I have a dimeric protein 3HHZ.to generate the dimer foll transformations
have to be madethe problem is that this is an identity matrix,so will
not change anything...can anyone help with this??
how can i get the asymmetric unit to generate dimer??
REMARK 350 APPLY THE FOLLOWING TO
Hi Kanika,
In 3HHZ.pdb, I find:
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 22-MERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, K, L, M, N,
REMARK 350AND CHAINS: O, R
REMARK 350 BIOMT1 1 1.00 0.00 0.00
my protein is 3m2m..iv downloaded the biological assembly 1 for this..
http://www.rcsb.org/pdb/explore/explore.do?structureId=3M2M
to generate dimer for this the BIOMT data is like this from the pdb
filei dont know how will this work if its an identity matrix..
REMARK 350 BIOMOLECULE: 1
I thought symexp() would accomplish this, no?
From:
http://pymol.sourceforge.net/newman/user/S0400xtal.html
Something like:
fetch 3hhz
symexp mysymm, 3hhz, (3hhz), 2.75
(I came up with 2.75 by trail-and-error as 2.5 generates no symmetry
mates and 3.0 generated too many)
In the case of 3m2m,
the symexp data may not always be consistent with the biomt
transformations..although they turn out to be..
considering the case of 3hh7...the biological unit and asymm unit are
same...to form a dimer of this protein...i cannot find a clue by biomt data
REMARK 350 APPLY THE FOLLOWING TO CHAINS:
Hi Chad, Kanika,
Symexp is for generating symmetry mates, not for (re)constructing
biological assemblies.
If the BIOMT record gives an identity matrix, it means that there is
no further information for building a biological unit. The biological
unit is most likely contained in the PDB file. Note
Hi,
i am working to generate a dimer of my protein..I have made a duplicate of
my proteinCan any one tell me how to rotate my molecule to get maximum
stability..???
Regards..
Kanika
--
Free Software Download: Index,
Hi, Kanika,
are you looking for biological units of proteins when you say stable
dimer? If this is the case, I recommend the page:
http://pdbwiki.org/index.php/Biological_unit
at the bottom of the page you can find four very useful servers for the
determination of biological units of proteins
