- Chimera-users - RBVI Mailing Lists

PDF Chimera documentation
by Elaine Meng 25 Apr '08

25 Apr '08

Hi everybody, For those of you who have asked about a PDF version of the documentation: we just made PDFs of the User's Guide and Programmer's Guide for the last production release (1.2470 Nov 2007). These are linked near the bottom of http://www.cgl.ucsf.edu/chimera/docindex.html (the page you get from clicking "Documentation" in the lefthand column of the Chimera home page). ** HOWEVER, these files have several limitations: - large size (User's Guide >600 pages, Programmer's Guide >2600 pages!) - suboptimal page ordering due to the nonlinear nature of the documentation - some redundancies, i.e., pages occurring more than once in the PDF document Because of these limitations, we recommend using the documentation in HTML form where possible, and printing from your Web browser to obtain hard copies of specific parts as needed. Also, the HTML documentation is updated constantly, whereas the PDF files may not be updated very often. 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

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Benchmark scores
by Sacha De Carlo 25 Apr '08

25 Apr '08

System : DELL Inspiron 530s, WinXP, 3Gb @ 800MHz Graphics : Radeon HD 2400 Pro 256Mb DDR3, driver version 6.14.0010.6764 Proc: Intel Dual E2160(a)1.8GHz Test date: 2008/4/25 Benchmark scores surface 648 mesh 554 contour 168 solid 248 recolor 115 Molecule Benchmark scores 1F4H (33805): 93.0 171.0 8.0 7.0 173.0 14.0 30.0

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Tile 3D EM maps
by Eduardo Sanz-Garcia 25 Apr '08

25 Apr '08

I found that "tile" only works with atomic coordinate models. Is there a way to "tile" 3D EM maps? Thank you

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Morph surfaces
by Thomas Goddard 24 Apr '08

24 Apr '08

Hi Craig, You can make a low resolution surface from atomic coordinates using the new molmap Chimera command (added in January 2008). You can create such a surface for each frame of your morph using the MD Movie dialog menu entry Per-Frame / Define Script. If your morph is model #2 the script would look like: molmap #2 8.5 where 8.5 is the desired resolution in Angstroms. To produce a smoother surface, to color it (transparent red), and to set the volume step size (the surface is a contour surface of a map computed from the molecule) the script would look like molmap #2 8.5 gridSpacing 1.5 volume #2 color 1,0,0,.5 step 1 The color spec is red,green,blue,opacity. The molmap command replaces a previous map for the molecule by default so the surfaces will not accumulate. More details on the molmap command are in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html You'll need a Chimera daily build to use this command: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom Craig Yoshioka wrote: > Hi Dr. Goddard, > > I'm Craig, a graduate student in Clint and Bridget's lab at Scripps. I > am trying to use Chimera to put together an animation movie. I have > fitted a couple of crystal structures into different EM maps and have > used the Morph Conformations to interpolate between them (excellent > btw). I want to do the animation using surfaces though, and have not > found a satisfactory way to do so. The surfacing command under the > actions menu seems to fail half the time, but provides far too detailed > a surface for this animation anyways. I really like the flexibility of > the surfacing used by the multi-scale model window (letting you set the > "resolution", etc.) but this surface does not update with the morph > conformations animation. I have taken to saving the morph conformations > pdb to the disk as all frames, and reopening it to get access to all the > intermediate PDBs. I then using multi-scale surfacing on this to > generate a large series of surfaces, and I generate the animation by > switching them on and off in series. This is, of course, very time > consuming. Is there a way for me to switch the algorithm used by the > surfacing in the actions menu to use the multi-scale models surfacing > instead? That way the animation would be much easier. > > thanks for your help, > > -Craig > >

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chimera on OS X 10.5
by Mark Moll 23 Apr '08

23 Apr '08

When I run Chimera on OS X 10.5 "Leopard", I get a ton of the following errors in /var/log/system.log: The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec(). Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__ () to debug. I first reported on this on November 2, 2007, but with the latest daily build this still happens. I removed all extensions, but that doesn't seem to make a difference. My own extension becomes painfully slow, because Chimera is constantly writing the above error message. I never get the error above with the version of python that comes with Leopard or with the version of python2.5 in MacPorts. Would it be possible to build Chimera's version of Python similar to these other versions of Python? Or does the problem lie elsewhere? -- Mark

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Dialog w/ sliders?
by Randy Heiland 22 Apr '08

22 Apr '08

I was wondering if there's a dialog in the gui code that has built-in sliders? E.g., currently our extension module subclasses ModelessDialog; however, our input panel has so many values that it would be convenient if it was embedded in a widget such that sliders appeared when it was resized smaller. thanks, Randy

