[phenixbb] Re: Generating BIOMT record for icosahedral symmetry

4 Oct 2025


      Hi Lei,
Here is another approach that may be easier if you have cryo-EM data.  If
you have a cryo-EM map for this structure, you can run "phenix.map_symmetry
my_map.mrc" and it should find the icosahedral symmetry and write out the
operators.
All the best,
Tom T


On Sat, Oct 4, 2025 at 4:34 PM Tom Terwilliger <
[email protected]> wrote:
...
Hi Lei,
Can you possibly try this: (1) create a model that has only one chain per
asymmetric unit of your virus (i.e., select all the "A" chains and remove
all the others).  Then (2) try the method that Guillaume suggested.
All the best,
Tom T
On Fri, Oct 3, 2025 at 7:44 PM Lei Chen  wrote:
...
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
...
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
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--
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: [email protected]
Tel: 505-431-0010
-- 
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: [email protected]
Tel: 505-431-0010