- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera-users Digest, Vol 54, Issue 16
by Jonathan Hilmer 18 Oct '07

18 Oct '07

Regarding Chimera movies in PowerPoint: I'm not sure exactly what the end result is like on a Mac, but using a standard Windows setup, PowerPoint will degrade the quality of any movie that you just drop into it. I haven't investigated exactly why this occurs, but it is noticeable. I was able to restore the full quality by embedding a Windows Media Player object into the PowerPoint file, with VB code that loads the movie of interest by default. This might not be an option for a Mac, but perhaps someone else might find it useful: I can give details on the method if anyone would like. As a useful secondary effect, by using an absolute pointer to the movie file rather than an embedded (and relative) link to the directory and file as PowerPoint usually stores, you can place movies in a central repository via http server: this makes it possible to have smaller, more mobile PowerPoint files that don't require a full copy of every included embedded movie. Regarding the quality of output from Chimera, it is possible to composite movies from individual frames. It's not a simple method, but it does remove all limitations on resolution, sampling, etc, and simplifies post-processing as well. One example of a Chimera-produced movie that might not have been possible another way can be found on our server (11MB, mpeg-4): ftp://guest@dratz2.chemistry.montana.edu/capsid_visuals/movies/non-capsid/20060401_both_02.zip Jonathan > Hi > > We have just installed Chimera on a MacPro running OS X 10.4. I would > like to be able to record simple movies of rotating peptides for use in > PowerPoint ( 2003) presentations. > > I have been able to record and insert the avi format into PowerPoint > and the movie does play correctly. But I am noticing a considerable > loss in resolution as compared to the original molecule in Chimera. > > Is there some adjustment I should be making in Movie Recorder to improve > the image resolution? > > Should I be running POV-Ray on these files? > > Thanks for any suggestions. > > > Gene > > (Eugene Coats)

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Model loops with modeller-chimera error
by Gatsogiannis, Christos 18 Oct '07

18 Oct '07

i'm getting this error when i try to run the "model loops"-tool: Error processing trigger "check for changes": TypeError: coercing to Unicode: need string or buffer, Popen found (see reply log for Python traceback info) and the progress-monitor stays by 0% - My chimera version is 1.2422 and my modeller version is 9v2 Thanks in advance Christos ################################################# Gatsogiannis Christos Dipl. Biol. Johannes Gutenberg University Mainz Institut of Zoology cryoEM-Lab +49-6131-39-23091 gatsogia(a)uni-mainz.de #################################################

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Questions on recording movies for use in PowerPoint
by Coats, Eugene 18 Oct '07

18 Oct '07

Hi We have just installed Chimera on a MacPro running OS X 10.4. I would like to be able to record simple movies of rotating peptides for use in PowerPoint ( 2003) presentations. I have been able to record and insert the avi format into PowerPoint and the movie does play correctly. But I am noticing a considerable loss in resolution as compared to the original molecule in Chimera. Is there some adjustment I should be making in Movie Recorder to improve the image resolution? Should I be running POV-Ray on these files? Thanks for any suggestions. Gene (Eugene Coats)

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Non-standard atom names
by Francesco Pietra 18 Oct '07

18 Oct '07

Problems with atom names in preparing a protein for docking. The protein (K ion channel) was obtained as monomer from Protein Data Bank and then as tetramer from Protein Quaternary Structure database through Chimera Fetch ID. The tetramer was stripped to leave --Two helices --Selectivity filter --Pore helix Prepare with Chimera 1.2422 (I had previously carried out successfully the tutorial) along defaults Tools .. Strct edit .. Dockprep All selected except "Delete non-complexed ions" Add hydrogens (also consider H-bonds) To write mol2 use untrasnformed coordinates; use Sybyl type H naming; write current selection to @SETS, Save reported: Correct charges are unknown for 15 non-standard atom names in otherwise standard residues (charges 0.0 assigned to these atoms. 1 model had non integral total charge. Looking at the mol2 file, I could only identify nine type of atoms assiggen 0.0000 charge: H, HD1, HD2, HE1, HE2, HG1, HG2, HH1, HH2 such as (for a small initial portion): 2 H .... 1 SER1 50 HD1 ... 4 LEU4 95 HD1 .... 7 LEU7 97 HD2 ... 7 LEU7 135 HG2 ... 10 THR10 150 HD1 ..... 11 LEU11 168 HE2 .... 12 GLN12 226 HH1 ... 16 ARG16 259 HD2 ... 18 LEU18 279 HD1 ... 20 LEU20 281 HD2 .. 20 LEU20 294 HD1 ... 21 LEU21 296 HD2 ... 21 LEU21 306 HG2 ... 22 ILE22 308 HG1 ... 22 ILE22 310 HD1 ... 22 ILE22 365 HD2 ... 25 LEU25 397 HG1 ... 27 ILE27 430 HG1 .. 30 ILE30 445 HD1 ... 31 LEU31 578 HE1 ... 40 GLU40 601 HD1 ... 42 ASP42 718 HG2 ... 51 ILE51 847 HG1 ... 59 VAL59 861 HG2 ... 60 VAL60 900 HG2 ... 63 THR63 926 HG2 ... 65 VAL65 974 HD1 ... 69 ASP69 1037 HG2 ... 73 ILE73 1039 HG1 ... 73 ILE73 1041 HD1 ... 73 ILE73 1063 HG1 ... 75 VAL75 Being new to these procedures, could you please indicate how to fix the issue? Thanks francesco pietra ____________________________________________________________________________________ Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/

