[Chimera-users] Charge data

Tue Apr 24 17:17:17 PDT 2012

Hi Nikolay,
	The short answer is:  keep looking!  You will find all the hydrogens  
after the heavy atoms.  Chimera outputs atoms in Mol2 files in the  
same order that they were encountered in the input.  Atoms added  
afterward are therefore placed after the original input atoms.   
Perhaps it would be better if it kept all residue atoms together, at  
least as an option, but right now it doesn't.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Apr 24, 2012, at 5:05 PM, Nikolay Igorovich Rodionov wrote:

> 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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