[chimera-dev] [Chimera-users] displacing atoms following a given vector
Eric Pettersen
pett at cgl.ucsf.edu
Thu May 22 15:18:52 PDT 2008
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 at cgl.ucsf.edu
> escribió:
>> Send Chimera-users mailing list submissions to
>> chimera-users at 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 at cgl.ucsf.edu
>>
>> You can reach the person managing the list at
>> chimera-users-owner at 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 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
>>>>
>>>>
>>>
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/
>> 20080522/72231393/attachment-0001.html
>>
>> ------------------------------
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>> End of Chimera-users Digest, Vol 61, Issue 20
>> *********************************************
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-dev/attachments/20080522/ba7c6670/attachment.html>
More information about the Chimera-dev
mailing list