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Lipid bilayer
by Francesco Pietra 12 Oct '07

12 Oct '07

How far (and how close to reality) can we go in building a lipid bilayer with Chimera for use with Amber and Dock? If possible, where to drop in Chimera? I mean a lipid bilayer for a model of ion channel, i.e. ca 30A thick. Thanks francesco pietra ____________________________________________________________________________________ Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545433

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Re: [Chimera-users] multalignviewer/4650 (associations dialog problem)
by Eric Pettersen 12 Oct '07

12 Oct '07

Hi Roberta, The bug you ran into is that the associations dialog wasn't handling non-polymer models correctly (some of your models had had all the protein removed, leaving just ligand). I've just put in enough of a fix so that your session can be used. If you get tomorrow's test build (following the "Test Builds" link off www.cgl.ucsf.edu/chimera) that will have the fix in it. It's not yet a complete fix because it only handles the case where you open the associations dialog _after_ the protein deletion has occurred (which is okay for you). I need to put in more work to make it handle the case where the deletion occurs after the associations dialog is open. When that fix is done you will get an automated mail about it as I change the bug report from "open" to "internal-fix" -- and then it will be available in the next test build. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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molecular modelization softwares
by DESPLAT Nelly 11 Oct '07

11 Oct '07

Dear sir or madam, I am currently studying at the Université Paul Sabatier of Toulouse (France), in a Bioinformatics program (master degree) and I have a report to write, concerning molecular modelization softwares. Could it possible to obtain additional informations about your software Chimera? I would like to know its price, the price of an additionial module, and also how its maintenance work. I thank you ahead of time for your help. Sincerely. Nelly DESPLAT _____________________________________________________________________________ Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail

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Visualizing an ion channel
by Francesco Pietra 11 Oct '07

11 Oct '07

Hi Elaine: Perhaps trivial, though new for me: How to assemble reliably the essentials (to get the teepee) of the four alpha subunits of an ion channel when the Protein Data Bank gives the pdb file for one on the subunits? For example 2A79, a mammalian Kv1.2 ion channel. Thanks francesco pietra ____________________________________________________________________________________ Check out the hottest 2008 models today at Yahoo! Autos. http://autos.yahoo.com/new_cars.html

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Chimera POVRAY and Vista?
by Frank Neese 09 Oct '07

