From s.molnar at sbcglobal.net Wed Dec 1 07:43:22 2004 From: s.molnar at sbcglobal.net (Stephen P. Molnar, Ph.D.) Date: Wed, 1 Dec 2004 10:43:22 -0500 Subject: [Chimera-users] Labeling Residues Message-ID: <20041201104322.61ebced6.s.molnar@sbcglobal.net> 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 From pett at cgl.ucsf.edu Wed Dec 1 10:35:22 2004 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 1 Dec 2004 10:35:22 -0800 Subject: [Chimera-users] Labeling Residues In-Reply-To: <20041201104322.61ebced6.s.molnar@sbcglobal.net> References: <20041201104322.61ebced6.s.molnar@sbcglobal.net> Message-ID: On Dec 1, 2004, at 7:43 AM, Stephen P. Molnar, Ph.D. wrote: > 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? Hi Stephen, I just want to make sure we're on the same page first: these substitution codes only work when using the Actions...Label...residue...custom dialog (i.e. not from other ways to place labels, such as the "label" command or by using the selection inspector). That said, the example works for me. If I have SER200 in 1qti selected, and I cut-and-paste that format into the labeling dialog and hit OK, the residue is labeled "wt S200" in the graphics window. What's the behavior when you do this? --Eric From meng at cgl.ucsf.edu Wed Dec 1 11:00:47 2004 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 1 Dec 2004 11:00:47 -0800 Subject: [Chimera-users] Labeling Residues In-Reply-To: <20041201104322.61ebced6.s.molnar@sbcglobal.net> References: <20041201104322.61ebced6.s.molnar@sbcglobal.net> Message-ID: <4F304D0E-43CB-11D9-8B82-0003933D1350@cgl.ucsf.edu> Hello, Eric already mentioned the most important point: that this is only the format used within the Custom Residue Label dialog (opened with Actions... Label... residue... custom in the Chimera menu). The string starting with "wt" mentioned in your mail is just an example from the man page. If you didn't want "wt" in your label, of course, it shouldn't appear in that string. The Custom Residue Label dialog doesn't actually require anyone to type in those slightly ugly strings by hand, however. If you really wanted the label to be SER200 for example, you would just select that serine residue, open the dialog from the menu, and then click the buttons name number (in that order) and then Apply. Hope this clarifies - Elaine --- Elaine C. Meng, Ph.D. meng at 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 On Dec 1, 2004, at 7:43 AM, Stephen P. Molnar, Ph.D. wrote: > 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 > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From s.molnar at sbcglobal.net Wed Dec 1 12:14:33 2004 From: s.molnar at sbcglobal.net (Stephen P. Molnar, Ph.D.) Date: Wed, 1 Dec 2004 15:14:33 -0500 Subject: [Chimera-users] Labeling Residues In-Reply-To: References: <20041201104322.61ebced6.s.molnar@sbcglobal.net> Message-ID: <20041201151433.129b7714.s.molnar@sbcglobal.net> Thanks, both you and Elaine, for your reply First of all, I had made the Action selections you outlined below. Now, I hate to be so dense (although, after a lifetime of practice at it, I think that I'm rather good at being dense), but how do I select the particular residue that I want to label in 1qti so that I can cut and paste the information. The reason that I want to label it in the first place is so that I can identify the residue in the graphics window. Certainly Select/Residue/Name lets me pick all of the serine residues in the protein, but I only want one of them labeled. I hope that I haven't made my question even more murky than it origionally was. Eagerly awaiting your further explanation. Thanks in advance. On Wed, 1 Dec 2004 10:35:22-0800 Eric Pettersen wrote: > > On Dec 1, 2004, at 7:43 AM, Stephen P. Molnar, Ph.D. wrote: > > > 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? > > Hi Stephen, > I just want to make sure we're on the same page first: these > substitution codes only work when using the > Actions...Label...residue...custom dialog (i.e. not from other ways to > place labels, such as the "label" command or by using the selection > inspector). That said, the example works for me. If I have SER200 in > 1qti selected, and I cut-and-paste that format into the labeling > dialog and hit OK, the residue is labeled "wt S200" in the graphics > window. What's the behavior when you do this? > > --Eric > -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariant http://www.geocities.com/FoundationForChemistry From