Hello Is there a way to write out the BIOMT matrices associated with the input symmetry symbol in the output PDB file saved by Chimerax? Thank you Haixin -- Haixin Sui, Ph.D Pronouns: he, his, him (What's This<https://oer.ny.gov/system/files/documents/2023/11/personal-pronouns.pdf>?) Principal Investigator Wadsworth Center NY State Department of Health Biggs Lab C311, Empire State Plaza Albany, NY 12237 (518) 474-4235 (o) haixin.sui@health.ny.gov<mailto:haixin.sui@health.ny.gov> www.wadsworth.org/research/laboratories/sui-laboratory/sui-laboratory<http://www.wadsworth.org/research/laboratories/sui-laboratory/sui-laboratory>
Hello Haixin, Based on our earlier emails I guess by "input" you mean the symmetry that you entered with the "sym" command. As far as I know, there is no way to output that as BIOMT matrix into a PDB file, sorry. Maybe if anybody else has an idea of how to do this (with any program), they can answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 1, 2025, at 2:16 PM, Sui, Haixin (HEALTH) via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Is there a way to write out the BIOMT matrices associated with the input symmetry symbol in the output PDB file saved by Chimerax? Thank you Haixin -- Haixin Sui, Ph.D Pronouns: he, his, him (What’s This?) Principal Investigator Wadsworth Center NY State Department of Health Biggs Lab C311, Empire State Plaza Albany, NY 12237 (518) 474-4235 (o) haixin.sui@health.ny.gov www.wadsworth.org/research/laboratories/sui-laboratory/sui-laboratory _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Haixin, Most of our effort is to support the mmcif format since the PDB does not even provide the old PDB format for many new entries. The sym command has an addMmcifAssembly option that adds the matrices to an mmcif file. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#addMmcifAssemb... Tom
On Jul 1, 2025, at 5:24 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Haixin, Based on our earlier emails I guess by "input" you mean the symmetry that you entered with the "sym" command. As far as I know, there is no way to output that as BIOMT matrix into a PDB file, sorry. Maybe if anybody else has an idea of how to do this (with any program), they can answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 1, 2025, at 2:16 PM, Sui, Haixin (HEALTH) via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Is there a way to write out the BIOMT matrices associated with the input symmetry symbol in the output PDB file saved by Chimerax? Thank you Haixin -- Haixin Sui, Ph.D Pronouns: he, his, him (What’s This?) Principal Investigator Wadsworth Center NY State Department of Health Biggs Lab C311, Empire State Plaza Albany, NY 12237 (518) 474-4235 (o) haixin.sui@health.ny.gov www.wadsworth.org/research/laboratories/sui-laboratory/sui-laboratory _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Elaine Meng -
Sui, Haixin (HEALTH) -
Tom Goddard