- Chimera-users - RBVI Mailing Lists

about problems with windows version
by Ricardo José Soares Torquato 07 Apr '08

07 Apr '08

Dear friends I got chimera program from website, and install on my notebook, and installed the last realese of windows version, my machine has a turion64 as a processor and WinXP pro as OS, but after the installation I try to run it, I got this message: ! Outline highlight not supported by hadware, in small windows. Can you help? thank's Ricardo

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Fitting multiple pdb models
by Pabhashi Fernando 07 Apr '08

07 Apr '08

Hi, I am at the moment trying Chimera, and quite like it! This is to get a clarification: I need to fit 6 independent pdb models that account for different domains of the protein into my EM map. How can I do this? And, is there an evaluation criterion for the fitting? Many thanks. Best wishes, Lasanthi ___________________________________________________________ Yahoo! For Good helps you make a difference http://uk.promotions.yahoo.com/forgood/

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Map image script
by Tom Goddard 07 Apr '08

07 Apr '08

Hi Richard, Here's a Python script that will make 6 thumbnail images of each map in a directory along +/- x, y and z axes. It sets the map contour level to the mean plus two standard deviations. To use it edit the line that sets the directory where the maps reside. Then start Chimera and open the Python file. Make sure not to cover the Chimera window while it is capturing images. The JPEG image file are placed in the same directory and have names matching the map files with suffixes 1,2,3,4,5,6. Tom # ---------------------------------------------------------------------------- # Make 6 views along +/- xyz axes of each map in a directory. # # Sets image size, background color, silhouette edges, and map contour level. # from chimera import runCommand as run run('windowsize 100 100') # Set image size. run('cd /tmp/emdb') # Go to directory containing maps run('set bg_color white') # White background from chimera import viewer viewer.showSilhouette = True # Turn on silhouette edges import os # Get all files that end with ".map" filenames = os.listdir('.') filenames = [f for f in filenames if f.endswith('.map')] # Create images for f in filenames: run('open %s' % f) # Open map # Set contour level to (mean + two standard deviations) from VolumeViewer import active_volume v = active_volume() m = v.matrix() level = m.mean() + 2*m.std() run('volume #0 level %.6g' % level) # Create 6 map images. fprefix = f.rstrip('.map') # Remove ".map" suffix run('copy file %s_1.jpg jpeg' % fprefix) run('turn y 90') run('copy file %s_2.jpg jpeg' % fprefix) run('turn y 90') run('copy file %s_3.jpg jpeg' % fprefix) run('turn y 90') run('copy file %s_4.jpg jpeg' % fprefix) run('turn y 90') run('turn x 90') run('copy file %s_5.jpg jpeg' % fprefix) run('turn x 180') run('copy file %s_6.jpg jpeg' % fprefix) run('close all')

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pov-ray problem
by Fabian Gmail 07 Apr '08

07 Apr '08

Dear chimera experts, I have some difficulties creating high-quality pictures with pov-ray I get them very dark, so in pockets for example I can not distinguish colors. How I could make a pov-ray picture less dark? Thanks a lot, Fabian Glaser -- 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 Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

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Chimera - Surface Residue Identification
by Thiruvarangan Ramaraj 07 Apr '08

07 Apr '08

Hello, I am new to Chimera, I am trying to identify the residues that lie on the surface of a antigen complex that are within certain distance from the antibody. Any help would be greatly appreciated. Thank You --------------------------------- You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.

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chimera explodes
by liane saiz 05 Apr '08

05 Apr '08

Hello everybody: I had some problems with chimera. I installed version 2470 but it explodes when I try to select anything with the following error: Segmentation fault (core dumped) I tried also version 1.2422 and I got the same error. All other features of chimera seems to work properly. In both cases the installation process seems normal. I'm running chimera in linux (ubuntu gutsy) with a 2.6.22-14-generic kernel. In other computer in the lab with the same linux distribution and kernel, all features in chimera 1.2470 work fine (including the select menu). Thanks in advance for any help. Liane

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Chimera crashes
by Ben Keshet 04 Apr '08

