July 2009 - Chimera-users - RBVI Mailing Lists

Faster raytracing
by "Bernhard Pätzold" 09 Jul '09

09 Jul '09

Hello I love Chimera and the only little bummer to me are the long rendering times for raytraced movies. I managed to get the PovRay version 3.7 which uses multiple cores running on our server. However now I am stuck and here comes my question. Is there away how I can get Chimera to use the newer Version of PovRay? Or can I somehow change my script so that I get only the .pov and .ini files for all the frames while the actual raytracing is skipped and I can do it subsequently with the newer Version? Currently the whole things has to happen on a windows system, but I hope that I'll get my ubuntu version soon up and running again, so hints and advices for both options are welcome. Thanks a lot in advance Berni -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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no bug reports
by Eric Pettersen 09 Jul '09

09 Jul '09

Since mail to chimera-bugs eventually gets delivered to crick and crick is down, we won't be receiving any bug reports until crick comes up. --Eric

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thermal ellipsoids
by Michael K. Gilson 08 Jul '09

08 Jul '09

Hi, Chimera and PyMol are showing very different thermal ellipsoid orientations for the same PDB file, and I have reason to believe that the PyMol display is the right one. Here are the first two lines of the PDB file I am reading in: Atom 1 O1 CUC 1 3.345 1.613 0.172 ANISOU 1 O1 CUC 1 619 156 528 150 43 -6 ATOM 2 O2 CUC 1 -1.699 0.125 2.792 ANISOU 2 O2 CUC 1 497 355 848 128 -68 204 I would appreciate help with this because Chimera appears to provide more detailed control of the coloring of the ellipsoids than PyMol does. I'll be happy to provide screenshots or other information. Regards, Mike

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Model translation
by David Chenoweth 08 Jul '09

08 Jul '09

Hi, Can anyone tell me the easiest way to translate an entire model by a defined amount (angstroms) in a defined direction. I have a slice of a nanotube and I would like to open it several times, translate each section, and make bonds between the translated sections in order to create a longer nanotube and then save the new coordinates as a new model. Thanks, Dave

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Re: [Chimera-users] Display Molecule Name
by cdlau＠ucsd.edu 08 Jul '09

08 Jul '09

Hi, Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible? Thanks, Chris On Thu, 2 Jul 2009, cdlau(a)ucsd.edu wrote: Hi, I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great. Thanks for your help, Chris Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name. - Greg

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Thermal ellipsoids
by Michael Day 07 Jul '09

07 Jul '09

Hi, I see thermal ellipsoid rendering was just enabled. This is another point (in a long list of points) in favor of using Chimera. Is there a plan to be able to display ellipsoid axis or octants as in ortep type renderings. This would be extremely useful in small molecule work. I've been using Chimera as an alternate when reporting structures in my lab and it has been very well received. The first question asked when I distributed a report today was about the axis and/or octants. Great work. Keep it up! Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------> >>

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Display of a vector in Chimera
by Charles Letner, Ph.D. 07 Jul '09

07 Jul '09

Hello, Is there a way to display a vector between two sets of coordinates in Chimera? If the approach is to write a python, any chance I could get a nudge in the right direction on chimera commands to work with? I've written a minimal amount of python code but not related to Chimera. Cheers, Chuck Charles Letner, Ph.D. Alpharetta, GA 30004 Email: chuck(a)theletners.com

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Re: [Chimera-users] minmize small molecule
by Elaine Meng 06 Jul '09