09 Oct '07

Dear Chimera team, First of all congratulations for a really nice program and thank you very much for making it available to the community! I like it a lot. I was nevertheless running into a problem when trying to create povray pictures on a windows vista PC. Is there anything i can do about it? With my best regards, sincerely yours, Frank Neese The output is below: running "C:\Program Files\Chimera\bin\povray.exe" "d:\HomeD\Research\Bonn\COLLAB - Gross\image.ini" "+Id:\HomeD\Research\Bonn\COLLAB - Gross\image.pov" "+Od:\HomeD\Research\Bonn\COLLAB - Gross\image.png" "+V" povray: cannot open the user configuration file C:\Users\neese\AppData\Roaming/.povray/3.6/povray.conf: No such file or directory povray: I/O restrictions are disabled. povray: cannot open an INI file, creating a temporary file 'C:\Users\Public\Desktop/pov36.ini'. povray: cannot write to C:\Users\Public\Desktop/pov36.ini: Permission denied Persistence of Vision(tm) Ray Tracer Version 3.6.1 (cl /nologo /Zc:forScope /Op- /GRX /EHc- /GF /G7 /MD /Zl /O2i) This is an unofficial version compiled by: UCSF Chimera <chimera(a)cgl.ucsf.edu> The POV-Ray Team(tm) is not responsible for supporting this version. POV-Ray is based on DKBTrace 2.12 by David K. Buck & Aaron A. Collins Copyright 1991-2003 Persistence of Vision Team Copyright 2003-2004 Persistence of Vision Raytracer Pty. Ltd. Primary POV-Ray 3.5/3.6 Developers: (Alphabetically) Chris Cason Thorsten Froehlich Nathan Kopp Ron Parker Contributing Authors: (Alphabetically) Steve Anger Eric Barish Dieter Bayer Steve A. Bennett David K. Buck Nicolas Calimet Aaron A. Collins Chris Dailey Steve Demlow Andreas Dilger Alexander Enzmann Dan Farmer Mark Gordon Christoph Hormann Mike Hough Chris Huff Kari Kivisalo Lutz Kretzschmar Jochen Lippert Pascal Massimino Jim McElhiney Douglas Muir Juha Nieminen Bill Pulver Eduard Schwan Wlodzimierz Skiba Robert Skinner Yvo Smellenbergh Zsolt Szalavari Scott Taylor Massimo Valentini Timothy Wegner Drew Wells Chris Young Other contributors are listed in the documentation. Support libraries used by POV-Ray: ZLib 1.2.3, Copyright 1995-1998 Jean-loup Gailly and Mark Adler LibPNG 1.2.16, Copyright 1998-2002 Glenn Randers-Pehrson LibJPEG 6b, Copyright 1998 Thomas G. Lane LibTIFF 3.8.0, Copyright 1988-1997 Sam Leffler, 1991-1997 SGI Redirecting Options All Streams to console..........On Debug Stream to console.........On Fatal Stream to console.........On Render Stream to console........On Statistics Stream to console....On Warning Stream to console.......On Parsing Options Input file: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov (compatible to version 3.61) Remove bounds........On Split unions.........On Library paths: C:\Program Files\Chimera\share\fonts Output Options Image resolution 512 by 384 (rows 1 to 384, columns 1 to 512). Output file: d:\HomeD\Research\Bonn\COLLAB - Gross/image.png, 24 bpp PNG Graphic display......On (gamma: 2.2) Mosaic preview.......Off CPU usage histogram..Off Continued trace......Off Tracing Options Quality: 9 Bounding boxes.......On Bounding threshold: 1 Light Buffer.........On Vista Buffer.........On Draw Vista Buffer....Off Antialiasing.........On (Method 1, Threshold 0.300, Depth 3, Jitter 1.00) Clock value: 0.000 (Animation off) 0:00:00 Parsing File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 Possible Parse Error: Could not find file 'transforms.inc' File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 File Context (5 lines): #include "transforms.inc" global_settings { charset utf8 max_trace_level 10 } Parse Error: Cannot open include file transforms.inc. File: d:\HomeD\Research\Bonn\COLLAB - Gross\image.pov Line: 6 Parse Warning: Check that the file is in a directory specifed with a +L switch or 'Library_Path=' .INI item. Standard include files are in the include directory or folder. Please read your documentation carefully. Total Scene Processing Times Parse Time: 0 hours 0 minutes 0 seconds (0 seconds) Photon Time: 0 hours 0 minutes 0 seconds (0 seconds) Render Time: 0 hours 0 minutes 0 seconds (0 seconds) Total Time: 0 hours 0 minutes 0 seconds (0 seconds)

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Re: [Chimera-users] surface/4623 (Chimera surfacing failure)
by Eric Pettersen 09 Oct '07

09 Oct '07

Hi Jeff, Chimera doesn't communicate depth-cuing/fog info to POV-Ray yet. I will open a bug report about it with you included on the recipient list. What you may want to do in the interim to get a better looking image is to reposition the lights in the scene to reduce the shadows. You use Tools->Viewing->Lights to bring up the interface for position the key (bright) and fill (dim) lights. I've attached two images where I've done that. In both the key light is just slightly overhead and centered. The fill light in one is coming from slightly below and centered, and in the other the fill light is off (you have to go to the "advanced" section of the lighting interface to turn off lights). --Eric

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