- Chimera-users - RBVI Mailing Lists

Dock PDB into low resolution EM map.
by Puey Ounjai 12 Jun '06

12 Jun '06

Dear all, I am trying to dock atomic coordinate of a protein derived from 3D X-ray crystal (PDB format) into lower resolution (about 20-25 A resolution) EM map (BRIX, XPLOR ASCII or SITUS format) from 2D crystal. 1. Does Chimera have this kind of fitting tool (PDB to volume) or I have to fit the coordinate by hand? If chimera can do this task, Which command should I use? 2. Does Chimera have any statistical evaluation for manual fitting? 3. How can you evaluate the % matching of 2 models in Chimera? Best regards, Puey Ounjai

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Fish-eye view
by Thomas Goddard 12 Jun '06

12 Jun '06

Hi Gabe, Fish-eye would be handy for presentation images. I submitted a request for this in 2003 to the Chimera bug/feature tracking system. Unfortunately it has not seen the light of day since. But I make fish-eye images once in while. I've attached one I just made for you as a test looking inside reovirus (1ej6). The trick is to bring up the Chimera Python shell, menu entry Tools / General Controls / IDLE and type a few things: >>> c = chimera.viewer.camera >>> c.viewDistance 30.0 >>> c.screenWidth 13.0 >>> c.viewDistance = 2 >>> The parameters that control the field of view are "viewDistance" (default 30) and "screenWidth" (default 13). I think view distance means how far your face is from your screen and screen width is how wide the Chimera window is -- maybe the defaults refer to centimeters. The defaults (narrow screen and far view) give a field of view of 25 degrees. Setting viewDistance = 2 gives a field of 150 degrees. Tom > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > From: Gabriel Lander <glander(a)scripps.edu> > Subject: odd request > Date: Fri, 9 Jun 2006 13:03:11 -0700 > > Hi Thom, > The P22 paper I presented at the biophysics conference in Salt Lake > City will be published on June 23rd in Science, so when that happens > I'll send the movie I made with Chimera your way. > We actually got the cover of the issue, and I worked with a graphics > artist here at scripps to put it together using his fancy graphics > software. One thing that really made the structure very visually > striking was the implementation of a fisheye lens. Although this > feature is not scientifically very useful, it would be a great artistic > addition to Chimera. I have no idea how difficult this would ever be > to implement or if it'd be worth it, but it's just a thought. I know > you get like a million suggestions a day, so obviously this would go > somewhere in the utmost bottom list of things to do. > I've attached the mockup we made for the cover to give you an idea of > what I'm talking about. > Cheers, > -gabe > > *** removed image ***

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Colored Rays
by Mark Cunningham 12 Jun '06

12 Jun '06

Elaine, thanks for your response to my question on the coordinate system problem. My problem, as you suggested, was not related to coordinate systems, rather there was a problem with GOLD writing extra coodinates (electron pair coordinates) to its output file, which caused the structures to have enormously large rmsd, so much until the GOLD ligand appeared to be in a different coordinate system relative to the reference ligand. After going in and deleting the extra coordinates, everything worked fine. But now I have another question. Occassionally, while visualizing and manipulating a protein structure (1XAP) with Chimera, I get colored rays (30-40) stretching across the screen. Is this a bug in the program? How can I stop this from happening? If I close Chimera, and open it again, it works for a while, and then sporadically the rays reappear. Thanks. Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

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Sporadic Colored Rays Across Screen
by Mark Cunningham 11 Jun '06

11 Jun '06

Elaine and Eric, thanks for your responses to my question on the coordinate system problem. My problem, as you suggested, was not related to coordinate systems, rather there was a problem with GOLD writing extra coodinates (electron pair coordinates) to its output file, which caused the structures to have enormously large rmsd, so much until the GOLD ligand appeared to be in a different coordinate system relative to the reference ligand. After going in and deleting the extra coordinates, everything worked fine. But now I have another question. Occassionally, while visualizing and manipulating a protein structure (1XAP) with Chimera, I get colored rays (30-40) stretching across the screen. Is this a bug in the program? How can I stop this from happening? If I close Chimera, and open it again, it works for a while, and then sporadically the rays reappear. Thanks. Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

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Reading Frame Problem
by markcunningham 10 Jun '06

10 Jun '06

Could someone please help with this. . Using Chimera, I am trying to calculate rmsd between an observed ligand versus GOLD docked ligand, however the problem is the ligands load into different reading frames. The format for both ligands is .mol2. How can I correct this problem, in other words load both ligands into the same reading frame so that I can then calculate their rmsd. Thanks. Mark

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Reading Frames
by Mark Cunningham 09 Jun '06

09 Jun '06

Hopefully someone can please respond to this before the weekend. I have Windows version of Chimera. I am using Chimera to run rmsd between observed ligands and GOLD calculated ligands. When I open both ligands ( with .mol2 format) with Chimera, they load in different reading frames, thus I can't make the rmds calculation. Please address this issue. The rmsd works fine otherwise, its just with the GOLD ligand files that I am getting the reading frame problems. Thanks very much. Mark Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

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Writing a .x3d file that other programs can read
by Esther Bullitt 07 Jun '06

