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#2907 closed defect (not a bug)
Chimera Modeller Issue
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
Hello, I am currently trying to make a model where I fuse three known structures together, however, modeller keeps giving me 0 results. To clarify, I am taking chain A of 5tby, chain A of 1zil, and finally chain A of gfl and trying to fuse them together. I have loaded those sequences into the same sequence window, added my own "custom sequence" which is just the 3 one after another with no end, and pressed Modeller (homology). The result is an empty modeller result panel. I have never had this issue before doing similar things, so I was wondering if there were anything on your end. Thanks Joseph Cirilo The Pennsylvania State University College of Medicine Biomedical Sciences PhD Candidate Dept. of Cellular and Molecular Physiology 2019 GSA Social Chair Tel: (570) 328-2616 Email: jcirilo@pennstatehealth.psu.edu<mailto:jcirilo@pennstatehealth.psu.edu>
Attachments (1)
Change History (10)
comment:1 by , 6 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
comment:2 by , 6 years ago
| Status: | accepted → feedback |
|---|
follow-up: 3 comment:3 by , 6 years ago
Hi Eric,
I did not realize there was even a difference between Chiimera and ChimeraX. I apologize for the email t the wrong group. I will try to send the report to the chimera team. Thanks!
As to what you were alluding to with muleteer modeling, how would I go about doing that in ChimeraX? I may also try that if it is easier.
Thanks!
Joe
Joseph Cirilo
The Pennsylvania State University College of Medicine
Biomedical Sciences PhD Candidate
Dept. of Cellular and Molecular Physiology
2019 GSA Social Chair
Tel: (570) 328-2616
Email: jcirilo@pennstatehealth.psu.edu<mailto:jcirilo@pennstatehealth.psu.edu>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, March 2, 2020 5:17:11 PM
Cc: Cirilo, Joseph; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #2907: Chimera Modeller Issue
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#2907: Chimera Modeller Issue
--------------------------------+----------------------------
Reporter: jcirilo@… | Owner: Eric Pettersen
Type: defect | Status: accepted
Priority: normal | Milestone:
Component: Sequence | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------+----------------------------
Changes (by Eric Pettersen):
* owner: (none) => Eric Pettersen
* platform: => all
* status: new => accepted
* component: Unassigned => Sequence
* project: => ChimeraX
Comment:
Hi Joseph,
Are you having this problem with Chimera or ChimeraX? Though you
sent this to chimerax-bugs, your description sounds more like Chimera
(e.g. Chimera has a "Modeller (homology)" menu entry and ChimeraX does
not). Also, in ChimeraX you could model the multimer directly and not have
to resort to the trick you're using. In either case, the log should have
info about the job ID/URL. If you could send me that I could then look on
our server and see what happened.
--Eric
Eric Pettersen
UCSF Computer Graphics
--
Ticket URL: <https://urldefense.com/v3/__https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2907*comment:1__;Iw!!Ls64Rlj6!i58fhAmbdMRRDlHemMcsmT7xepi4_O0VnxpbmC1c09j-duvBX0iKVMN1cnRKV-M60t_cu18$ >
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ChimeraX Issue Tracker
follow-up: 4 comment:4 by , 6 years ago
For reference, however, this is what I see when I try to do the modeling. It does not give an error code, just no model is produced,
Thanks,
Joe
Joseph Cirilo
The Pennsylvania State University College of Medicine
Biomedical Sciences PhD Candidate
Dept. of Cellular and Molecular Physiology
2019 GSA Social Chair
Tel: (570) 328-2616
Email: jcirilo@pennstatehealth.psu.edu<mailto:jcirilo@pennstatehealth.psu.edu>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, March 3, 2020 9:06:30 AM
To: pett@cgl.ucsf.edu; Cirilo, Joseph
Subject: Re: [ChimeraX] #2907: Chimera Modeller Issue
== CAUTION: External Sender ==
This message came from outside of Penn State Health & College of Medicine.
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#2907: Chimera Modeller Issue
--------------------------------+----------------------------
Reporter: jcirilo@… | Owner: Eric Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Sequence | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------+----------------------------
Comment (by jcirilo@…):
{{{
Hi Eric,
I did not realize there was even a difference between Chiimera and
ChimeraX. I apologize for the email t the wrong group. I will try to send
the report to the chimera team. Thanks!
As to what you were alluding to with muleteer modeling, how would I go
about doing that in ChimeraX? I may also try that if it is easier.
Thanks!
