[chimerax-users] chimeraX questions on representation

[Dr. Eddie]

Awesome, thanks!

On Tue, Oct 16, 2018 at 2:51 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Eddie,
> ChimeraX (and Chimera for that matter) connect atoms in standard residues
> using a connectivity template.  Therefore the atoms have to have standard
> names.  Some hydrogens in your file don’t have their PDB-standard names,
> and therefore wind up unconnected.  I have committed a fix for this — if
> there are unconnected hydrogens after the template pass then Chimera(X)
> does an additional connect-by-distance pass.
> A second problem with the file is that it uses ATOM records for
> everything, including solvent, ions, and the lipid bilayer.  ATOM records
> are for polymeric residues and imply connectivity between consecutive
> residues with the same chain ID.  Therefore the non polymeric components of
> the file should have been using HETATM records.  I have attached an edited
> version of your file with appropriate HETATM records.  It should work much
> better in tomorrow’s fixed build.
>
> —Eric
>
>
>
> On Oct 16, 2018, at 11:31 AM, Dr. Eddie <eackad at gmail.com> wrote:
>
> Thanks for the help! As for the pdb, I've attached it. It shows fine in
> vmd and pymol.
> Thanks,
> Eddie
>
> On Tue, Oct 16, 2018 at 1:19 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> On Oct 15, 2018, at 8:35 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>
>>  I don’t know why your H’s are disconnected specifically, but it’s almost
>> surely some issue with the input file.
>>
>>
>> If you provided the input file, we might be able to offer advice on how
>> to get ChimeraX to handle it better.  One thing you might try sight unseen
>> is to remove the LINK/CONECT records in the file (assuming it’s a PDB file).
>>
>> —Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>>
>>
>>
>>
>>
>
> --
> Eddie
> <popc.3a4.ionf.pdb>
>
>
>

-- 
Eddie
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