07 Jun '06

Hi, I am having trouble exporting a .x3d file in a format which programs that convert .x3d data to VRML data can read. The error message for one of them is: Xj3D Version: 1_0 Device found: Mouse-0 Device found: Keyboard-0 Error: Unexpected Exception: Unknown field name: chimera:hither for node: org.web3d.vrml.renderer.ogl.nodes.navigation.OGLViewpoint@1080876 Error: Failed to load file -- The ultimate goal is to have a VRML file that includes both the EM surface map and the pdb subunit structure together in a file that can be read by one of the companies that laser etches the structure into a glass cube. Some companies can read the pdb, some the VRML, but none can read both. Chimera says the .x3d can be converted into .vrml if there are no clipping planes or perspective, which there are not. But I still get this error. Any suggestions, pls? thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics, Room W302 Boston University School of Medicine 715 Albany Street (mail only; couriers use 700 Albany Street) Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041

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1.2251 snapshot release
by Eric Pettersen 06 Jun '06

06 Jun '06

Hi all, There is a new snapshot release (1.2251) available, with a potpourri of new features, listed below. The release is for all platforms, but on Mac we had a little difficulty getting things to work for OS X 10.3, so this release is 10.4 only, but the next production release will include 10.3 support. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu --- 1.2251 release (changes since 1.2199 release) GENERAL: Session files are smaller, use less memory, and start faster. CIF/mmCIF files can be read (or fetched by ID from RCSB) Electron density maps can be fetched by PDB ID from Electron Density Server Virus Particle Explorer (VIPER) files can be fetched by ID VIPER input automatically starts Multiscale Models and constructs viral capsid Thinner default ribbons Files opened by scripts (either Python or Chimera commands) are now searched for relative to the script location, not Chimera's startup location. Can switch to sequential stereo mid-session without having used --stereo at startup (except on certain Windows systems) New stereo mode: anaglyph (offset red/cyan-tinged views, like 3D movies) NEW TOOLS: Add Charge (Structure Editing) - assigns partial charges to atoms; Amber (Cornell et al. 1995) charges used for standard residues, Amber's Antechamber module (now included with Chimera) used to calculate charges for nonstandard residues Build Structure (Structure Editing) - under construction but basic functions work; not much documentation ReadStdin (Utilities) - allows communication with Chimera through standard input/output TOOL CHANGES: AddH (Structure Editing) - new options including how to treat histidines Adjust Torsions (Structure Editing) - interface reorganized to show atoms defining a torsion in order 1-2-3-4 - options added to control decimal places and show degree symbol in angle labels Dock Prep (moved to Structure Editing) - option added to delete alternate locations of atoms - hydrogen addition and charge addition details split off into separate tools called from Dock Prep (AddH and Add Charge, respectively) - terminal carboxylates/amines completed as appropriate Effects (Viewing Controls) - background transparency option added (previously only available as --bgopacity startup option) Minrms Plot (Structure Comparison) - Show Alignment option added MPOSE extension removed (Structure Comparison) Multalign Viewer (Structure Comparison) - .ali extension interpreted as PIR format - .pfam extension no longer indicates Stockholm format, instead indicates Pfam format ("Plain Pfam format" at the Sanger Institute Pfam site) - changed default residue letter/region colors for improved readability - improved editing response time - editing no longer pushes residues that are not in the active region - added control over whether a region depiction spans gaps - option to associate a structure chain with the best-matching sequence in the alignment (when criteria for automatic association are not met) - new Edit menu allowing sequence reordering and deletion, gap column addition and deletion COMMAND CHANGES: ribbonjr removed NEW COMMANDS: addcharge - assign partial charges to atoms (command-line implementation of new Add Charge tool) intersurf - generate and display interface surfaces (command-line implementation of Intersurf) setattr - set a new or existing attribute to a specified value surftransparency - adjust molecular surface transparency COMMAND CHANGES: longbond - now takes an atom or model specification to restrict the calculation to certain models TUTORIALS: figures added to Getting Started tutorials

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Stereographics support
by Eduardo Sanz Garcia 01 Jun '06

01 Jun '06

Hi, We've recently purchased a Stereographics E-2 Emitter to go with our Mac G5 equipped with an NVIDIA Quaddro FX 4500 Graphics Card. As far as we know, the hardware is hooked up correctly, but when we try to run Chimera using command "./chimera --stereo", the following error appears: 'Unable to find hardware stereo support TOGL Couldn't get visual' We called the Stereographics company regarding this error and they mentioned that our software should have "blue line code" enabled. They couldn't give me more details because they said they were unfamiliar with Chimera. Could someone enlighten us with how we can get Chimera to run with stereo enabled? Thanks.

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-S option in ksdssp command
by kovzany＠go.com 01 Jun '06

01 Jun '06

Dear All, I'm trying to get an output with protein secondary structure assignment into a text file, using ksdssp command, unfortunately everytime I get error like this: Computing secondary structure assignments for model #0 using ksdssp (Kabsch and Sander Define Secondary Structure of Proteins) with the parameters: energy cutoff <default> minimum helix length <default> minimum strand length <default> -S option not yet available My question is: am I doing something wrong, or -S option is not yet implemented, despite it is described in ksdssp.html help file? thanks, PK

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