December 2004 - Chimera-users - RBVI Mailing Lists

re H-Bonds in ViewDock
by Vidana.Epa＠csiro.au 02 Feb '05

02 Feb '05

Hi Chimera users, I've started to use Chimera recently. When using ViewDock it struck me that it would be very useful, after loading a .mol2 file of ligands and computing H-bonds between them and the receptor, to be able to list the number of H-bonds as a column in the ViewDock ListBox. Or, is it somehow possible to do this already? (One way to fix this might be to have a script that will write the number of H-bonds computed for each molecule in a new .mol2 file, and then read in this modified .mol2 file .... Has anybody done something in this fashion?) Thanks very much. Cheers, Vidana. Vidana C. Epa CSIRO, Division of Health Sciences & Nutrition, 343 Royal Parade, Parkville, Victoria 3052, AUSTRALIA. tel.: (61) - 3 - 9662 - 7345 fax.: (61) - 3 - 9662 - 7347 email: Vidana.Epa(a)csiro.au

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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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Chimera-users December 2004