- Chimera-users - RBVI Mailing Lists

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

15 Aug '08

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

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

14 Aug '08

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

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version 1.2540 stability
by James Fethiere 14 Aug '08

14 Aug '08

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

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

14 Aug '08

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

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Color zone with transparency
by Tom Goddard 14 Aug '08

14 Aug '08

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

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Two transparent models
by Tom Goddard 14 Aug '08

14 Aug '08

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

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Hydrogens in proteins
by Walter Novak 14 Aug '08

14 Aug '08

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

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opening CASTp results
by Walter Novak 14 Aug '08

14 Aug '08

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

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calculation of volume
by Navnit Kumar Mishra 13 Aug '08

13 Aug '08

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

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

12 Aug '08

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

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

12 Aug '08

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

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

11 Aug '08

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

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protonating the protein
by Elaine Meng 11 Aug '08

11 Aug '08

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

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Volume planes tool
by Elaine Meng 08 Aug '08

08 Aug '08

Hi Jeff, Here is another idea, still not exactly what you were asking for, but perhaps worth a look. You can use the Per-Model Clipping tool (under Tools... Depiction) to show a thin slab of the data, and you can interactively rotate and translate the slab any way you want relative to the data with the mouse. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/ per-model.html Just choose which model to clip, enable clipping, turn on slab mode and adjust clipping with mouse. You may also want to adjust the contour level in Volume Viewer. I tried it on emd_1274.map in the production release (1.2540). You can use it on solid, surface, or mesh volume displays. Below I attach an image of a slab surface display together with an unclipped solid display (a second copy of the same data). There is also a command to control per-model clipping in a script, mclip. It lets you specify location/orientation in the data coordinate system or the viewing coordinate system. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mclip.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Chimera: doubt on axes measurement
by Giovanni Cardone 08 Aug '08

08 Aug '08

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

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Protonating the protein
by Francesco Pietra 07 Aug '08

07 Aug '08

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

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

07 Aug '08

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

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ConSurf display in Chimera
by Elaine Meng 06 Aug '08

06 Aug '08

Hello everybody, The ConSurf Server <http://consurf.tau.ac.il/> now provides results as Chimera Web data: a single click displays the color-coded query structure and multiple sequence alignment in your locally installed copy of Chimera. For a screenshot and example Web data file, see: http://www.cgl.ucsf.edu/chimera/consurf/consurf.html More about Chimera Web data: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.ht… Special thanks to Elana Erez and the Ben-Tal and Pupko groups at Tel Aviv University, and to Fabian Glaser. Enjoy! Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] mouse selection problem
by Eric Pettersen 06 Aug '08

06 Aug '08

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

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Text statistics from Matchmaker
by nettles 04 Aug '08

04 Aug '08

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

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

01 Aug '08

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

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

01 Aug '08

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

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import GRID contour map
by Sebastian Kruggel 01 Aug '08

01 Aug '08

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

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

01 Aug '08

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

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

01 Aug '08

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

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