[chimerax-users] Questions on job status

[Will Grubbe]

Ok. Thank you for the help! I will try to figure it out.

On Fri, Aug 26, 2022 at 3:45 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Will,
> Thanks for the job IDs, that was helpful.  So your jobs are failing but
> ChimeraX isn't alerting you to that -- which is a bug we need to fix.  The
> reason for the failure is that in order to fill in those missing residues,
> ChimeraX needs to know what those residues are, which apparently is not
> contained in the IFNL1_complex.cif file that you are using.  You either
> need to edit that file to insert the complete sequence, or open a separate
> sequence file containing the complete sequence and associate the structure
> with that sequence.  It should automatically associate due to the high
> similarity, but if it doesn't you would have to use the
> "Structure→Associations..." item in the sequence context menu to make the
> association.  Anyway, once you have the structure associated with the
> complete sequence, you should be able to successfully model the loop.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Aug 26, 2022, at 8:57 AM, Will Grubbe via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Thank you for the response Elaine. It was a Modeller online job to fill in
> some missing residues of a protein complex. I kept ChimeraX open the whole
> time on my computer but can't find anything updated, either on the desktop,
> in the downloads, or in the results folder I specified. I don't see
> anything in the log list either - perhaps I am doing something wrong. I do
> have job IDs if that helps -
> Webservices job id: EZ1QP7XJZLIY0BVI
> Webservices job id: 488559BRXJ20I5U4
> Webservices job id: L4AM4PK7N293HQ1L
>
> On Thu, Aug 25, 2022 at 6:59 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>> HI WIll,
>> It would help if you would say what kind of job you submitted.
>> Modeller?  AlphaFold prediction? In either case you would normally keep the
>> same ChimeraX session open and results would automatically open in ChimeraX
>> when they return. If you quit out of ChimeraX while Modeller is still
>> running, currently you can't get the results later.  If it seems to take a
>> really long time, maybe it just failed and you should look in the Log to
>> see if there was a message.
>>
>> AlphaFold prediction is different since it doesn't run on our website but
>> instead on Google Colab.  If there were any results returned before you
>> quit from ChimeraX, they should be in folders under
>> ~/Downloads/ChimeraX/AlphaFold/ on your machine.  Maybe the Colab timed out
>> before returning any results, however.  Even if you were trying to fill in
>> just a few residues, if you were predicting the whole complex it is
>> potentially a very long job.
>>
>> For Alphafold predict, make sure you are using a recent ChimeraX daily
>> build -- in mid-July we improved it to use ColabFold which is a much faster
>> version.  Also in the last day or two, a new option to specify the results
>> folder location was added.
>> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict
>> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html*predict__;Iw!!BpyFHLRN4TMTrA!8ApevkHLkrkKHr8pkkOX-szCFb-HkzoxMVky3sxpkDyIS1gCzW4qaI55jCpJyb9vudpPKGxqps99XWSiP2ga$>
>> >
>> <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog
>> <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog__;!!BpyFHLRN4TMTrA!8ApevkHLkrkKHr8pkkOX-szCFb-HkzoxMVky3sxpkDyIS1gCzW4qaI55jCpJyb9vudpPKGxqps99XQeQ_eBU$>
>> >
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> > On Aug 25, 2022, at 3:29 PM, Will Grubbe via ChimeraX-users <
>> chimerax-users at cgl.ucsf.edu> wrote:
>> >
>> > Hello, I've submitted a few jobs using ChimeraX and am wondering how to
>> check the status of them. I just need to fill in a few residues in a
>> protein complex with known sequence - where can I find the results when
>> they are done?
>> > Thank you for your help,
>> > Will
>>
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