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"Floating exception" error message
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

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(no subject)
by Dong-Yan Tan 27 Jun '08

27 Jun '08

Dear all, We have just installed chimera-1.2470-linux.exe in our Linux computer (SUSE LINUX 9.0 ). We keep getting error message "Floating exeptions" when we are just trying to open a PDB file and the program quits automatically. Has anyone encountered such a problem or have clues about where to look for solutions? Thanks a lot. Dong-Yan -- Dong-Yan Tan Laboratory of Dr. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine Bronx, NY 10461 Tel: 718-430-3451 Email: dtan(a)aecom.yu.edu

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hydrophobic pocket
by bala 27 Jun '08

27 Jun '08

Dear Chimerian's, How do i detect hydrophobic pockets in a protein using chimera ?. Thanks in advance, Bala

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Re: [Chimera-users] Question about avi files in chimera
by Tom Goddard 27 Jun '08

27 Jun '08

Hi Jaap, The AVI files produced by Chimera movie recorder use the MSMPEG-4v2 (Microsoft MPEG4 version 2) video codec and the encoding is done by the open source ffmpeg program. The file size depends on the movie recorder "bit rate" setting (default 2000 Kbits/sec = 250 Kbytes/sec = 15 Mbytes/min). Changing this setting allows you to trade off file size versus image quality. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.… Tom Jaap Brink wrote: > > Hi Tom, > > > > I was wondering given the size difference in avi files that chimera > generates versus other program (Video Edit Magic for instance), which > video codec is being used? I searched the list of embedded software > packages in chimera and found the library of libavcodecs. > > > > Thanks in advance, > > > > Jaap >

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upcoming production release
by Greg Couch 26 Jun '08

26 Jun '08

Hello, We are currently getting ready to put out another chimera production release. At this point, we consider the daily builds to be release candidates, so please download one and try it out. Not all of the daily builds will be production releases, in particular, the Mac OS X Aqua version is not quite ready, and will be a snapshot release. And the Linux off-screen OpenGL version is experimental and will probably stay as a daily build. Greg Couch UCSF Computer Graphics Lab Daily builds: <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html> New features: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html>

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Re: [Chimera-users] how to draw lines in Chimera
by Elaine Meng 24 Jun '08

24 Jun '08

On Jun 24, 2008, at 4:24 PM, Qing Xie wrote: > Hi, > I'm trying to draw a bunch of axes from center (0,0,0). I could do > this > in 'O' by calling this macro: > > begin_object symax > colour blue > stick_xyz 139.05, -0.00, -16.25, -139.05, 0.00, 16.25, 0.25 > stick_xyz -111.40, 43.12, 73.02, 111.40, -43.12, -73.02, 0.25 > stick_xyz -107.48, 80.74, 39.10, 107.48, -80.74, -39.10, 0.25 > stick_xyz -66.72, 119.11, -31.00, 66.72, -119.11, 31.00, 0.25 > stick_xyz 50.41, 73.78, -107.77, -50.41, -73.78, 107.77, 0.25 > stick_xyz 100.65, 0.20, -97.31, -100.65, -0.20, 97.31, 0.25 > stick_xyz -68.88, 113.16, 45.26, 68.88, -113.16, -45.26, 0.25 > stick_xyz -39.02, 80.98, -107.34, 39.02, -80.98, 107.34, 0.25 > stick_xyz 10.15, 0.20, -139.64, -10.15, -0.20, 139.64, 0.25 > stick_xyz 50.47, -73.42, -108.00, -50.47, 73.42, 108.00, 0.25 > end_object symax > > Since I had to use some features in Chimera, do you know what > commands I > should combine to do similar things above? > Thank you! > Sincerely, > Qing Hi Qing, You can make a BILD file defining the objects, for example containing the following: .color medium blue .cylinder 139.05 -0.00 -16.25 -139.05 0.00 16.25 1 .cylinder -111.40 43.12 73.02 111.40 -43.12 -73.02 1 .cylinder -107.48 80.74 39.10 107.48 -80.74 -39.10 1 .cylinder -66.72 119.11 -31.00 66.72 -119.11 31.00 1 .cylinder 50.41 73.78 -107.77 -50.41 -73.78 107.77 1 .cylinder 100.65 0.20 -97.31 -100.65 -0.20 97.31 1 .cylinder -68.88 113.16 45.26 68.88 -113.16 -45.26 1 .cylinder -39.02 80.98 -107.34 39.02 -80.98 107.34 1 .cylinder 10.15 0.20 -139.64 -10.15 -0.20 139.64 1 .cylinder 50.47 -73.42 -108.00 -50.47 73.42 108.00 1 and open it in Chimera to create the objects. I also attached this below as the file sticks.bild to be opened directly in Chimera. I didn't think 0.25 looked that good, but you can edit the file to whatever radius (and color, etc.) that you want. The BILD language also includes many other objects: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.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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Re: [Chimera-users] find levels and morph conformations
by Thomas Goddard 24 Jun '08

