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<p>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.<br>
</p>
<p> -- Greg<br>
</p>
<div class="moz-cite-prefix">On 8/26/2022 1:47 PM, Will Grubbe via
ChimeraX-users wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAN6o79sbnUHbUVQ-Rk5ic1ZFM-Tdq-DHEv4bcPGU-fCFkGb61w@mail.gmail.com">
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<div dir="ltr">Ok. Thank you for the help! I will try to figure it
out. </div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Aug 26, 2022 at 3:45
PM Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu"
moz-do-not-send="true" class="moz-txt-link-freetext">pett@cgl.ucsf.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;">Hi Will,
<div><span style="white-space:pre-wrap"> </span>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.</div>
<div><br>
</div>
<div>
<div>--Eric</div>
<div><br>
</div>
<div><span style="white-space:pre-wrap"> </span>Eric
Pettersen</div>
<div><span style="white-space:pre-wrap"> </span>UCSF
Computer Graphics Lab</div>
<div><br>
</div>
<div><br>
<blockquote type="cite">
<div>On Aug 26, 2022, at 8:57 AM, Will Grubbe via
ChimeraX-users <<a
href="mailto:chimerax-users@cgl.ucsf.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">chimerax-users@cgl.ucsf.edu</a>>
wrote:</div>
<br>
<div>
<div dir="ltr">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 -
<div>Webservices job id: EZ1QP7XJZLIY0BVI<br>
Webservices job id: 488559BRXJ20I5U4<br>
Webservices job id: L4AM4PK7N293HQ1L</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Aug 25,
2022 at 6:59 PM Elaine Meng <<a
href="mailto:meng@cgl.ucsf.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">meng@cgl.ucsf.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px
0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">HI WIll,<br>
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.
<br>
<br>
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.<br>
<br>
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.<br>
<<a
href="https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html*predict__;Iw!!BpyFHLRN4TMTrA!8ApevkHLkrkKHr8pkkOX-szCFb-HkzoxMVky3sxpkDyIS1gCzW4qaI55jCpJyb9vudpPKGxqps99XWSiP2ga$"
rel="noreferrer" target="_blank"
moz-do-not-send="true">https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict</a>><br>
<<a
href="https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog__;!!BpyFHLRN4TMTrA!8ApevkHLkrkKHr8pkkOX-szCFb-HkzoxMVky3sxpkDyIS1gCzW4qaI55jCpJyb9vudpPKGxqps99XQeQ_eBU$"
rel="noreferrer" target="_blank"
moz-do-not-send="true">https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Aug 25, 2022, at 3:29 PM, Will Grubbe
via ChimeraX-users <<a
href="mailto:chimerax-users@cgl.ucsf.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">chimerax-users@cgl.ucsf.edu</a>>
wrote:<br>
> <br>
> 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? <br>
> Thank you for your help,<br>
> Will <br>
<br>
</blockquote>
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