Re: [chimera-dev] [Chimera-users] displacing atoms following a given vector
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@cgl.ucsf.edu escribió:
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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)
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Message: 1 Date: Wed, 21 May 2008 16:06:07 -0400 From: Magali Cottevieille <mc3077@columbia.edu> Subject: [Chimera-users] Stereo projection To: chimera-users@cgl.ucsf.edu Message-ID: <483480AF.9020604@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@columbia.edu magali.cottevieille@gmail.com
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Message: 2 Date: Wed, 21 May 2008 16:18:26 -0500 From: Steven Ludtke <sludtke@bcm.edu> Subject: [Chimera-users] Stereo projection To: chimera-users@cgl.ucsf.edu Cc: mc3077@columbia.edu Message-ID: <0F963AC8-7667-4B76-B8E2-0DC9855E406C@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@columbia.edu> Date: May 21, 2008 3:06:07 PM CDT To: chimera-users@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@columbia.edu magali.cottevieille@gmail.com
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
--------------------------------------------------------------------- ------- Steven Ludtke, PhD | Baylor College of Medicine sludtke@bcm.tmc.edu | Associate Professor & Co- Director stevel@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
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Message: 3 Date: Wed, 21 May 2008 14:25:09 -0700 (PDT) From: Greg Couch <gregc@cgl.ucsf.edu> Subject: Re: [Chimera-users] Stereo projection To: Magali Cottevieille <mc3077@columbia.edu> Cc: chimera-users@cgl.ucsf.edu Message-ID: <Pine.OSF. 4.63.0805211409520.1818353@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
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Message: 4 Date: Thu, 22 May 2008 10:51:29 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [Chimera-users] findhbond/5750 (FindHBond failure) To: Tyler Arbour <tyler.arbour@gmail.com> Cc: Chimera BB <chimera-users@cgl.ucsf.edu> Message-ID: <A4A9CFED-F357-4943-AB11-43D644C07DF0@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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Eric Pettersen