- Chimera-users - RBVI Mailing Lists

Protonating the protein
by Francesco Pietra 07 Aug '08

07 Aug '08

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

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

07 Aug '08

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

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ConSurf display in Chimera
by Elaine Meng 06 Aug '08

06 Aug '08

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

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

06 Aug '08

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

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Text statistics from Matchmaker
by nettles 04 Aug '08

04 Aug '08

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

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

01 Aug '08

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

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

01 Aug '08

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

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import GRID contour map
by Sebastian Kruggel 01 Aug '08

01 Aug '08

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

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

01 Aug '08

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

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

01 Aug '08

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

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Distance Lines
by hsosa＠aecom.yu.edu 31 Jul '08

31 Jul '08

Hi , I want to make a solid line (with chosen color) between two atoms. Kind of like the line that appears when measuring distances between atoms, but without the distance legend. Is there an easy way to do that ? Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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PDB morphing
by Dougherty, Matthew T. 28 Jul '08

28 Jul '08

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

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Distance between helices
by Thomas Goddard 28 Jul '08

28 Jul '08

HI Tom How do I compute and show the distance between 2 regions (2 alpha helixes) of 2 crystal structures (docked in the density maps), similar portions of each is already highlighted/selected to show the DNA binding region (without showing the atoms). THanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Re: [Chimera-users] BIOMT matrix in Chimera?
by Elaine Meng 28 Jul '08

28 Jul '08

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

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

28 Jul '08

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

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

25 Jul '08

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

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

25 Jul '08

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

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nogui vrml export?
by Paul 25 Jul '08

25 Jul '08

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

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superimposing active sites
by Elaine Meng 24 Jul '08

24 Jul '08

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

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making MD movie
by bala 24 Jul '08

24 Jul '08

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

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

23 Jul '08

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

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

23 Jul '08

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

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Making a spin movie
by Tom Goddard 23 Jul '08

23 Jul '08

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

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

23 Jul '08

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

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

22 Jul '08

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

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