06 Jul '09

Hello, It looks like the Cu is part of the small molecule. Sorry, in my first reply I thought it was just a separate monatomic ion (not covalently bonded to anything) that happened to be near the small molecule, such as in the binding site of a protein. Covalent organometallic compounds cannot be minimized in Chimera. Chimera uses Antechamber/GAFF to assign parameters to nonstandard residues such as small molecules, and this process is only meant to handle organic molecules made of C, N, O, H, S, P, F, Cl, Br and I. To minimize this type of compound, you would need to use some other program, sorry. Elaine On Jul 6, 2009, at 12:48 PM, Venkataraman Kabaleeswaran wrote: > changed the atom type, but got the following error message? > > > Running ANTECHAMBER command: /net/earth/disk3/vk/pgm/chimera/bin/ > antechamber/exe/antechamber -i /tmp/tmpXaquvp/ante.in.mol2 -fi mol2 - > o /tmp/tmpXaquvp/ante.out.mol2 -fo mol2 -c gas -nc -1 -df 0 -j 5 -s 2 > (LIG) Running: "/net/earth/disk3/vk/pgm/chimera/bin/antechamber"/exe/ > bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f > ac -j part > (LIG) > (LIG) For atom[10]:Mg, the best APS is not zero, exit > (LIG) Running: "/net/earth/disk3/vk/pgm/chimera/bin/antechamber"/exe/ > atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff > (LIG) > (LIG) Running: "/net/earth/disk3/vk/pgm/chimera/bin/antechamber"/exe/ > atomtype -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d "/net/ > earth/disk3/vk/pgm/chimera/bin/antechamber"/dat/antechamber/ > ATOMTYPE_GAS.DEF > (LIG) > (LIG) > (LIG) No Gasteiger parameter for atom[9]:Mg :DU, exit(0) > Failure running ANTECHAMBER for residue LIG > Check reply log for details > > Kabaleeswaran Venkataraman > > -------------------------------------------------------------- > Arise, Awake and stop not until goal is Reached > - Swami Vivekananda > -------------------------------------------------------------- > > > --- On Mon, 7/6/09, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] minmize small molecule > To: "Venkataraman Kabaleeswaran" <vkabs(a)yahoo.com> > Cc: chimera-users(a)cgl.ucsf.edu > Date: Monday, July 6, 2009, 8:07 PM > > Hello, > The "Minimize Structure" tool in Chimera uses MMTK. In general, it > works on (polyatomic) nonstandard residues because Antechamber is > can generate parameters for those, but unfortunately there is a hard > limitation on the types of monatomic atoms that are handled. > > From the Minimize Structure documentation: > "Only the ions in ff99 are handled: Na+, K+, Rb+, Cs+, Mg2+, Ca2+, > Zn2+, and Cl–" > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.… > > > > You could change the Cu to one of those, say Mg, by editing your > structure input file or by using Build Structure (Modify Atom > section). If you are concerned about the effect on the nearby > atoms, you could make sure to freeze that part of the structure so > that it is not allowed to move during minimization. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > 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 Jul 6, 2009, at 10:35 AM, Venkataraman Kabaleeswaran wrote: > > > > > Hi > > I wanted to optimize the geometry of small molecule by > minimization for docking. > > > > I have not seen any option in chimera but even I did tried with > the small molecule I have as nonstandard aminoacid, but it give me > error mmtrk could not Cu atom type. > > > > Is it any small script or through chimera I could able to optimize > the small molecule? > > thanks > > > > Kabaleeswaran Venkataraman > >

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building a backbone model from deposited Calpha coordinates
by Mark Girvin 06 Jul '09

06 Jul '09

I'm sure that this has been asked before, but with limited web bandwidth while traveling, and not finding it in the downloaded help, will ask again anyway (pls feel free to ignore) -- what would you suggest as the best way to coax a ribbon diagram out of deposited Calpha coordinates? Thanks either way, - Mark (further apologies if this turns into a double posting - seemed to bounce the first try). -- Mark Girvin Biochemistry Department Albert Einstein College of Medicine 1300 Morris Park Ave. Bronx, NY 10461 http://www.bioc.aecom.yu.edu/labs/girvlab

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minmize small molecule
by Venkataraman Kabaleeswaran 06 Jul '09

06 Jul '09

Hi I wanted to optimize the geometry of small molecule by minimization for docking. I have not seen any option in chimera but even I did tried with the small molecule I have as nonstandard aminoacid, but it give me error mmtrk could not Cu atom type. Is it any small script or through chimera I could able to optimize the small molecule? thanks Kabaleeswaran Venkataraman -------------------------------------------------------------- Arise, Awake and stop not until goal is Reached - Swami Vivekananda --------------------------------------------------------------

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