May 2008 - Chimera-dev - RBVI Mailing Lists

add h
by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

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Re: [chimera-dev] [Chimera-users] displacing atoms following a given vector
by Eric Pettersen 22 May '08

22 May '08

Hi JD, You would displace the atoms of molecule 'm' by the vector (1,2,3) like so: v = chimera.Vector(1,2,3) for a in m.atoms: a.setCoord(a.coord() + v) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 22, 2008, at 1:12 PM, Jean-Didier Maréchal wrote: > Dear All, > > I have been flying through the developer's guide but can't find what I > look for, sorry. > > I have a given molecule and a vector in cartesian coordinates (e.g. a > normal mode but not necessarily) indicating a direction of > displacement > for the different atoms of the molecules. I would like to write a > script > that displaces the atoms following this vector. I am prettysure that > some modules of chimera should allow me to do that, but I can't find > which ones. Could you give me a hand on this please? > > ALl the best > JD > > > El jue, 22-05-2008 a las 12:00 -0700, chimera-users- > request(a)cgl.ucsf.edu > escribió: >> 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. Stereo projection (Magali Cottevieille) >> 2. Stereo projection (Steven Ludtke) >> 3. Re: Stereo projection (Greg Couch) >> 4. Re: findhbond/5750 (FindHBond failure) (Eric Pettersen) >> >> >> --------------------------------------------------------------------- >> - >> >> Message: 1 >> Date: Wed, 21 May 2008 16:06:07 -0400 >> From: Magali Cottevieille <mc3077(a)columbia.edu> >> Subject: [Chimera-users] Stereo projection >> To: chimera-users(a)cgl.ucsf.edu >> Message-ID: <483480AF.9020604(a)columbia.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi, >> >> Is there any way, with two projectors piloted by two graphic >> cards, to >> send from Chimera the stereo left eye view onto one, and the stereo >> right eye view onto the other one ? These two projectors are meant >> to be >> used with filters and special glasses to create a 3D view. >> Thanks for your help! >> >> -- >> Magali Cottevieille, Ph.D. >> Howard Hughes Medical Institute, >> Department of Biochemistry and Molecular Biophysics, >> 630 W 168th St, P&S Black Building 2-221 >> New York, NY 10032 >> >> Ph: (+1) 212-305-9521 >> Fax: (+1) 212-305-9500 >> >> Email: mc3077(a)columbia.edu >> magali.cottevieille(a)gmail.com >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 21 May 2008 16:18:26 -0500 >> From: Steven Ludtke <sludtke(a)bcm.edu> >> Subject: [Chimera-users] Stereo projection >> To: chimera-users(a)cgl.ucsf.edu >> Cc: mc3077(a)columbia.edu >> Message-ID: <0F963AC8-7667-4B76-B8E2-0DC9855E406C(a)bcm.edu> >> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >> >> Yes, we have done this before, though I don't remember with absolute >> certainty if we >> did it with chimera. You don't use 2 video cards normally, but rather >> 1 card with 2 >> outputs. Also, you will need one of the 'professional' cards where >> the >> driver supports >> stereo in a window ie- NVidia Quadro (we didn't try ATI). The NVidea >> stereo drivers then >> have a mode for this type of stereo, or at least that's my memory, it >> was a year or two >> ago when we demonstrated this. You need: >> >> 2 identical projectors which permit geometry correction so their >> corners can be exactly aligned >> 2 polarizer plates. we got (http://www.3dstereo.com/viewmaster/pj- >> pfilt-3x3.html >> ) for $20 a pair >> linear polarizing glasses (from the same site) >> Quadro or similar GFX card >> >> Note that with this type of stereo, you could technically make this >> work with any old dual >> output 3-D card, but you would have to write the visualization >> software so it would open >> 2 display windows with slightly different orientations that you could >> then manually (or >> automatically) position on each of the 2 projectors. >> >> We did this just as an initial proof of concept, and haven't managed >> to get back to it again, >> though we keep meaning to, as it is MUCH cheaper than the commercial >> solutions. Oh, one warning, >> the polarizer plates mentioned above are plastic, and the light >> energy >> put out by your typical >> projector is quite substantial. We actually melted one of the >> polarizers on our first attempt, >> despite using much of it's 3x3 inch surface area. ie - use a low >> power >> projector, or put the >> polarizer between thick glass plates or somesuch... >> >>> From: Magali Cottevieille <mc3077(a)columbia.edu> >>> Date: May 21, 2008 3:06:07 PM CDT >>> To: chimera-users(a)cgl.ucsf.edu >>> Subject: [Chimera-users] Stereo projection >>> >>> Hi, >>> >>> Is there any way, with two projectors piloted by two graphic >>> cards, to >>> send from Chimera