meng at cgl.ucsf.edu Wed Dec 1 12:17:22 2004 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 1 Dec 2004 12:17:22 -0800 Subject: [Chimera-users] Labeling Residues In-Reply-To: <20041201151433.129b7714.s.molnar@sbcglobal.net> References: <20041201104322.61ebced6.s.molnar@sbcglobal.net> <20041201151433.129b7714.s.molnar@sbcglobal.net> Message-ID: <02942844-43D6-11D9-BE81-0003933D1350@cgl.ucsf.edu> Hello Dr. Molnar, There are a multitude of different ways to make selections. Here is the general "selection" man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html In brief, if you knew where it was on the screen, you could pick it with the mouse (Ctrl-click). If you only know the number you could select it in the command line: select :200 (if no chain ID), or select :200.a (if the residue is in chain A) (you have to give the chain ID if there is one, since there could be another residue 200 in some other chain). Yet another way is to use the sequence panel. (first open the Model Panel from the Favorites menu, and then in the Model Panel choose the model of interest on the left and click the "sequence..." button on the right). sequence panel man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html In the sequence panel: when you mouse over the sequence, the actual numbers in the structure are reported. You can just highlight (in the sequence panel) the residue you want; the default behavior is to select that residue in the structure. Hope this helps, Elaine On Dec 1, 2004, at 12:14 PM, Stephen P. Molnar, Ph.D. wrote: > Thanks, both you and Elaine, for your reply > > First of all, I had made the Action selections you outlined below. > > Now, I hate to be so dense (although, after a lifetime of practice at > it, I think that I'm rather good at being dense), but how do I select > the particular residue that I want to label in 1qti so that I can cut > and paste the information. The reason that I want to label it in the > first place is so that I can identify the residue in the graphics > window. Certainly Select/Residue/Name lets me pick all of the serine > residues in the protein, but I only want one of them labeled. > > I hope that I haven't made my question even more murky than it > origionally was. > > Eagerly awaiting your further explanation. > > Thanks in advance. > > -- > Stephen P. Molnar, Ph.D. Life is a fuzzy set > Foundation for Chemistry Stochastic and multivariant > http://www.geocities.com/FoundationForChemistry From pett at cgl.ucsf.edu Wed Dec 1 13:37:46 2004 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 1 Dec 2004 13:37:46 -0800 Subject: [Chimera-users] Command-line MatchMaker Message-ID: <3DED7B48-43E1-11D9-9266-000393CD9B40@cgl.ucsf.edu> > 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 From pett at cgl.ucsf.edu Mon Dec 6 09:52:36 2004 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 6 Dec 2004 09:52:36 -0800 Subject: [Chimera-users] release candidate Message-ID: <9CDABC60-47AF-11D9-B544-0003933D1350@cgl.ucsf.edu> 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 at cgl.ucsf.edu From meng at cgl.ucsf.edu Wed Dec 8 10:13:17 2004 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 8 Dec 2004 10:13:17 -0800 Subject: [Chimera-users] Re: [chimera-dev] add h In-Reply-To: <41B64828.40400@jhu.edu> References: <41B64828.40400@jhu.edu> Message-ID: 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 at cgl.ucsf.edu Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: defineType.txt URL: -------------- next part -------------- From pett at cgl.ucsf.edu Wed Dec 8 10:58:55 2004 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 8 Dec 2004 10:58:55 -0800 Subject: [Chimera-users] Re: [chimera-dev] add h In-Reply-To: References: <41B64828.40400@jhu.edu> Message-ID: <356E639C-494B-11D9-BD8D-000393CD9B40@cgl.ucsf.edu> On Dec 8, 2004, at 10:13 AM, Elaine Meng wrote: > 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) Wanted to add one little addendum. In the current version of Chimera (1.2056), the first "addh" (before the Define Attribute) is actually necessary -- it is necessary to force Chimera to compute the atom types before overriding them with your own. This will be corrected in the upcoming production release in mid/late December. There are other ways to force the computation besides addh; finding h-bonds or going into ball-and-stick mode (the atom radius depends on the atom type) are a couple of other ways. Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu From goddard at cgl.ucsf.edu Fri Dec 10 16:11:50 2004 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Fri, 10 Dec 2004 16:11:50 -0800 (PST) Subject: [Chimera-users] Chimera export surfaces as VRML questions Message-ID: <200412110011.iBB0Bo4J1962626@guanine.cgl.ucsf.edu> 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 From goddard at cgl.ucsf.edu Fri Dec 10 16:11:50 2004 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Fri, 10 Dec 2004 16:11:50 -0800 (PST) Subject: [Chimera-users] Chimera Multiscale using VRML? Message-ID: <200412110023.iBB0N2fL1857219@guanine.cgl.ucsf.edu> 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/framemulti.html 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 From goddard at cgl.ucsf.edu Mon Dec 13 10:56:44 2004 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 13 Dec 2004 10:56:44 -0800 (PST) Subject: [Chimera-users] Chimera Multiscale using VRML? Message-ID: <200412131856.iBDIuiIZ1833023@guanine.cgl.ucsf.edu> 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 } ] } From Vidana.Epa at csiro.au Thu Dec 16 21:54:58 2004 From: Vidana.Epa at csiro.au (Vidana.Epa at csiro.au) Date: Fri, 17 Dec 2004 16:54:58 +1100 Subject: [Chimera-users] re H-Bonds in ViewDock Message-ID: <58F49C25B66F4C4DA7FE79B9E79C89B905255E@exvicn1-mel.nexus.csiro.au> 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 at csiro.au -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Fri Dec 17 16:43:38 2004 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 17 Dec 2004 16:43:38 -0800 Subject: [Chimera-users] production release Message-ID: 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 at cgl.ucsf.edu http://www.cgl.ucsf.edu From swamidass at gmail.com Mon Dec 20 13:47:41 2004 From: swamidass at gmail.com (S Joshua Swamidass) Date: Mon, 20 Dec 2004 13:47:41 -0800 Subject: [Chimera-users] Chimera Guassian Cube Extension In-Reply-To: References: Message-ID: 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: cube.tgz Type: application/x-gzip-compressed Size: 3660 bytes Desc: not available URL: From swamidass at gmail.com Mon Dec 20 13:49:33 2004 From: swamidass at gmail.com (S Joshua Swamidass) Date: Mon, 20 Dec 2004 13:49:33 -0800 Subject: [Chimera-users] Mol2 Trajectory Reader? Message-ID: 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 From goddard at cgl.ucsf.edu Mon Dec 20 14:37:56 2004 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 20 Dec 2004 14:37:56 -0800 (PST) Subject: [Chimera-users] Chimera Guassian Cube Extension In-Reply-To: (message from S Joshua Swamidass on Mon, 20 Dec 2004 13:47:41 -0800) References: Message-ID: <200412202237.iBKMbutu1734472@guanine.cgl.ucsf.edu> Hi Joshua, I tried your Gaussian cube file reader and it worked fine. I'll look at including it in Chimera. I may want to create the atoms when the file is read. Also the documentation says the number of atoms can be negative indicating it is an orbital cube file. I may want to handle that case, or at least give a sensible error message if such a file is read. Thanks for contributing your code. Tom From pett at cgl.ucsf.edu Tue Dec 21 18:18:51 2004 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 21 Dec 2004 18:18:51 -0800 Subject: [Chimera-users] Mol2 Trajectory Reader? In-Reply-To: References: Message-ID: On Dec 20, 2004, at 1:49 PM, S Joshua Swamidass wrote: > 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. Hi Joshua, I guess I'm curious as to what package puts out trajectories in Mol2 format... The difficulty of adding a format is directly proportional to how fast you need to have the trajectory read. Reading the entire trajectory at startup in interpreted Python is not too difficult to code. Using a C/C++ Python module to read the trajectory and/or reading the frames on demand both increase the coding effort. If you provided me with examples of Mol2-format trajectories, I could probably have support for them done in about a month or possibly less, given the various other demands on my time. Performance would be similar to the multi-MODEL PDB trajectory case, since the entire trajectory would be read in on startup, but using the C++ layer. I've appended an outline of how to add a new trajectory format, in case you want to give it a stab yourself... Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu Adding a New Trajectory Format ---------------------------------------------- Movie actually uses the Trajectory module (chimera/share/Trajectory) to read the various formats. Trajectory has a subdirectory named "formats" that in turn has subdirectories for each supported format (the subdirectories are Python modules). By convention the module name for each format is the name of the format with the initial letter of each word capitalized and all other letters lowercase (e.g. the MMTK module's name is Mmtk). A format's module is typically structured so that the code that interfaces with Trajectory's generic format handling is in the __init__.py file, and the code specific to supporting reading the format's files is in another file -- usually named after the format itself (e.g. Gromos.py). __init__.py: The __init__.py file needs to support the following things: 1) If the name of the format as displayed to the user is different from the module name (which, due to capitalization, it usually is) then there has to be a global variable named "formatName" that is initialized to the display name of the format. 2) A class named ParamGUI needs to be defined that handles presenting the file-loading interface for that format to the user. It must have two methods: 2.1) __init__, which receives a Tkinter.Frame instance argument. The __init__ method should populate the frame with widgets for gathering the input information for the format from the user. 2.2) loadEnsemble, which takes as arguments a starting frame number, ending frame number, and callback function. loadEnsemble needs to compose a list of the arguments that were provided by the user to the widgets defined in the __init__ function, and then call this module's global loadEnsemble method (see below) with that list as the first argument and the start/end frame number and callback as the remaining three arguments. 3) A global loadEnsemble function that generates an ensemble instance (discussed later). This function is not only called by the ParamGUI.loadEnsemble method, but also when the user uses a "metafile" to specify the input parameters. This function takes fours arguments: a format-specific list of input parameters, a starting frame number, ending frame number, and callback function to start the Movie interface. This function should call the Movie-interface callback with the generated ensemble as an argument. This function should also remember the provided format-specific values as preferred defaults for future uses of the format. The code for a format's __init__.py file is very similar from format to format. The easiest way to write your own is to grab another format's __init__.py file and modify it. The __init__.py file for the Gromos format is a good example since it uses multiple input files and and has a non-file parameter as well, so it pretty much covers all the bases in what you might need. The format-specific .py file: This file defines an "ensemble" class that gets instantiated from __init__.py's loadEnsemble function. The ensemble class needs to support the following methods: 1) An __init__ method that takes the format's input parameters and start/end frames as arguments. The __init__ method may read input files or do whatever is necessary to support the other instance methods (i.e. call into a C/C++ module to read the files -- the Amber format does this). 2) A GetDict method that takes a string argument. The string specifies what data should be returned. The possible string values are: 2.1) atomnames -- return a list of the atom names; a residue's atoms must be consecutive 2.2) elements -- return a list of the atom elements. These should be instances of chimera.Element (which can be initialized with a string (e.g. "Fe") or a number). Trajectory's determineElementFromMass function may be useful here if the format doesn't specify the atomic number directly or it can't be easily determined from the atom name. 2.3) resnames -- return a list of the residue names 2.4) bonds -- return a list of "bonds": two-tuples of indices into the atomnames list 2.5) ipres -- a list of the first atom of each residue (indices into atomnames, but unlike previous indices these are 1-based, so the first element of ipres will always be 1) 3) A __getitem__ method taking a frame-number argument (starting with 1): return a list of 3-tuples corresponding to the xyz coordinates of the atoms in that frame (same order as atomnames). The coordinates should be in angstroms. 4) A __len__ method that returns the total number of frames in the trajectory (not just the number of frames between the user-specified start/end frames).