[chimerax-users] Trouble displaying missing structure dashed lines in cartoon mode

[Jonathan Jih]

That makes a lot of sense - thanks for the explanation Eric!

Is there perhaps a way to disable automatic SEQRES generation when saving
pdbs within ChimeraX? I noticed that when I load a pdb with no SEQRES info
(thereby having missing structure pseudobonds display correctly), upon
resaving that pdb, new SEQRES info is automatically generated causing the
issue to rear again. I then have to go back and manually delete SEQRES for
each one of the pdbs I generate.

Appreciate all the help.

Jonathan

On Wed, Jan 11, 2023 at 2:37 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Just for the curious bystanders, the problem is that the SEQRES records --
> which are supposed to supply the complete sequence of the polymer --
> indicated that the far-apart residues were consecutive in sequence.
> ChimeraX therefore suppressed the display of the missing-structure
> pseudobond.
>
> --Eric
>
> On Jan 11, 2023, at 12:35 PM, Jonathan Jih via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi Eric,
>
> I can confirm that opening 1www does display pseudobonds properly. I
> played around with my pdb files, and it seems if the issue can be resolved
> if I either: 1) delete or modify a residue in ChimeraX and then resave the
> pdb, or 2) if I fully delete the SEQRES header of each pdb file.
>
> In any case, I'll send you separately two test pdbs I've created. Thanks
> for the prompt response!
>
> Jonathan
>
> On Wed, Jan 11, 2023 at 10:33 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> Hi Jonathan,
>> So if you open a structure such as 1www, are the missing-structure
>> pseudobonds displayed?  If they are, then I would need access to one of
>> your PDB files (or part of of one) that demonstrates the problem -- which
>> you could send to me directly.
>>
>> --Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>>
>>
>> On Jan 11, 2023, at 2:35 AM, Jonathan Jih via ChimeraX-users <
>> chimerax-users at cgl.ucsf.edu> wrote:
>>
>> Hello ChimeraX team,
>>
>> I'm having quite a bit of trouble displaying missing structure dashed
>> lines when my models are shown in cartoon mode. This is despite the
>> "missing structure" sub-model box being ticked in the model panel.
>>
>> I recall finding a workaround for this nearly a year ago on ChimeraX 1.3,
>> but I cannot for the life of me remember how I did so (now using ChimeraX
>> 1.5). Interestingly, old sessions that I saved in 1.3 and 1.4 with whatever
>> workaround I applied back then display the missing structure dashed lines
>> properly in 1.5. However, opening the exact same pdb files from those older
>> sessions in 1.5 yields no dashed lines in cartoon mode. Full atom mode
>> appears fine.
>>
>> I also found this thread (
>> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003273.html),
>> which seems to indicate the issue has been fixed, so not sure if I'm just
>> doing something wrong?
>>
>> My OS is Windows 11 if that matters. Thanks in advance for the help!
>>
>> Jonathan
>>
>>
>> --
>> Biochemistry, Biophysics, and Structural Biology (BBSB)
>> Molecular Biology Institute, University of California, Los Angeles
>>
>>
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>>
>
> --
> Biochemistry, Biophysics, and Structural Biology (BBSB)
> Molecular Biology Institute, University of California, Los Angeles
>
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-- 
Biochemistry, Biophysics, and Structural Biology (BBSB)
Molecular Biology Institute, University of California, Los Angeles

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