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From: Ruchi Sachdeva (ruchi.imt_at_gmail.com)
Date: Wed Jun 27 2007 - 01:15:28 CDT

Hi all,

Im trying to generate a tetramer of aquaporin using the following
transformation matrix provided in the pdb file.
**********************
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 96.76000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 96.76000
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 96.76000
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 96.76000
REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000
******************

i used the following commands in tk console for the purpose
****************
set m1 {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}
set sel1 [atomselect top "protein and chain A"]
$sel1 move $m1
$sel1 writepdb aqp1.pdb
****************

Similarly three more pdb files were created with other matrices. Then i put
all the files in a single pdb file . On viewing the structure in vmd, I
found only three chains i.e. a trimer rather than a tetramer. Then I noticed
that structures formed with matrices 2 & 4 had identical coordinates,
resulting in only three chains.

I followed the same procedure for other pdb's of aquaporins and found same
error.

Please somebody can tell me what may be the mistake in the procedure?

Any help will be appreciated

Thanks