August 2007 - Chimera-users - RBVI Mailing Lists

modeling non-standard amino acids
by Dan Wendt 14 Aug '07

14 Aug '07

Hello, My name is Daniel Wendt and I work for Biomarin Pharmaceuticals in Novato, Ca. I'm trying to use Chimera's modeling software to predict structural changes that are imparted on my 22 amino acid peptide by the insertion of two non-standard changes to the peptide bond. In one case, I am adding a methyl group to the backbone amide bond. In another case, I'm removing a carbonyl from the backbone amide bond. This peptide then needs to be cyclized by the formation of a intra-disulfide bond. I do have x-ray crystal structure data of my cyclized peptide bound to one of its receptors. Do you know how one goes about doing this? Do you have any references that might help? Thank you in advance! Daniel Wendt Senior Scientist BioMarin Pharmaceutical Novato, Ca 94949 (415) 506-6131 This message is intended only for the confidential use of the intended recipient(s). If you have received this communication in error, please notify the sender by reply e-mail, and delete the original message and any attachments. Any unauthorized disclosure, copying, or distribution of this message (including the attachments), or the taking of any action based on it, is strictly prohibited.

2 1

mrc maps
by Gorelik, Tatiana 13 Aug '07

13 Aug '07

Dear Chimera-team, Can I load several .mrc maps at a time and rotate them one against another? Thanks, Tatiana ************************************ Tatiana Gorelik, PhD, Institut für Physikalische Chemie Johannes Gutenberg-Universität Mainz Welderweg 11 55099 Mainz Germany Tel.: 0049 6131 39 22347 Fax: 0049 6131 39 23768 e-mail:gorelik@uni-mainz.de ************************************

5 6

macintosh/stereographics/boot camp
by Dougherty, Matthew T. 11 Aug '07

11 Aug '07

There are some difficulties deep in the apple graphics driver implementation that prevent X11 and openInventor and openGL stereographics. I can report that mac-bootcamp-windows running with a quadro fx 4500 (card supplied by apple, other cards have the wrong firmware); does correctly do stereographics under XP windows correctly with no noted problems. ========================================================================= Matthew Dougherty *** 713-433-3849 National Center for Macromolecular Imaging ========================================================================= =========================================================================

1 0

chimera on AMD workstation
by Vinay Kumar 10 Aug '07

10 Aug '07

Hello all, recently we bought a AMD workstation. I tried to install chimera_linux x86_64 on it. But it did not install. went through installation instructions. still did not work. i would like you to give me some suggestions and some variations that i could try to install chimera. Thank you Elaine, for your post on spheres. shall inform when my adventures have a result. regards, Vinay

2 2

Teaching with Chimera
by Fabian Glaser 09 Aug '07

09 Aug '07

Dear Chimera team, I'd like to use both chimera and chimera tutorials for a new "Structural Bioinformatics practical course" I am preparing here at the Technion in Israel. I will of course acknowledge appropriately. Is there any legal limitation for using chimera for this purpose? Thanks for creating such a fantastic tool Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL E-mail: fglaser(a)tx.technion.ac.il Tel: +972-4-829-3701 Cell: +972-52-2357731

2 1

writing translation/rotation
by Thomas C. Marlovits 08 Aug '07

08 Aug '07

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

3 2

how to select spheres for docking?
by Vinay Kumar 06 Aug '07

06 Aug '07

Hello all, I have a few queries to ask. hoping you all will reply. i use DOCK6.0, the dms program under DOCK, can create and execute a total of 9999 spheres. I would want to know, how do i selectively select spheres using chimera? Is it possible to select certain residues and generate the molecular surface for it? and use it for docking?? My previous problem with chimera got resolved. Thank you Greg. I had to change the OS from RHL9.0 to fedora core. with regards, Vinay ps- please ignore if off-topic. i have posted the same query on dock mailing list. still awaiting a reply there.

2 1

Re: [Chimera-users] odd glare when volume rendering
by Tom Goddard 03 Aug '07

03 Aug '07

Hi Jeff, Aha! Now I see Chimera is working as expected and I can reproduce the glare on my computer. If you have depth cueing set to "No color", which is the default, *and* you use a light background color, then Chimera interprets "no color" as white. With a dark background color, I use black, "no color" for depth cueing is interpreted as black. So all I had to do was set by background color to a light shade to see the glare. So this is bad behavior. The white depth cue color does not work with volume rendering -- it is way too powerful -- all the far planes in the data become slightly white, and this ends up making a very white brick. Oddly, I have already fixed the problem, accidently! My current development version of Chimera (not on the web) has a new blending mode for volumes. I made the change to address a serious problem you raised earlier that the brightness in volume rendering changes a lot when you change step size. The new mode fixes that and will be the default in the next snapshot. Coincidentally the new blending mode also makes white fog work as expected without an overly powerful effect. I have also added better handling of large EM tomography maps -- file loads report progress and can be canceled, default initial display can show a single z plane, the z plane slider is built into volume viewer, hdf5 format map files can be written which contain subsampled versions of the map allowing rapid display of the data at any scale. I'm testing all this on an 2048^3 map. A snapshot should be out in a month or so, though if you really want bleeding edge stuff I could probably give you an earlier version for mac os. Tom William Jeffrey Triffo wrote: > hello, > > I am getting an odd glare when I use solid rendering in VolumeViewer - > it is orientation dependent, which makes me think it has to do with > lighting? I am using build 2416; is it possible to forward a screenshot > to the list? > > thanks, > >

1 1

odd glare when volume rendering
by William Jeffrey Triffo 02 Aug '07

02 Aug '07

hello, I am getting an odd glare when I use solid rendering in VolumeViewer - it is orientation dependent, which makes me think it has to do with lighting? I am using build 2416; is it possible to forward a screenshot to the list? thanks, -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

2 3

Problem with Gasteiger charges of a formally charged ligand
by cdeligka＠purdue.edu 02 Aug '07

02 Aug '07

Dear all, I tried to calculate the Gasteiger charges of peroxynitrite anion using Chimera (I tried the version that was recently released as well as some previous ones). This is my PDB file: HEADER HETATM 1 O 2 2 1.225 0.000 1.819 HETATM 2 N 2 2 0.138 0.000 1.281 HETATM 3 O 2 2 0.138 0.000 -0.086 HETATM 4 O 2 2 1.359 0.000 -0.746 The formal charge of this molecule is -1. For some reason Chimera generates the Gasteiger charges for the molecule but these charges correspond to a formal charge of zero and not -1. If I try the other method AM1-BCC the charges that are calculated do correspond to a formal charge of -1. In my calculations I do need the Gasteiger charges and so I cannot use the ones that are calculated by AM1-BCC. If you have any suggestions please let me know. Are you aware of any other software that might be able to do this calculation? Thank you all, Christos

2 1