[chimerax-users] Questions on job status

[Greg Couch]

The issue of mmCIF files missing sequence information is unfortunately 
not uncommon.  For example, if you are using Phenix, it used to be 
(maybe still is) the case that you have to go through the step of 
preparing the data for submission to the PDB for it to incorporate the 
sequence information into the mmCIF file.  Having the actual sequence, 
especially when it is known, helps  ChimeraX help you.

     -- Greg

On 8/26/2022 1:47 PM, Will Grubbe via ChimeraX-users wrote:
> 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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