04 Apr '08

Hi, I have been using Chimera on my desktop successfully - great program. However, when I run Chimera on my laptop, Chimera tends to crash, usually when the screen saver starts. the message I have is: chimera failed abnormally; the exit code was :3. I am not sure how to open the debug mode (I tried to right-click ==> properties and change the target by adding '--debug' but I am getting an error message that the name is not valid. my machine is Dell Vostro 1500 with XP with a GeForce 8400M GS video card. Any suggestion are welcome. Thanks, Ben

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surface color command
by Michael DiMattia 04 Apr '08

04 Apr '08

Hello, Is there a command for "surface color"? The menu window that lets you color a molecule radially. I'm wondering if there is a command-version of this task so that I can put it into a script. I looked up "surface color" in the Chimera help files but I don't see a command. Thanks! Mike

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Re: [Chimera-users] Chimera-users Digest, Vol 60, Issue 4
by Boyle, Joseph J 03 Apr '08

03 Apr '08

Hello, Is it possible to use Chimera to dock a small ligand into a binding pocket pdb - and if so how is the ligand imported into the protein pdb file ? Yours Sincerely, Joseph Boyle ________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu on behalf of chimera-users-request(a)cgl.ucsf.edu Sent: Thu 03/04/2008 8:41 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 60, Issue 4 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: Smooth Trajectory in MD Movie Tool (Eric Pettersen) 2. Re: Smooth Trajectory in MD Movie Tool (Yan Liang) 3. chimera manual (bala) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Apr 2008 16:37:42 -0700 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Smooth Trajectory in MD Movie Tool To: Yan Liang <liangyan(a)cems.umn.edu> Cc: Chimera forum <chimera-users(a)cgl.ucsf.edu> Message-ID: <7524F1C4-94F1-487C-A67F-FA6A5B4778DB(a)cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Yan, You _could_ write a script to do the averaging, but you would pretty much have to be an expert on how Chimera handles trajectory data to be able to write it in any reasonable amount of time. Since I am such an expert, I've written the script for you and attached it to this message. To do the averaging, simply have your trajectory open and then open the script (either with the File...Open menu or with the "open" command). Note that the script rewrites the coordinates of the trajectory. The only way to restore the trajectory to the "unaveraged" state is by reopening the original files. The main parameter in the script you might want to change is the "window" variable, which controls how many adjacent frames contribute to the averaging. The value in the script right now is 2, which means that the two frames to each side of a frame contribute to the average (with further-away frames contributing less). --Eric ? On Apr 2, 2008, at 2:36 PM, Yan Liang wrote: > Thank you very much Eric. I have tried "Hold selection steady" > function, and it helps a lot to reduce the overall movement of the > large molecule. But as for the residuals, they are still very shaky. > > I am thinking about writing a script to average the movement of > each atom, but I have no experience in Chimera scripting. Do you > think it is possible to write such scripts in Chimera? Thanks. > > Sincerely, > > Yan Liang > Graduate Student > Department of Chemical Engineering and Materials Science > University of Minnesota > > > > On Apr 2, 2008, at 1:42 PM, Eric Pettersen wrote: >> Hi Yan, >> Chimera doesn't yet support smoothing per se. What you can do is >> use "Hold selection steady" in MD Movie's Actions menu to hold one >> or more atoms (possibly all atoms) as steady as possible across >> the trajectory -- which will mostly eliminate the translational >> component of the "shakiness". This "holding steady" is most >> useful for small-molecule trajectories and replica-exchange >> trajectories. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/> >> >> >> On Apr 2, 2008, at 10:44 AM, Yan Liang wrote: >>> Hi >>> >>> I am using Chimera to make a MD movie. The problem is the movie >>> is too >>> shaky. Is it possible to smooth the trajectory by writing a Per- >>> Frame >>> script in MD Movie tool? >>> >>> Thanks, >>> >>> Yan Liang >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

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chimera manual
by bala 03 Apr '08

03 Apr '08

Hello all, I want to have the pdf version of chimera manual/user guide. I am not finding it anywhere ?. Where can i find it. The only pdf i see is the chimera quick reference guide. Thanks, Bala

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