- Chimera-users - RBVI Mailing Lists

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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