VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Fri Aug 12 2005 - 14:57:51 CDT

Steve,

   The BIOMT records are explained in a little more detail than on the main PDB site at http://www.rcsb.org/pdb/lists/pdb-l/199907/msg00010.html.
It appears that each 3X3 grid consisting of a group of BIOMT1/2/3 records is a rotation matrix. The last column is a translation vector. For your example, the first set just gives the reference subunit (multiply each atom's XYZ coordinates by the unit matrix, and translate by (0,0,0). The second set says to change the sign of every X and Z coordinate (i.e. rotate around y by 180 deg) then translate the whole thing by (74.19668, 0 71.18338) to get the second subunit.
   For VMD, you'd load the PDB file in, which defines the reference subunit coordinates.

>set temp [atomselect top all]

defines a variable "temp" that references this atom selection, in this case every atom. Now you can apply the reflections:

>$temp move [transaxis y 180]

and then the translation

>$temp moveby {74.19668 0.0 71.18338}

At this point, you could write out the transformed coordinates with

>$temp writepdb second_sub.pdb

Then, you can either load both PDB files into VMD (which I tried, it looks like it works), or use your favorite text editor to concatenate the two files--I would just include the atomic coordinates and the last "END" record.

Chris

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu]On Behalf
> Of Steve Ding
> Sent: Thursday, August 11, 2005 5:10 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: help with BIOMT
>
>
> Hi all,
> I was trying to follow thread
> (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/2621.h
> tml) that
> tried to explain how to use use the "BIOMT" function, but I couldn't
> follow. I'm new to using VMD, so please have some patience.
> The PDB file
> I have displays a dimer, but I would like for it to display a tetramer
> (PDB 1I1R). Below is the REMARK 350:
> REMARK 350
>
>
> REMARK 350 BIOMOLECULE: 1
>
>
> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
>
>
> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000
> 0.00000
>
> REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000
> 0.00000
>
> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000
> 0.00000
>
> REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000
> 74.19668
>
> REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000
> 0.00000
>
> REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000
> 71.18338
>
>
> Is it that the first three lines of BIOMT are for chain A and
> the second
> three lines are for chain B? I tried to use the commands listed in the
> previous thread in the Tk console, but all I got was an
> error. Any help
> would be greatly appreciated.
>
> Steve
>