[phenixbb] Re: Generating BIOMT record for icosahedral symmetry

Hi Lei, I was glad to hear that getting the symmetry from phenix.map_symmetry and reformatting the output to the PDB BIOMT format worked for you. In an off-list conversation with Tom, he mentioned that phenix.find_ncs could be used as an alternative to the awk script for the reformatting of the output. E.g. phenix.find_ncs symmetry_from_map.ncs_spec find_ncs.output_files.ncs_format=biomt would output find_ncs.biomt with the BIOMT records. Regards, Mitch On Fri, Oct 3, 2025 at 8:56 AM Mitchell Miller wrote:

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 wrote:

...

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