April 2008 - Chimera-users - RBVI Mailing Lists

Splitting surfnet surfaces and calculate enclosed volume.
by Jean-Didier Maréchal 08 Apr '08

08 Apr '08

Hi everyone, I would like to calculate the volume of the main pocket provided by a surfnet calculation performed on a given selection. The resulting calculation returns me different pockets of variable sizes. And I have two small questions: 1. Is there a way to split the resulting surfaces in individual size ranked entities so that I can calculate the volume of each of them? 2. What would be the easiest way to call the mv accelerator function from the python shell (whether by a command emulation or a directly importing a module)? Cheers, JD On Tue, 2008-03-25 at 12:00 -0700, chimera-users-request(a)cgl.ucsf.edu wrote: > 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. pdb to density map function (Jeff Triffo) > 2. Re: pdb to density map function (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 24 Mar 2008 20:56:21 -0700 > From: Jeff Triffo <triffo(a)rice.edu> > Subject: [Chimera-users] pdb to density map function > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <47E877E5.4020501(a)rice.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > hi, > > I think I recall seeing information about a pdb -> density map function > (like an MRC density map). is this currently implemented/contained > within Chimera? I can use an outside program to do this, but if it is > already in Chimera I would prefer to do that. > > thanks, > > -Jeff > > > > ------------------------------ > > Message: 2 > Date: Tue, 25 Mar 2008 09:03:29 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] pdb to density map function > To: Jeff Triffo <triffo(a)rice.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <638CF385-92E5-4E11-8875-C5D9682073F5(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > > On Mar 24, 2008, at 8:56 PM, Jeff Triffo wrote: > > hi, > > I think I recall seeing information about a pdb -> density map > > function > > (like an MRC density map). is this currently implemented/contained > > within Chimera? I can use an outside program to do this, but if it is > > already in Chimera I would prefer to do that. > > thanks, > > -Jeff > > > > Hi Jeff, > Yes, there is a "molmap" command in recent versions: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html > > In addition, the "Fit in Map" tool can use the same functionality to > simulate a map from atomic coordinates and then use map-in-map fitting: > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/ > fitmaps.html > > These features were added after the November production release but > are available in recent daily builds: > http://www.cgl.ucsf.edu/chimera/alpha-downloads.html > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 59, Issue 24 > *********************************************

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Re: [Chimera-users] Chimera with 3d (6-axis) mouse?
by Tom Goddard 08 Apr '08

08 Apr '08

Hi Mario, We haven't distributed any game controller support in Chimera. Conrad Huang in our lab recently tried head tracking with a Wii remote. We've tried Wii remote control of Chimera using just mouse emulation. We've tried a force feedback device called a Phantom (from Sensable) for placing markers in density maps. That was distributed with Chimera on Windows in the past but is not currently working, though I am just now fixing it. Greg Couch in our lab has experimented with a game pad API and a consumer device. So we have some interest in alternative input devices but it is mostly just in the tinkering stage. Tom Mario J. Borgnia wrote: > This reminds me that several years ago Alwyn Jones introduced the use > of gamepads to control the display. Is this available in Chimera? > Tom Goddard wrote: >> Hi Lee, >> >> I added Chimera support for the Space Navigator 6-degree-of-freedom >> input device (costs only $60) for Mac and Windows. >> >> http://www.3dconnexion.com/ >> >> I expect it will work with other 3dconnexion devices such as your >> Space Explorer. If you download the current Chimera daily build >> >> http://www.cgl.ucsf.edu/chimera/alpha-downloads.html >> >> for Windows or Mac OS and have the 3dconnexion driver installed, the >> device will move and rotate Chimera models. >> >> I have only two button assignments: Button1 or Fit centers the >> models and scales them to fit in the window, Button2 toggles a mode >> allowing simultaneous rotation and translation (default off is called >> "dominant" mode by 3dconnexion). The Windows Control Panel or Mac OS >> System Preferences lets you change the assignments of the device >> buttons. You may not have any assigned to be "Button2" unless you >> change those settings. >> >> There are also a few keyboard shortcuts that change modes. >> Shortcuts or Accelerators are turned on with menu entry Tools / >> General Controls / Accelerators On. Shortcut "nf" turns on "fly >> through" mode. Instead of the device behaving as if you are holding >> the models it is used to control the viewer position (ie. pushing >> forward flies you forward rather than pushing the models away from >> you). It is hard to control -- needs more programming work. >> Shortcut "na" allows the device to move both inactive (frozen) and >> active models. This can be useful if you are docking a molecule into >> a map with the mouse and changing view points of both molecule and >> map using the space navigator. Shortcut "nd" toggles >> translate/rotate only mode (i.e. "dominant" mode). I just added that >> today so it won't be in Chimera until tonight's builds. >> >> Tom