the stereo left eye view onto one, and the stereo >>> right eye view onto the other one ? These two projectors are meant >>> to be >>> used with filters and special glasses to create a 3D view. >>> Thanks for your help! >>> >>> -- >>> Magali Cottevieille, Ph.D. >>> Howard Hughes Medical Institute, >>> Department of Biochemistry and Molecular Biophysics, >>> 630 W 168th St, P&S Black Building 2-221 >>> New York, NY 10032 >>> >>> Ph: (+1) 212-305-9521 >>> Fax: (+1) 212-305-9500 >>> >>> Email: mc3077(a)columbia.edu >>> magali.cottevieille(a)gmail.com >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> --------------------------------------------------------------------- >> ------- >> Steven Ludtke, PhD | Baylor College of Medicine >> sludtke(a)bcm.tmc.edu | Associate Professor & Co- >> Director >> stevel(a)alumni.caltech.edu | National Center For Macromolecular >> Imaging >> V: (713)798-9020 | Dept of Biochemistry and Mol. >> Biol. >> F: (713)798-1625 | >> | Those who Do, Are >> http://ncmi.bcm.edu/~stevel | The converse also applies >> >> >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 21 May 2008 14:25:09 -0700 (PDT) >> From: Greg Couch <gregc(a)cgl.ucsf.edu> >> Subject: Re: [Chimera-users] Stereo projection >> To: Magali Cottevieille <mc3077(a)columbia.edu> >> Cc: chimera-users(a)cgl.ucsf.edu >> Message-ID: <Pine.OSF. >> 4.63.0805211409520.1818353(a)guanine.cgl.ucsf.edu> >> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed >> >> On Wed, 21 May 2008, Magali Cottevieille wrote: >> >>> Hi, >>> >>> Is there any way, with two projectors piloted by two graphic >>> cards, to >>> send from Chimera the stereo left eye view onto one, and the stereo >>> right eye view onto the other one ? These two projectors are >>> meant to be >>> used with filters and special glasses to create a 3D view. >>> Thanks for your help! >> >> Chimera supports stereo using workstation graphics cards, i.e., >> NVidia >> Quadro FX and ATI/AMD FireGL cards. We don't have a recent FireGL >> card >> (and driver), so the rest of this email will be about the NVidia >> Quadro FX >> cards and driver. >> >> The Quadro FX graphics cards have two video outputs and the driver >> lets >> you display the left eye on one output and the right eye on the >> other. >> The higher end cards have SLI support (on FireGL it's called >> CrossFire) >> which lets you use two matched graphics cards together. It is >> unclear to >> me how or if SLI/CrossFire and stereo work together, but I would >> expect >> them to. >> >> Greg >> >> >> ------------------------------ >> >> Message: 4 >> Date: Thu, 22 May 2008 10:51:29 -0700 >> From: Eric Pettersen <pett(a)cgl.ucsf.edu> >> Subject: Re: [Chimera-users] findhbond/5750 (FindHBond failure) >> To: Tyler Arbour <tyler.arbour(a)gmail.com> >> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> >> Message-ID: <A4A9CFED-F357-4943-AB11-43D644C07DF0(a)cgl.ucsf.edu> >> Content-Type: text/plain; charset="us-ascii" >> >> Hi Tyler, >> The problem is that Chimera "knows" the atom types of standard >> residues and doesn't try to compute them from scratch. Therefore it >> assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the >> find-hbond computation as it looks for the planarity of the ND1 and >> sees it bonded to nothing! >> For what you want to do, you want to get that atom's residue >> changed. Do this: >> >> 1) Control-double click on the ND1 atom >> 2) Chose "Modify Atom" from the resulting popup menu. >> 3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral" >> 4) Change "Bonds" to 3 >> 5) In the "Residue Name" section, use the "new residue" option with >> "NH3" as the name and chain "het" >> 5) Click the Change button >> >> That should give you what you want. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> On May 22, 2008, at 10:25 AM, Tyler Arbour wrote: >> >>> Wow, I didn't expect a response for this...great! I was actually >>> just trying to create a figure representing a computational model >>> that I am using. Starting from the crystal structure, I wanted to >>> actually change the histidinal N to a simple NH3 molecule. I am >>> just trying to get familiar with Chimera--I usually use DS >>> Viewerpro for modifying structures, and it doesn't seem like >>> Chimera is well-suited to this type of modification. If you have >>> any advice on an easy way to make this conversion so that I have a >>> nice figure, I'd greatly appreciate it! Thanks. >>> >>> Tyler >>> >>> On May 22, 2008, at 11:17 AM, Eric Pettersen wrote: >>> >>>> Hi Tyler, >>>> Your structure seems to have a histidine residue (residue 159 in >>>> chain A) that consists solely of an ND1 atom! How did you manage >>>> that? >>>> >>>> --Eric >>>> >>>> >>>> Eric Pettersen >>>> UCSF Computer Graphics Lab >>>> http://www.cgl.ucsf.edu >>>> >>>> >>> >> >>

