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
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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@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



------------------------------

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
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


_______________________________________________
Chimera-users mailing list

----------------------------------------------------------------------------
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





------------------------------

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


------------------------------

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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