Hi Lei,
I don't know what is the recommended workflow, but here is an awk script I
wrote to help a student who wanted to view the symmetry in chimeraX.
Regards,
Mitch
------0readme.txt-------
To make BIOMT records from a map, run phenix.map_symmetry followed by
the awk conversion script to write BIOMT records.
phenix.map_symmetry J30_class_00_final_volume.mrc symmetry=I nproc=30
awk -f ncs-to-BIOMT.awk symmetry_from_map.ncs_spec > BIOMT-rec.txt
after that copy those records into the PDB header along with the
details of which chains to apply the symmetry to like
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 350
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
<---- Clip --->
REMARK 350 BIOMT1 60 0.809017 -0.500000 -0.309017 194.18424
REMARK 350 BIOMT2 60 -0.500000 -0.309017 -0.809017 508.38093
REMARK 350 BIOMT3 60 0.309017 0.809017 -0.500000 72.49131
Then in chimeraX, if you load the PDB file as object 1, you can symmetry
expand it via
sym #1 biomt
-----------------
In case the attachment gets stripped from the e-mail, the contents of
ncs-to-BIOMT.awk file are:
/new_operator/{ myopt++ ;
getline ; getline ; r11=$2; r12=$3; r13=$4 ;
getline ; r21=$2; r22=$3; r23=$4 ;
getline ; r31=$2; r32=$3; r33=$4 ;
getline ; t1=$2 ; t2=$3 ; t3=$4 ;
printf "REMARK 350 BIOMT1 %2d %9.6f %9.6f %9.6f
%14.5f\n",myopt,r11,r12,r13,t1 ;
printf "REMARK 350 BIOMT2 %2d %9.6f %9.6f %9.6f
%14.5f\n",myopt,r21,r22,r23,t2 ;
printf "REMARK 350 BIOMT3 %2d %9.6f %9.6f %9.6f
%14.5f\n",myopt,r31,r32,r33,t3 }
On Fri, Oct 3, 2025 at 7:38 AM Lei Chen
Dear All,
I am currently working on depositing a PDB file for an icosahedral virus and have built the pdb for one asymmetric unit (ASU).
I am wondering how I can compile or obtain the BIOMT record. I haven't found a detailed protocol online.
Thank you, Lei _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s