24 Jun '08

Hi Ed, The Morph Conformations tool works with submodels. It will not work between two models or submodels that have different numbers of chains. The error message you get means that you are giving it models with different numbers of chains. Tom Edward Brignole wrote: > Tom, > > ... I'd like to use morph conformations between two pdbs each > composed of the same submodels/chains. I've tried to do this through the > dialog but it displays an error telling me "cannot interpolate the > models have different numbers of chains". The only way I can see to do > this is to write the pdb as a mol2 so that all atoms are in a single > model without submodels, open the mol2, and run morph conformations. > Is there another method or is this the simplest? > > Thanks, > Ed

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selecting/displaying zones
by Elaine Meng 24 Jun '08

24 Jun '08

On Jun 24, 2008, at 11:56 AM, Thomas C. Marlovits wrote: > > Am using Chimera and would like to do the following: > - would first like to focus on specific side chain residues (for > example lysines) > - at a specific atom of either one or all lysines present in my > sample, I would like to draw a region of interest (which should be > a sphere with a given distance ... then make it rather transparent > like soap bobbles ...) ... the idea of this is to highlight areas > within a given distance away from this atom > - then I would like to read out all other side chains that are > within such an area ( in a table or so) ... and eventually > highlight them with specific colors ... > > Elaine, is there an easy way to do this ? > Tx, > -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) Hi Thomas, You can definitely (1) select the atoms or residues within a specified cutoff of some other atoms and write a list of what is selected to the Reply Log or to a file. Slightly trickier is (2) displaying a "bubble." (1) The following command selects all atoms within 4.5 angstroms of atom NZ in lysine 92, chain A (example structure 2gbp): select :92.a@nz za<4.5 to select the whole residues with any atom in the zone, use "z" or "zr" instead of "za", and to use all the atoms of that lysine, just omit "@nz" from the command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#zones This selection process can also be done by Ctrl-clicking to select the atom and then using Select... Zone. You can write out a list of the selection with Actions... Write List (click Log if you want to send it to the Reply Log instead). The default is a list of all the atoms individually, but you can set it to "residues" instead to just get one line of output per residue. The command to do that same thing is "writesel" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/writesel.html (2) The "bubble." I imagine something like Volume Eraser would be nice (check it out: Tools... Volume Data... Volume Eraser). However, that does not let you specify particular coordinates for the center. You have to move it around by hand. Volume Eraser really just makes a big atom and gives it a transparent color. You could add an atom in Build Structure (under Tools... Structure Editing), color it a transparent color, and change its radius with "vdwdefine" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ editing.html#build http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html It doesn't let you enter specific coordinates for the atom. However, if you add the atom as a "new model" you can match it to different locations on the first. For example, if the new atom is model 1 and the structure of interest (say 2gbp) is model 0: rep sphere #1 colordef tpink 1 .6 .6 .6 color tpink #1 vdwdef 3.0 #1 vdwdef +1 #1 vdwdef +1 #1 match #1 #0:147.a@nz select #1 za<5 & #0 [... etc. ...] The radius would just be for display purposes. You'd still have to specify the zone distance when selecting. A couple of failed ideas: (a) You can make a spherical surface of specified radius with the command "shape" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html but you cannot directly specify coordinates for the center or easily modify radius after it has been created. (b) Create a spherical object in BILD format. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Disadvantages are inability to make it transparent and having to delete/recreate the object just to change its radius. 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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how could u know the order of atoms?
by Kamal Al Nasr 23 Jun '08

23 Jun '08

Dear Sir/Madam, I am using Chimera viewer..and it is a great viewer ever... I kindly have a question... how could you know (from PDB file) the coorect bonding between atoms? I mean that how could you know that this atom is connected with CA not N nor C.....do u have all these bonds stored already in a database? or you use atom positions to determine that? I appreciate your time.... Kamal

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connectivity
by Jean Didier Pie Marechal 18 Jun '08

18 Jun '08

Dear all, I would like to use chimera to generate inputs for gaussian QM/MM calculations (ONIOM). One of the element I need is the connectivity of the atoms. I looked around the programmer's guide but couldn't find the right module that takes this in charge. what is the way to have access the connectivity of a given molecule? All the best, 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, Juny 18, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 18 > 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. Find contour level to enclose a specified volume (Thomas > Goddard) 2. Re: Find contour level to enclose a specified volume > (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 17 Jun 2008 15:44:57 -0700 > From: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: [Chimera-users] Find contour level to enclose a specified > volume > To: "'Chimera BB'" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <48583E69.5090608(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Ed Brignole asked about setting a volume contouring level so that > the > resulting surface encloses a desired volume (cubic Angstroms). > Attached > is a Python script that does this in two ways. The first way is > fast > but approximate finding the level such that the number of enclosed > grid > points times the voxel volume equals the requested volume. > Estimating > the enclosed volume of the surface this way can give a much > different > result than actually computing analytically the volume within the > surface. The second approach computes surfaces at different > contour > levels and calculates analytically the volume. It uses bisection > to > find the correct contour level. This approach can be slow, about > 30 > seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface > triangles. Most of that time (80%) is actually computing the > enclosed > volume. That should be very fast but the code is checking for > holes in > the surface in a rather slow way. Both methods use the step size > (subsampling) set in the volume dialog. > > Tom >

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