notice that some actions in Chimera can be undid, such as "undo selection" or "undo move". Can every action be undid in Chimera? For example, I colored a selection zone in a different color. But I want to undo this action and recover each atom's previous color. Thank you very much! With best regards, Lesheng

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