Generating BIOMT record for icosahedral symmetry - phenixbb - phenix-online.org

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Generating BIOMT record for icosahedral symmetry

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Lei Chen

3 Oct 2025 3 Oct '25

12:37 p.m.

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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Mitchell Miller

3 Oct 3 Oct

1:56 p.m.

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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Guillaume Gaullier

2:50 p.m.

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

_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Lei Chen

4 Oct 4 Oct

1:44 a.m.

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

_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Tom Terwilliger

10:34 p.m.

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 _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise

script I the sender and know the content is safe.

...
När du har kontakt med oss på Uppsala universitet med e-post så innebär

det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

...
E-mailing Uppsala University means that we will process your personal

data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

-- 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

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Tom Terwilliger

10:53 p.m.

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 _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise

script I the sender and know the content is safe.

...
När du har kontakt med oss på Uppsala universitet med e-post så innebär

det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

...
E-mailing Uppsala University means that we will process your personal

data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

-- 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

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Mitchell Miller

5 Oct 5 Oct

2:13 p.m.

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

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Lei Chen

6 Oct 6 Oct

1:23 a.m.

Thank you Mitch and Tom! Your advice is really helpful ! Best, Lei On Sun, Oct 5, 2025 at 10:13 PM Mitchell Miller wrote:

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

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Guillaume Gaullier
Lei Chen
Mitchell Miller
Tom Terwilliger