[Chimera-users] Charge data

Tue Apr 24 17:05:48 PDT 2012

Thank you, I will try that. Also, I was just comparing the charge data of a subunit between one set generated using Chimera with AMBER and the other using pdb2pqr with PARSE. I noticed that the chimera generated file did not have records for hydrogen atoms even though they were explicitly added using addh. Is this due to an error on my part, or has it something to do with the 2mol formatting?

To give you an idea of what I am talking about here is the data for the first amino acid:

        --- > .2mol
     68 N           26.7840   15.9620   -1.4880 N.4       4 SER1        0.1849
     69 CA         25.7660   16.9460   -1.9070 C.3       4 SER1        0.0567
     70 C            25.2870   16.6990   -3.3350 C.2       4 SER1        0.6163
     71 O           26.1060   16.6940   -4.2710 O.2       4 SER1       -0.5722
     72 CB         26.3460   18.3420   -1.7240 C.3       4 SER1        0.2596
     73 OG        26.8010   18.5430   -0.4010 O.3       4 SER1       -0.6714

       --- > .pqr
ATOM      1  N    SER P   1      78.482   33.268   37.386 -0.7800 1.5000
ATOM      2  CA   SER P   1      77.464   34.252   36.967 -0.0000 2.0000
ATOM      3  C    SER P   1      76.985   34.005   35.539  0.5500 1.7000
ATOM      4  O    SER P   1      77.804   34.000   34.603 -0.5500 1.4000
ATOM      5  CB   SER P   1      78.044   35.648   37.150  0.0000 2.0000
ATOM      6  OG   SER P   1      78.499   35.849   38.473 -0.4900 1.4000
ATOM      7  H2   SER P   1      78.147   32.756   38.163  0.3900 1.0000
ATOM      8  H    SER P   1      78.673   32.645   36.625  0.3900 1.0000
ATOM      9  HA   SER P   1      76.672   34.153   37.584  0.0000 0.0000
ATOM     10  HB3  SER P   1      77.336   36.321   36.945  0.0000 0.0000
ATOM     11  HB2  SER P   1      78.811   35.764   36.522  0.0000 0.0000
ATOM     12  HG   SER P   1      78.357   35.015   39.006  0.4900 1.0000

I wrote a new PDB file for the altered molecule using the "write pdb" option and the hydrogen atoms were present in that file, so I know they are on my model.

Nikolay Rodionov

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
Sent: Tuesday, April 24, 2012 4:36 PM
To: Nikolay Igorovich Rodionov
Cc: Chimera BB
Subject: Re: [Chimera-users] Charge data

Hi Nikolay,
You're welcome, I'm glad Chimera does some of what you want!

Hmmm, that's a good question.  I think it could be done by opening the structure, using only commands to carefully translate (and rotate, if needed) by some exact amount, then saving the transformed coordinates.

You would have to determine the needed amounts of motion.  I guess pure translation would be relatively simple if you know the current coordinates of the helix center you want to make the origin:  if (a,b,c) you could use commands:

move x -a
move y -b
move z -c

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>

As for finding out helix center and axis if you don't already know them, commands "measure center" "measure inertia" and/or ("define axis" "define centroid" + Save button on axis/centroid table) may be useful:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Apr 24, 2012, at 3:14 PM, Nikolay Igorovich Rodionov wrote:

> Thank you so much, you've helped me a lot within the last week. I have one more question, is it possible to set a new origin for the axis? I have a helical molecule which was built from HETAM transformations so the origin is at the located in the center of the original molecule. I would like the move the origin to the center of the helix.
> Nikolay Rodionov
>

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