[chimerax-users] Saving biomt record for generated icosahedral

Fri Nov 20 18:46:02 PST 2020

Thank you Tom for the confirmation.

  Ibrahim
________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Friday, November 20, 2020 9:43 PM
To: Moustafa, Ibrahim M. <ria2 at psu.edu>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Saving biomt record for generated icosahedral

Hi Ibrahim,

  You are right that ChimeraX cannot save BIOMT remarks in a PDB file.  In fact ChimeraX does not even read BIOMT remarks from PDB files.  ChimeraX uses mmCIF format primarily and reads the structure assembly matrices from mmCIF format but currently cannot write those matrices when you add them with the sym command.  In the future we plan to have ChimeraX write mmCIF assembly matrices.  The old PDB format will be dropped by the PDB in coming years -- I suspect you cannot even deposit a virus capsid model in PDB format.  They have been trying for years to replace the old format because it is poor at handling large structures due to limits of 100,000 atoms and 62 chains.

  At any rate, you should use Chimera if you need to read and write BIOMT matrices in the old PDB format.

Tom

On Nov 20, 2020, at 6:33 PM, Moustafa, Ibrahim M. <ria2 at psu.edu<mailto:ria2 at psu.edu>> wrote:

Hi Elaine,

  As you mentioned, I need the BIOMT record to be the header in pdb containing ASU coordinates.  The BIOMT record of a certain model is specific to generate a full model that fits corresponding EM map (using a coordinate system of the map). I was able to do it in chimera with "biomtSet true" in the "sym" command. I thought the same could be done in ChimeraX but apparently it is not.

   Thank you,
    Ibrahim
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>>
Sent: Friday, November 20, 2020 9:22 PM
To: Moustafa, Ibrahim M. <ria2 at psu.edu<mailto:ria2 at psu.edu>>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>>
Subject: Re: [chimerax-users] Saving biomt record for generated icosahedral

Hi Ibrahim,
ChimeraX doesn't generate BIOMT records, but you can save PDB and mmCIF files with the "save" command or menu: File... Save.
<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fsave.html%23formats&data=04%7C01%7Cria2%40psu.edu%7Cd3c480129ef84b56bb7008d88dc45154%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637415221608931635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gmVGMzXsGJxhRI6OE7YLDededC5SXyp4a8W%2FUFOg4BE%3D&reserved=0<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fsave.html%23formats&data=04%7C01%7Cria2%40psu.edu%7Cbb2efa38b6d843e9234908d88dc745dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637415234311352414%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=JekuQ6b%2B7Iw9%2F4cXWnrgY6jvZfPo89RLoY30ZMmoD2k%3D&reserved=0>>

Maybe I am misunderstanding the question. If you already built the full model, then you don't need the BIOMT records, right?  They are only needed to generate the full model from the asymmetric unit, if I understand correctly.  But maybe you want to generate BIOMT records so that you only need to save the asymmetric unit as a PDB file and then put those BIOMT records in the file.

I am no expert on icosahedral capsids and symmetry operations, so the following is a guess:

Don't all icosahedral capsids have the same BIOMT records?  For example, see this page:
<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fviperdb.scripps.edu%2FIcosahedral_Matrices.php&data=04%7C01%7Cria2%40psu.edu%7Cd3c480129ef84b56bb7008d88dc45154%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637415221608931635%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=d%2BEKtfrRP1%2BFjBTeS0sAmkZifDDBwPGoIhvYllmoXME%3D&reserved=0<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fviperdb.scripps.edu%2FIcosahedral_Matrices.php&data=04%7C01%7Cria2%40psu.edu%7Cbb2efa38b6d843e9234908d88dc745dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637415234311362410%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=llmfKncmEN6LldC3KpUKWFrjRoD%2FgAgUahbHibzdgq0%3D&reserved=0>>

... which seems to agree with what I see in the PDB file for one example icosahedral capsid structure, 1POV.  So maybe as long as you have the asymmetric unit coordinates in the proper frame of reference, you can just copy the BIOMT records from any of those PDB files, such as 1POV.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 20, 2020, at 5:41 PM, Moustafa, Ibrahim M. <ria2 at psu.edu<mailto:ria2 at psu.edu>> wrote:
>
> Hi all,
>   I built a full icosahedral model from ASU in chimeraX, how can I save the coordinates and BIOMT record of the generated full-model?
>     Thanks for helping.
>   Ibrahim
>

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