VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Fri Mar 23 2001 - 09:38:46 CST

Hi,

As far as I can tell from the PDB file format specification (you can read
it at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html),
there is no standard for what is to appear in that section of an ATOM record.
VMD does not attempt to parse that data. If you want to use it, say, color
your atoms, you'll have to write a script to parse it yourself, then import
the data into VMD.

For example, say you had parsed the data with a Tcl script and had the numbers
in a Tcl list, call it 'val'. Then you could set, say, the occupancy of all
the atoms to your 'val' data by typing the following at the command line:

        set sel [atomselect top all]
        $sel set occupancy $val

The only other approach I could suggest would be to take the program you are
using and try to get it to put those data in a different field of the PDB
record.

Regards,

Justin

 

On Thu, Mar 22, 2001 at 03:12:53PM -0800, Yunfeng Hu wrote:
> I guess you are talking about the column such as 93.62, 96.09. My question
> is about the next one which has 57, 44 and so on. They are produced by a
> particular program. I want to color the atoms based on that number.
> Thanks.
>
> Yunfeng
>
>
> On Thu, 22 Mar 2001, Justin Gullingsrud wrote:
>
> > Hi,
> >
> > The next to last column is, I think the B-factor (or Beta, in VMD
> > terminology). Thus, if you make a selection like
> >
> > beta > 60
> >
> > you should get just the first 4 atoms.
> >
> > You can color by beta as well, and change the color using the color
> > scale controls in the Color menu.
> >
> > Justin
> >
> >
> > On Mon, Mar 19, 2001 at 07:33:01PM -0800, Yunfeng Hu wrote:
> > > I have a pdb file like this
> > > ATOM 5 CB HIS 3 -16.235 -1.096 -33.335 1.00 93.62 57
> > > POC
> > > ATOM 6 CG HIS 3 -16.801 -2.279 -34.053 1.00 96.09 57
> > > POC
> > > ATOM 7 ND1 HIS 3 -16.128 -3.477 -34.152 1.00 97.72 57
> > > POC
> > > ATOM 34 OE2 GLU 6 -14.184 5.483 -27.224 1.00 74.34 44
> > > POC
> > > ATOM 36 CA VAL 7 -20.215 0.594 -25.878 1.00 54.93 20
> > > POC
> > > ATOM 40 CG1 VAL 7 -22.049 1.281 -24.309 1.00 53.91 20
> > > POC
> > > ATOM 40 CG1 VAL 7 -22.049 1.281 -24.309 1.00 53.91 67
> > > POC
> > > ATOM 46 CB ALA 8 -21.668 -2.539 -29.245 1.00 43.10 57
> > > POC
> > >
> > > I wonder if I can select the group of atms based on the number difference
> > > of the next to the last collum.
> > > Thanks!
> > >
> > > Yunfeng
> > >
> >
> > --
> >
> > Justin Gullingsrud 3111 Beckman Institute
> > H: (217) 384-4220 I got a million ideas that I ain't even rocked yet...
> > W: (217) 244-8946 -- Mike D
> >
> 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D