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Code source for Multi-touch
by Gergely Nagy 20 May '08

20 May '08

Dear Chimera Dev Team, I am referring to my email that I wrote in the beginning of April where I told about our diploma work. Just to sum it up in a couple of lines, we have a multi-touch screen (30") and we would like to make Chimera work with it. We would like to work with Chimera, because at the Center of Integrative Genomics at the University of Lausanne and at the Swiss Institute of Bioinformatics people use this software so this adaptation would even be useful besides that it would be our diploma work. So a couple of questions arise. Would it be possible to have the entire source code? We are ready to sign an NDA or any other contract if necessary. I am asking this because I am having difficulties to imagine how we could make the changes without being able to check how it works in the program. If there is a way to do it rapidly then of course we won't need the entire code source. The library that handles the touch events (touchDown, touchUpdate, touchRemove) is written in C++ (would wrap it of course). It gives basically the coordinates of the touches and updates the coordinates when dragging the finger. So we would need to replace mouse events with those and make zooming, translating and rotating functions available by using only the fingers. We would also make a new menu bar with only a couple of functions to be able to demonstrate the concept. So please tell us what would be possible and what wouldn't so we can evaluate the situation and make the right decisions immediately. Thanks a lot for taking the time to reply. Best regards, Gergely Nagy Marco Pambianchi

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Error on command-line startup: OSX 10.5
by Bernard Heymann 05 May '08

05 May '08

When I start up Chimera from the command line under Leopard, I get a lot of messages such as: 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. Chimera still runs, but I thought this is probably something to be dealt with sooner than later. I did some digging and came across the following technical note from Apple: http://developer.apple.com/technotes/tn2005/tn2083.html The reference to the fork message is at the bottom of the page. I also found on another site the following advice for an X11 application: "I've updated the OSX Readme TclTk build example to include an extra configure option: --disable-corefoundation Since the example is for an X11 TclTk build, CoreFoundation isn't really necessary, so this is OK." Because Chimera uses Tk, I thought this might be something to try to avoid these error messages and possible instability down the line. Bernard Heymann Rm 1515, 50 South Dr, NIH, Bethesda, 20892-8025 Tel 301-451-8241, Fax 301-480-7629

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Chimera-dev May 2008