Joe
Joseph Cirilo
The Pennsylvania State University College of Medicine
Biomedical Sciences PhD Candidate
Dept. of Cellular and Molecular Physiology
2019 GSA Social Chair
Tel: (570) 328-2616
Email:
jcirilo@pennstatehealth.psu.edu<mailto:jcirilo@pennstatehealth.psu.edu>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, March 2, 2020 5:17:11 PM
Cc: Cirilo, Joseph; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #2907: Chimera Modeller Issue
== CAUTION: External Sender ==
This message came from outside of Penn State Health & College of Medicine.
Please use caution when opening attachments or links.
#2907: Chimera Modeller Issue
--------------------------------+----------------------------
Reporter: jcirilo@… | Owner: Eric Pettersen
Type: defect | Status: accepted
Priority: normal | Milestone:
Component: Sequence | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------+----------------------------
Changes (by Eric Pettersen):
* owner: (none) => Eric Pettersen
* platform: => all
* status: new => accepted
* component: Unassigned => Sequence
* project: => ChimeraX
Comment:
Hi Joseph,
Are you having this problem with Chimera or ChimeraX? Though you
sent this to chimerax-bugs, your description sounds more like Chimera
(e.g. Chimera has a "Modeller (homology)" menu entry and ChimeraX does
not). Also, in ChimeraX you could model the multimer directly and not
have
to resort to the trick you're using. In either case, the log should have
info about the job ID/URL. If you could send me that I could then look
on
our server and see what happened.
--Eric
Eric Pettersen
UCSF Computer Graphics
--
Ticket URL:
<https://urldefense.com/v3/__https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2907*comment:1__;Iw!!Ls64Rlj6
!i58fhAmbdMRRDlHemMcsmT7xepi4_O0VnxpbmC1c09j-duvBX0iKVMN1cnRKV-M60t_cu18$
>
ChimeraX
<https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimerax/__;!!Ls64Rlj6
!i58fhAmbdMRRDlHemMcsmT7xepi4_O0VnxpbmC1c09j-duvBX0iKVMN1cnRKV-M6-4d830I$
>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://urldefense.com/v3/__https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2907*comment:3__;Iw!!Ls64Rlj6!hFVnuba0LgydmUG3v2AsIGI3jscjJP50YC6a0zG_WkRPA_KPiMnTHJqh0WBkmwp1Ut1Gxzk$ >
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ChimeraX Issue Tracker
comment:5 by , 6 years ago
For now, scratch the idea of using ChimeraX. It seems to generate homo-multimers okay, but not hetero-multimers. I will look into that.
As for Chimera, I was asking you for the information from the Reply Log (Favorites→Reply Log). When you run the Modeller job, part of the output in the reply log should look something like: "Opal job URL: http://webservices.rbvi.ucsf.edu/appModeller9v8Service1583264051417-1393740528". That's the information I need to see what happened on the server.
--Eric
comment:6 by , 6 years ago
My apologies!
Here is the reply log.
#0, chain A: myosin-7
#0, chain B: myosin-7
#0, chain C: myosin light chain 3
#0, chain D: myosin light chain 3
#0, chain E: myosin regulatory light chain 2, ventricular/cardiac muscle isoform
#0, chain F: myosin regulatory light chain 2, ventricular/cardiac muscle isoform
#1, chain A: GCN4
#1, chain B: GCN4
#2, chain A: green fluorescent protein
#2, chain B: green fluorescent protein
seq (len 2206): 1zil chain A
target (len 2206): 5TBY (#0) chain A
seq (len 2206): 1gfl chain A
target (len 2206): 5TBY (#0) chain A
seq (len 2206): HMM LZ GFP
target (len 2206): 5TBY (#0) chain A
seq (len 2206): 5TBY (#0) chain A
target (len 2206): HMM LZ GFP
seq (len 2206): 1zil chain A
target (len 2206): HMM LZ GFP
seq (len 2206): 1gfl chain A
target (len 2206): HMM LZ GFP
seq (len 2206): 5TBY (#0) chain A
target (len 2206): HMM LZ GFP
seq (len 2206): 1zil chain A
target (len 2206): HMM LZ GFP
seq (len 2206): 1gfl chain A
target (len 2206): HMM LZ GFP
Target seq: HMM LZ GFP
Template structures:
5TBY (#0)
1zil (#1)
1gfl (#2)
Run on web, the license key is: MODELIRANJE
Now, modeller is running on the web over Opal...
