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

[Jonathan Jih]

Sounds great. Thanks!!

On Wed, Jan 11, 2023 at 3:59 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hmmm, oops. :-). Tomorrow's daily build will not put out SEQRES records
> for chains where it doesn't know the complete sequence.
>
> --Eric
>
> On Jan 11, 2023, at 2:41 PM, Jonathan Jih <jihmailed at gmail.com> wrote:
>
> 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
>
> De Novo Modeling Solutions <http://www.denovomods.com/>
> projects at denovomods.com | (831) 419-7729
>
>
>

-- 
Biochemistry, Biophysics, and Structural Biology (BBSB)
Molecular Biology Institute, University of California, Los Angeles

De Novo Modeling Solutions <http://www.denovomods.com/>
projects at denovomods.com | (831) 419-7729
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