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Chimera with 3d (6-axis) mouse?
by Lee Parsons 08 Apr '08

08 Apr '08

Hello I was wondering if there is any support for using a 3d mouse with chimera. In particular, I have a 3dconnexion space explorer, and it does not seem to work in chimera for windows. I have not found anything in the archives pertaining to this, or even its logitech ancestor the "magellan". thank you

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problem with opening pdb-files
by Ackermann, Bianca 08 Apr '08

08 Apr '08

Hello! When I download my pdb-files from the PDB homepage and open it in Chimera (File type all (guess type) or PDB) the structure appears in a normal way first. But after a few seconds or when I start working with the molecule, the structure breaks up and there are just orderless bars and lines. Perhaps you can help me with this problem? Thank you in advance. Greetings, Bianca Ackermann Institut für Mikrobiologie und Weinforschung AG Unden Becherweg 15 D - 55099 Mainz Tel.: +49-6131-3923553

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essential dynamics
by bala 07 Apr '08

07 Apr '08

Hello all, I have done a pca analysis using ptraj program of amber. I want to view the result of the same. Is there any that i can do it with chimera. I am aware that it can be down analyzed vmd. But i am more comfortable with chimera and i would be happy to perform the analysis in chimera if i can. Thanks, Bala

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Re: [Chimera-users] Chimera - Surface Residue Identification
by Elaine Meng 07 Apr '08

07 Apr '08

On Apr 7, 2008, at 9:33 AM, Thiruvarangan Ramaraj wrote: > Thanks for your reply. > I can find out the residues from one chain that are from certain > distances from another chain. But it will give all the residues, > instead I want only the residues that are in the surface of the > chain. Is there any way to do identify the residues that lie on the > surface of a chain. > > I tried to use surfcat, but it is not working, I am sure I am not > doing it correct. > Any help would be greatly appreciated. > Thank You > Sincerely > Thiru Dear Thiru, You can just add another step that says a residue just have a certain amount of surface area. Some new surface-area features were recently added to Chimera, so I recommend getting a daily build. First you would need to use "surfcat" and show the surfaces you want. I don't know what you tried, or what chains are in your structure, so I can't give exact steps. However, here is an example. If you have chains A,B,C and you want one surface around A and another around B,C together, you would use these commands: surfcat group1 :.a surfcat group2 :.b:.c surface group1 surface group2 Then, use Select by Attribute ("Select... by Attribute Value" in the Chimera menu): in that tool, choose attributes of "residues" and in the "Attribute" menu, choose the name of the surface area attribute. The name is areaSAS if you want solvent-accessible surface area, areaSES if you want solvent-excluded surface area. The values in the structure are shown in a histogram, and you would move the vertical bars to enclose the range of values you want the residues to have. Lots of residues have a tiny amount of surface area, so you would probably want to set the minimum at some positive number. Click Apply to select that set of residues. Then you can narrow the set of residues to only those in the zone, for example: select :.a & :.b zr<4.5 & sel (like my previous example plus "& sel" which means "and also already selected"). In the future it should be easier, with a command something like select :.a & :.b zr<4.5 & :/areaSES>50.0 (avoiding the separate "Select by Attribute" step) but currently, there is a bug that prevents using areaSAS and areaSES in the command line. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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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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