Multi-chain single macromolecule .pdb file read as two molecules
Hello, I have a homo-oligomeric model that I've refined using phenix and the ISOLDE tool in ChimeraX that's read during deposition as 2 separate molecules, a larger 14mer and a smaller tetramer. It's read as one molecule in Coot, Chimera and Pymol but read as two distinct molecules in ChimeraX exactly like the deposition. I found this curious and thought that perhaps you might have some idea of what's wrong with the file. There is nothing that appears obviously incorrect to me in the text of the .pdb file, all TER cards follow the chains and all amino acids and their identifiers are in sequence and correct. I'd appreciate any ideas you may have and I'm happy to send the file to you if you prefer. Thank you, Kind regards, Lenye Dlamini Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.
Hi Lenye, When you say "molecules", do you actually mean "models", i.e. the file creates multiple models in ChimeraX? Are there MODEL/ENDMDL records in the file? Is there and END record (not ENDMDL record) that's not at the end of the file? Yes, sending the PDB would be helpful... --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 28, 2023, at 1:27 PM, Lenye Dlamini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I have a homo-oligomeric model that I've refined using phenix and the ISOLDE tool in ChimeraX that's read during deposition as 2 separate molecules, a larger 14mer and a smaller tetramer. It's read as one molecule in Coot, Chimera and Pymol but read as two distinct molecules in ChimeraX exactly like the deposition. I found this curious and thought that perhaps you might have some idea of what's wrong with the file. There is nothing that appears obviously incorrect to me in the text of the .pdb file, all TER cards follow the chains and all amino acids and their identifiers are in sequence and correct.
I'd appreciate any ideas you may have and I'm happy to send the file to you if you prefer.
Thank you, Kind regards, Lenye Dlamini Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer <http://www.uct.ac.za/main/email-disclaimer> or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php <https://csirt.uct.ac.za/page/report-an-incident.php>. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Hello Eric, Thanks for your response Yes I mean models. There is an "END" at the end of the file and no "ENDMDL" anywhere on the file. Kind regards, Lenye Dlamini ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Monday, January 30, 2023 9:50 PM To: Lenye Dlamini <DLMLEN001@myuct.ac.za> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Multi-chain single macromolecule .pdb file read as two molecules CAUTION: This email originated outside the UCT network. Do not click any links or open attachments unless you know and trust the source. Hi Lenye, When you say "molecules", do you actually mean "models", i.e. the file creates multiple models in ChimeraX? Are there MODEL/ENDMDL records in the file? Is there and END record (not ENDMDL record) that's not at the end of the file? Yes, sending the PDB would be helpful... --Eric Eric Pettersen UCSF Computer Graphics Lab On Jan 28, 2023, at 1:27 PM, Lenye Dlamini via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello, I have a homo-oligomeric model that I've refined using phenix and the ISOLDE tool in ChimeraX that's read during deposition as 2 separate molecules, a larger 14mer and a smaller tetramer. It's read as one molecule in Coot, Chimera and Pymol but read as two distinct molecules in ChimeraX exactly like the deposition. I found this curious and thought that perhaps you might have some idea of what's wrong with the file. There is nothing that appears obviously incorrect to me in the text of the .pdb file, all TER cards follow the chains and all amino acids and their identifiers are in sequence and correct. I'd appreciate any ideas you may have and I'm happy to send the file to you if you prefer. Thank you, Kind regards, Lenye Dlamini Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprotect-za.mimecast.com%2Fs%2F_ER2CNxKq0i0N07GXFm8jQk&data=05%7C01%7Cdlmlen001%40myuct.ac.za%7C8b53751ab9e64d137a5408db03631d98%7C92454335564e4ccfb0b024445b8c03f7%7C0%7C0%7C638107496512969304%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MkUHSJqUiwNM86jM0sVpaCeyTfvZNX%2BmKJ3vvkUxT18%3D&reserved=0> or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprotect-za.mimecast.com%2Fs%2FrmC3CO7Xr8spApny4TvKeno&data=05%7C01%7Cdlmlen001%40myuct.ac.za%7C8b53751ab9e64d137a5408db03631d98%7C92454335564e4ccfb0b024445b8c03f7%7C0%7C0%7C638107496512969304%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2Qjhs62d%2BbbzK3O5DsvIFhPFuHWsle9shDMFddvtiEQ%3D&reserved=0>. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprotect-za.mimecast.com%2Fs%2F1gWACP1KvQUK4KWkMi1Lqa3&data=05%7C01%7Cdlmlen001%40myuct.ac.za%7C8b53751ab9e64d137a5408db03631d98%7C92454335564e4ccfb0b024445b8c03f7%7C0%7C0%7C638107496512969304%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4E8XSqkiy3Bnq5YkvRfl1nrd3mjQRQXExbXFqBu8cKY%3D&reserved=0> Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.
Okay, well, you would need to send me the file for me to figure out why this happens. You can either send it to me directly in email or use Help→Report a Bug in ChimeraX and attach the file. --Eric
On Jan 31, 2023, at 9:24 AM, Lenye Dlamini <DLMLEN001@myuct.ac.za> wrote:
Hello Eric,
Thanks for your response Yes I mean models. There is an "END" at the end of the file and no "ENDMDL" anywhere on the file.
Kind regards, Lenye Dlamini From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Monday, January 30, 2023 9:50 PM To: Lenye Dlamini <DLMLEN001@myuct.ac.za <mailto:DLMLEN001@myuct.ac.za>> Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Multi-chain single macromolecule .pdb file read as two molecules
CAUTION: This email originated outside the UCT network. Do not click any links or open attachments unless you know and trust the source.
Hi Lenye, When you say "molecules", do you actually mean "models", i.e. the file creates multiple models in ChimeraX? Are there MODEL/ENDMDL records in the file? Is there and END record (not ENDMDL record) that's not at the end of the file? Yes, sending the PDB would be helpful...
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 28, 2023, at 1:27 PM, Lenye Dlamini via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello,
I have a homo-oligomeric model that I've refined using phenix and the ISOLDE tool in ChimeraX that's read during deposition as 2 separate molecules, a larger 14mer and a smaller tetramer. It's read as one molecule in Coot, Chimera and Pymol but read as two distinct molecules in ChimeraX exactly like the deposition. I found this curious and thought that perhaps you might have some idea of what's wrong with the file. There is nothing that appears obviously incorrect to me in the text of the .pdb file, all TER cards follow the chains and all amino acids and their identifiers are in sequence and correct.
I'd appreciate any ideas you may have and I'm happy to send the file to you if you prefer.
Thank you, Kind regards, Lenye Dlamini Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprotect-za...> or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprotect-za...>. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprotect-za...> Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer <http://www.uct.ac.za/main/email-disclaimer> or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php <https://csirt.uct.ac.za/page/report-an-incident.php>.
participants (2)
-
Eric Pettersen -
Lenye Dlamini