[Chimera-users] displacing atoms following a given vector
Jean-Didier Maréchal
JeanDidier.Marechal at uab.es
Thu May 22 13:12:53 PDT 2008
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 at 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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 21 May 2008 16:06:07 -0400
> From: Magali Cottevieille <mc3077 at columbia.edu>
> Subject: [Chimera-users] Stereo projection
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <483480AF.9020604 at 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 at columbia.edu
> magali.cottevieille at gmail.com
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 21 May 2008 16:18:26 -0500
> From: Steven Ludtke <sludtke at bcm.edu>
> Subject: [Chimera-users] Stereo projection
> To: chimera-users at cgl.ucsf.edu
> Cc: mc3077 at columbia.edu
> Message-ID: <0F963AC8-7667-4B76-B8E2-0DC9855E406C at 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 at columbia.edu>
> > Date: May 21, 2008 3:06:07 PM CDT
> > To: chimera-users at 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 at columbia.edu
> > magali.cottevieille at gmail.com
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
> ----------------------------------------------------------------------------
> Steven Ludtke, PhD | Baylor College of Medicine
> sludtke at bcm.tmc.edu | Associate Professor & Co-Director
> stevel at 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 at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Stereo projection
> To: Magali Cottevieille <mc3077 at columbia.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <Pine.OSF.4.63.0805211409520.1818353 at 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 at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] findhbond/5750 (FindHBond failure)
> To: Tyler Arbour <tyler.arbour at gmail.com>
> Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <A4A9CFED-F357-4943-AB11-43D644C07DF0 at 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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