- Chimera-users - RBVI Mailing Lists

(no subject)
by Levy, Hazel C. 02 Jul '08

02 Jul '08

Hi, I am a postdoctoral researcher and an enthusiastic Chimera user. We are trying to finish up a manuscript to submit tomorrow to JSB and we have been frantically trying to figure out how to convert from Chimera's "contour level" to the more conventional "sigma level" for density map viewing at different noise levels. We understand that the higher the contour level the smaller the map volume displayed (less noisy), but we are not quit sure how to report this as a sigma level. Each map that we are comparing has a different contour range assigned, I am wondering if sigma level corresponds to some proportion of the maximum volume. Please let us know how to do this conversion or please point us in the direction toward the person that can help us. Thanks you so much...this information will settle a long-standing mystery for us. Hazel Levy

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Mutate by D- res...
by Yasser Almeida Hernández 30 Jun '08

30 Jun '08

Can Chimera mutate by D-residues? If this is possible, how i can do it? Thanks... -- Yasser Almeida Hernández Estudiante, 4to Año Bioquímica Facultad de Biología Universidad de la Habana

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Dummy atoms
by Jean Didier Pie Marechal 30 Jun '08

30 Jun '08

Dear all, I think the question was already posted but I can't find it. I would like to make an atom I placed as an helium to a Dummy: What is the corresponding atom type in Chimera? 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: Dimarts, Juny 24, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 21 > 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. Re: how could u know the order of atoms? (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 23 Jun 2008 14:22:31 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] how could u know the order of atoms? > To: Kamal Al Nasr <k_alnasr(a)yahoo.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <8901DE4E-D117-4B18-968B-D3095AD735D4(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Jun 19, 2008, at 10:08 AM, Kamal Al Nasr wrote: > > > Dear Sir/Madam, > > > > I am using Chimera viewer..and it is a great viewer ever... > > Thanks! I'm glad you like it. > > > 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? > > For standard amino and nucleic acids, Chimera has templates > containing the correct connectivity. For non-standard residues it > bases the connectivity on inter-atomic distances, with a few added > heuristics (e.g. hydrogens can only have one bond). > > The templates are accessible in the Python layer with the > chimera.restmplFindResidue() function. You can look in the > Rotamers > extension for examples of its use. The distance-based connectivity > > function is also available for an entire molecule as > chimera.connectMolecule(). It takes the molecule as its only > argument and adds bonds to it. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >

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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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"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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