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@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
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:
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
>