Basically, you probably want to use the xformCoord() function in this situation rather than the coord() function. coord() returns coordinates in the original reference frame of the molecule (basically the same as the coordinates from the original input file). xformCoord() returns coordinates in Chimera's global reference frame, i.e. after rotations and translations have been applied. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jul 18, 2008, at 7:40 AM, Jean Didier Pie Marechal wrote:
Hi everyone,
I am stuck with a script and my mistake seems to come from my poor understanding on how to treat atom coordinates with multiple models. I join to this e-mail a chimera file with a simple system to illustrate my problem.
In the file, I have two indentique phenyl moleculer each of them in different models and I would like to stock the center of mass of both molecules in a list. I wrote this very simple script using the way of calcuting the center of mass you provided me recently.
import chimera import BuildStructure from chimera import runCommand as run from chimera import selection, Vector from chimera import openModels, Molecule, Point
#Stock the two fragments in the list FRAG run("select") frag=[] for i in chimera.selection.currentResidues(): frag.append(i)
#Calculate center of mass of both entities #stocked in the list MAS mas=[] for i in range(len(frag)): sum=0 center = Vector(0, 0, 0) for a in frag[i].atoms: sum += a.element.mass center += a.element.mass * Vector(*a.coord().data()) mas.append(Point(center[0]/sum,center[1]/sum,center[2]/sum)) print i,mas[i]
The results I have are 0 20.0465 70.3735 23.9063 1 20.0465 70.3735 23.9064
Basically, the coordinates of the center of mass are the same? What did I do wrong in the way I treated this problem?
Thanks a lot for any answer,
All the best JD
Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es
----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Dijous, Juliol 17, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 63, Issue 17
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Today's Topics:
1. Re: Possible image saving bug (Greg Couch) 2. Possible image saving bug (Elaine Meng)
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Message: 1 Date: Thu, 17 Jul 2008 10:35:26 -0700 (PDT) From: Greg Couch <gregc@cgl.ucsf.edu> Subject: Re: [Chimera-users] Possible image saving bug To: Walter Novak <wnovak@brandeis.edu> Cc: Chimera forum <chimera-users@cgl.ucsf.edu> Message-ID: <Pine.OSF. 4.63.0807171001010.1939086@guanine.cgl.ucsf.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
On Thu, 17 Jul 2008, Walter Novak wrote:
Hi All,
I submitted a bug report on this, but the behavior is both odd and reproducible for me. Using the latest production release and trying to save an image using supersampling, the image is not stitched back together appropriately. It is odd, because it always happens for a certain session file I have. It doesn't seem to happen if I open a new molecule and make a picture. I can provide the session file if needed. First image is using 3x3 and second is 6x6.
I see from the bug report that you're using Mac OS X 10.5. We are having "issues" with the new X11 application in 10.5. And we have seen that slightly different X11 applications are installed on otherwise identical Macs and that reinstalling from the Mac OS X Install Disk fixed a non-chimera bug.
Also, I have read on the web that if you install the 10.4 X11 application on 10.5, then OpenGL applications will work better. Since that is not an option for everyone, we are spending more time to improve the Aqua version that is available as a Snapshot release on the chimera download page. It has different bugs, but the graphics is better. So you should try it out and see how well it works for you.
Greg Couch UCSF Computer Graphics Lab
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Message: 2 Date: Thu, 17 Jul 2008 10:40:13 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: [Chimera-users] Possible image saving bug To: wnovak@brandeis.edu Cc: Chimera BB <chimera-users@cgl.ucsf.edu> Message-ID: <B15630DD-299C-4B48-A8B4-469FA8995872@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Hi Wally, I also had this tiling problem. We think it may be something about
X11 in Mac OS 10.5 (possibly just 10.5.4), as the problem has not been observed with 10.4/X11.
Two workarounds that were successful in my case (I don't know if they will fix all instances of the problem):
(A) simply show the Command Line before saving the image. I tried hiding it again after that, but then the problem reoccurred, albeit in a more subtle fashion.
(B) save the session, restore it in the aqua version of Chimera (still on Mac OS 10.5.4 but not using X11) and save the image. Yeah, (A) is easier, but I didn't discover that one until this morning, after receiving your mail.
I hope these solutions are general! Sorry about the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
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