[chimerax-users] Multi-chain single macromolecule .pdb file read as two molecules

[Eric Pettersen]

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 at 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 at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>>
> Sent: Monday, January 30, 2023 9:50 PM
> To: Lenye Dlamini <DLMLEN001 at myuct.ac.za <mailto:DLMLEN001 at myuct.ac.za>>
> Cc: chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu> <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at 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 at cgl.ucsf.edu <mailto:chimerax-users at 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
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