[Molvis-list] Symmetry operations (expanding the 'BioUnit') in Jmol?

[Dan Bolser]

>  Dan Bolser wrote:
>  > Can I apply general symmetry operations to the ASU using Jmol?
>  >
>  > I would like to apply the various 'BioUnit' matrices from the PDB on a
>  > particular structure (specifically 1nf4).
>  >
>  > I was just wondering if this was possible.


2008/4/22 Angel Herraez <angel.herraez at uah.es>:
> Dan, I'd say the answer is yes, but I'm no expert in symmetry.
>
>  I've done something of the sort once, but all depends on your
>  definition of BioUnit and whether it is specified in the PDB file
>  itself.

Yes - I only want to use the symmetry matrices from the "REMARK
300/350" section of the PDB header. See below for the exact matrices
in this example.


>  You should post your question to jmol-users list.

OK - I CC'ed that list in this reply (I hope that is OK). Actually
that reminds me - anyone interested is invited to contribute their
favourite mailing lists to the list here:

http://biodatabase.org/index.php/List_of_mailing_lists_for_biologists


Dan.

REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 16CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I,
REMARK 350 J, K, L, M, N, O, P
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


Dang... I just realised the above symmetry does *not* describe the
biological unit of this structure!


Lets look at 1jgc instead:


REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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        0.00000
REMARK 350   BIOMT2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   3  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT2   3  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT3   3  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   4  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT2   4 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT3   4  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   5 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   5  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   5  0.000000  0.000000 -1.000000        0.00000
REMARK 350   BIOMT1   6  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   6  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT3   6  0.000000  0.000000 -1.000000        0.00000
REMARK 350   BIOMT1   7  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT2   7  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT3   7  0.000000  0.000000 -1.000000        0.00000
REMARK 350   BIOMT1   8  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT2   8 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT3   8  0.000000  0.000000 -1.000000        0.00000

I would like to apply these matrices using Jmol ... if possible