[phenixbb] Re: Generating BIOMT record for icosahedral symmetry

Dear Guillaume, I am working on a T=4 icosahedral virus. phenix.find_ncs gave me too many NCS operators, likely including the ones within one ASU. Thank you though. Best, Lei On Fri, Oct 3, 2025 at 10:50 PM Guillaume Gaullier wrote:

Hello Lei,

If you have an atomic model of the whole symmetric assembly, then this command should produce what you want:

phenix.find_ncs find_ncs.input_files.ncs_in_type=chains find_ncs.output_files.ncs_format=biomt find_ncs.input_files.ncs_in=your-atomic-model.cif

I hope this helps,

Guillaume

________________________________ From: Mitchell Miller Sent: Friday, October 3, 2025 3:56:05 PM To: Lei Chen Cc: [email protected] Subject: [phenixbb] Re: Generating BIOMT record for icosahedral symmetry

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

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