Wrote /var/folders/s6/kly45srj6t55wt4bsswykr980000gn/T/tmpHJILbf/template_struc/5TBY_0_0.pdb
Wrote /var/folders/s6/kly45srj6t55wt4bsswykr980000gn/T/tmpHJILbf/template_struc/1zil_1_0.pdb
Wrote /var/folders/s6/kly45srj6t55wt4bsswykr980000gn/T/tmpHJILbf/template_struc/1gfl_2_0.pdb
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling
Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job URL: http://webservices.rbvi.ucsf.edu/appModeller9v8Service15832675536851251259923
Traceback (most recent call last):
File "/Applications/Chimera.app/Contents/Resources/share/chimera/tasks.py", line 179, in runStatusCB
task.statusCBList[0]()
File "/Applications/Chimera.app/Contents/Resources/share/WebServices/appWebService.py", line 129, in statusCB
pgs = 100.0 * self.progressCB( self.backend.getStdOut() )
File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 306, in getStdOut
return self.getURLContent(stdOut_URL)
File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_client.py", line 327, in getURLContent
f = urllib2.urlopen(url)
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 154, in urlopen
return opener.open(url, data, timeout)
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 435, in open
response = meth(req, response)
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 548, in http_response
'http', request, response, code, msg, hdrs)
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 473, in error
return self._call_chain(*args)
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 407, in _call_chain
result = func(*args)
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/urllib2.py", line 556, in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 404: Not Found
Joseph Cirilo
The Pennsylvania State University College of Medicine
Biomedical Sciences PhD Candidate
Dept. of Cellular and Molecular Physiology
2019 GSA Social Chair
Tel: (570) 328-2616
Email: jcirilo@pennstatehealth.psu.edu<mailto:jcirilo@pennstatehealth.psu.edu>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, March 3, 2020 2:38:40 PM
Cc: Cirilo, Joseph; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #2907: Chimera Modeller Issue
== CAUTION: External Sender ==
This message came from outside of Penn State Health & College of Medicine.
Please use caution when opening attachments or links.
#2907: Chimera Modeller Issue
--------------------------------+----------------------------
Reporter: jcirilo@… | Owner: Eric Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Sequence | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------+----------------------------
Comment (by Eric Pettersen):
For now, scratch the idea of using ChimeraX. It seems to generate homo-
multimers okay, but not hetero-multimers. I will look into that.
As for Chimera, I was asking you for the information from the Reply Log
(Favorites→Reply Log). When you run the Modeller job, part of the output
in the reply log should look something like: "Opal job URL:
https://urldefense.com/v3/__http://webservices.rbvi.ucsf.edu/appModeller9v8Service1583264051417-1393740528__;!!Ls64Rlj6!jWZaQvwXwm02srZO1STKK1_s1jd4EV8Ru0380IBA8PcopLbAUrCIfTPDvBPJ0Y2ec_oBCQk$ ".
That's the information I need to see what happened on the server.
--Eric
--
Ticket URL: <https://urldefense.com/v3/__https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2907*comment:5__;Iw!!Ls64Rlj6!jWZaQvwXwm02srZO1STKK1_s1jd4EV8Ru0380IBA8PcopLbAUrCIfTPDvBPJ0Y2eg0Z4RQ4$ >
ChimeraX <https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimerax/__;!!Ls64Rlj6!jWZaQvwXwm02srZO1STKK1_s1jd4EV8Ru0380IBA8PcopLbAUrCIfTPDvBPJ0Y2epfXU8os$ >
ChimeraX Issue Tracker
follow-up: 6 comment:7 by , 6 years ago
| Status: | feedback → accepted |
|---|
So this is the tail end of the standard output of your Modeller job:
pick_re_612_> Number of MODEL atoms, selected restraints; 17824 127259
single_mod_E> Obj. func. (10258930.000) exceeded max_molpdf (10000000.000)
Summary of failed models:
HMM_LZ_GFP.B99990001.pdb Obj. func. (10730943.000) exceeded max_molpdf (10000000.000)
HMM_LZ_GFP.B99990002.pdb Obj. func. (10056025.000) exceeded max_molpdf (10000000.000)
HMM_LZ_GFP.B99990003.pdb Obj. func. (11483168.000) exceeded max_molpdf (10000000.000)
HMM_LZ_GFP.B99990004.pdb Obj. func. (11785519.000) exceeded max_molpdf (10000000.000)
HMM_LZ_GFP.B99990005.pdb Obj. func. (10258930.000) exceeded max_molpdf (10000000.000)
Mr. Google points me to this page: https://salilab.org/archives/modeller_usage/2006/msg00134.html
which basically says that all the generated models were discarded as bad. You could either tried other positions for the templates, or you could try what that web link says and increase the cutoff. You would have to run Modeller locally though, since Chimera's web execution does not allow custom scripts (it's local-execution mode does).
--Eric
comment:8 by , 6 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
comment:9 by , 5 years ago
Actually modeling heteromultimers in ChimeraX does work, it's just that it's complicated enough that I myself got confused. Basically, you have to have a structure to serve as the multimer template, with the chains in the approximately correct spatial relationship, then you have to have an alignment for each chain you want to model.
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Hi Joseph,
--Eric