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CHIMERA script for CONSURF
by Fabian Gmail 20 Apr '08

20 Apr '08

Hi all, I am very interested to write a script to deal with the color-coding of CONSURF server (http://consurf.tau.ac.il/index.html) a 9 layer colour from maroon-to-cyan. I basically would like to know how I could translate the code into RGB colors and color the structure accordingly. Any suggestions will be greatly appreciated, 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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Re: [Chimera-users] [chimera-dev] Chimera in windows: seeing samba mounted disk
by Eric Pettersen 18 Apr '08

18 Apr '08

Hi JD, Under the leftmost column of the file browser there should be a pop- up menu of drives. You should be able to pick F: from that. Let me know if that's not working for you. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 18, 2008, at 7:15 AM, Jean-Didier Maréchal wrote: > Dear all, > > I usual use chimera on my linux box, but for some practicities, I need > to use it in windows. > > I realized though that I can not access the disk F: of my windows box > which is a mounted disk from the linux one. Would it be difficult that > the file browser of chimera recognize samba mounted disk? Our is > ther a > trick I miss? > > All the best, > JD

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Command line change active to show models
by Jean-Didier Maréchal 18 Apr '08

18 Apr '08

Hi everyone, I was wondering if it was possible to change the "Active models" list that lays below the command line, to a "showed models" list. I know that I can pilot this through the model panel, however, I think that, for the work I do, a direct access to this option would be more useful. Thanks a lot, JD On Thu, 2008-04-17 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. CHIMERA script for CONSURF (Fabian Gmail) > 2. History feature for command line between sessions (Boaz Shaanan) > 3. Re: CHIMERA script for CONSURF (Elaine Meng) > 4. Re: CHIMERA script for CONSURF (Elaine Meng) > 5. Re: CHIMERA script for CONSURF (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Apr 2008 10:11:42 +0300 > From: Fabian Gmail <fabian.glaser(a)gmail.com> > Subject: [Chimera-users] CHIMERA script for CONSURF > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <4806F82E.7010605(a)gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi all, > > I am very interested to write a script to deal with the color-coding of > CONSURF server (http://consurf.tau.ac.il/index.html) a 9 layer colour > from maroon-to-cyan. I basically would like to know how I could > translate the code into RGB colors and color the structure accordingly. > > Any suggestions will be greatly appreciated, > > 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 > > > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Apr 2008 08:52:31 GMT > From: Boaz Shaanan <bshaanan(a)bgu.ac.il> > Subject: [Chimera-users] History feature for command line between > sessions > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <f652ac011b292.48070fcf(a)bgu.ac.il> > Content-Type: text/plain; charset="utf-8" > > Hi, > > ?The history of commands in the command line mode is retained within a session and is very convenient but I was wondering whether there is a feature that will allow you to recall commands from previous sessions (such as in O for example - it generates an .o-history file which is being constantly updated and is very convenient). If not, is it possible to request the addition of such a feature ? There are many ways to implement this of course and I'm sure you'll find the best way, if it's not already there lurking in Chimera. > > ?? Cheers, > > ????????????? Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > Phone: 972-8-647-2220 ; Fax: 646-1710 > Skype: boaz.shaanan? >

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showing buried pocket
by Eric Pettersen 18 Apr '08

18 Apr '08

On Apr 17, 2008, at 8:59 AM, Gareth Young wrote: > So I've been trying to make an 'inverted surface'. Basically I have > a cavity inside a protein which is almost completely surrounded and > so it is hard to illustrate it to others without removing parts of > the protein (which I could of course do). Does Chimera have a > function to mark the inside of a cavity with a surface, then > allowing the user to remove the protein and just leave the surface > so as to illustrate the size and shape of the cavity in relation to > the protein. > > Have I explained that clearly enough??? Hi Gareth, If this is a standard PDB you can fetch the structure from the CASTp database (File->Fetch By ID...) which will bring up an interface that will allow you to browse the pockets of the structure, with only the browsed pocket being surfaced. If you have a non-standard PDB, you will need to identify some residues near the pocket (let's say they were residues 15 to 19) and then use a command like: ~surf :15-19 z>5 to hide surfaces further than 5 angstroms from those residues, which should hide most of the "outside" surface. Then: ~disp will hide the structure. If you don't know the pocket residues, you might clip through the outside surface with the Side View clip planes and then use the mouse-hovering popup balloons to identify some residues. If your pocket has a channel to the outside, you might want to get a clean cut through the channel by using per-model clipping on the surface and orienting the clip plane so that it cuts the channel. The Per-Model Clipping tool is in the Depiction tools category. I'd like to get Chimera to handle CASTp results for non-standard PDBs, but haven't gotten to that yet. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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