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Opened 5 years ago
Closed 5 years ago
#3974 closed defect (can't reproduce)
Something broke in the PBD look up
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
HI guys, at some point last week the PDB lookup broke in Chimera X. I was able to import included Robetta results with all proteins one day (included image) and next day the same file generated the ignored bad PDB record found on line 2 (included image). I tested this on Windows and Mac versions. Please advise. Best, Christian Hans-Christian Reinecker MD Associate Professor of Medicine University of Texas Southwestern Medical Center Department of Medicine Division of Digestive and Liver Diseases Department of Immunology Center for Genetics of Host Defense J5.149 5959 Harry Hines Boulevard Dallas, TX 75390-8887 Phone: 214-645-5430 Fax: 214-648-2022 Hans-Christian.Reinecker@UTSouthwestern.edu ________________________________ UT Southwestern Medical Center The future of medicine, today.
Attachments (11)
Change History (21)
by , 5 years ago
| Attachment: | SLFN5 partial_threads_domain_43823_cluster_1.pdb added |
|---|
comment:1 by , 5 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
comment:2 by , 5 years ago
| Status: | accepted → feedback |
|---|
Hi Christian,
I guess I don't understand the problem. Opening your PDB file does produce warnings about the REMARK records, since they are in nonstandard format, but that doesn't affect the structures at all. You (and I) get 12 structures, overlaid on one another. Did you want them to appear the same as the image you sent? If the image is something you created in ChimeraX after some work, saving a PDB file will not preserve colors or representations, only coordinates. You would have to save a ChimeraX session file to preserve the work you'd done.
Perhaps you could explain further.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
comment:3 by , 5 years ago
Thanks for the fast answer. Here are the files so that it is clearer. I used Robetta output file to generate the included image in Chimera X. All was imported correctly fom the PBD file containing all the proteins. A few our later opening the same file threw up the errors and only the protein models generated from the input are displayed in ChimeraX not the similar structures identified.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, November 23, 2020 11:09 AM
Cc: Hans-Christian Reinecker <Hans-Christian.Reinecker@UTSouthwestern.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3974: Something broke in the PBD look up
EXTERNAL MAIL
#3974: Something broke in the PBD look up
-------------------------------------------------+-------------------------
Reporter: Hans-Christian.Reinecker@… | Owner: Eric
| Pettersen
Type: defect | Status: accepted
Priority: normal | Milestone:
Component: Input/Output | 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 => Input/Output
* project: => ChimeraX
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3974#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
SLFN5 partial_threads_domain_43823_cluster_1-1.pdb
by , 5 years ago
| Attachment: | SLFN5 partial_threads_domain_43823_cluster_1-1.pdb added |
|---|
Added by email2trac
by , 5 years ago
| Attachment: | SLFN5 partial_threads_domain_43823_cluster_1-2.pdb added |
|---|
Added by email2trac
comment:4 by , 5 years ago
Hi, I am trying to send files and jpegs, but I am getting all kind of reject emails, so I am not sure what gets through. I opened a PDB file that contains my modelled protein and the aligned proteins from robetta.bakerlab.org. All opened fine in ChimeraX with all the additional proteins imported. A few hours later the same file created the error messages and no additional protein models were imported just my modeled protein. Access to the PDB data base seems broken so no models are imported. I installled ChimeraX also on a Mac but also there the file/models are not imported/opened correctly anymore.
Best, Christian
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, November 23, 2020 11:18 AM
Cc: Hans-Christian Reinecker <Hans-Christian.Reinecker@UTSouthwestern.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3974: Something broke in the PBD look up
EXTERNAL MAIL
#3974: Something broke in the PBD look up
-------------------------------------------------+-------------------------
Reporter: Hans-Christian.Reinecker@… | Owner: Eric
| Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------------------+-------------------------
Changes (by Eric Pettersen):
* status: accepted => feedback
Comment:
Hi Christian,
I guess I don't understand the problem. Opening your PDB file
does produce warnings about the REMARK records, since they are in
nonstandard format, but that doesn't affect the structures at all. You
(and I) get 12 structures, overlaid on one another. Did you want them to
appear the same as the image you sent? If the image is something you
created in ChimeraX after some work, saving a PDB file will not preserve
colors or representations, only coordinates. You would have to save a
ChimeraX session file to preserve the work you'd done.
Perhaps you could explain further.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3974#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
comment:5 by , 5 years ago
ChimeraX Is doing exactly what it is supposed to do with SLFN5 partial_threads_domain_43823_cluster_1.pdb. The file contains 12 structures and 13 badly formatted REMARK records (basically comments) that get ignored. I open it and see: Is that what you get? Was that the only file in your Robetta results, or were there others? --Eric
follow-up: 3 comment:6 by , 5 years ago
Hi Eric, I don't see anything in your email after I open it and see: Weird that the alignment clusters were imported initially but not anymore? Best Christian
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, November 23, 2020 12:40 PM
To: Hans-Christian Reinecker <Hans-Christian.Reinecker@UTSouthwestern.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3974: Something broke in the PBD look up
EXTERNAL MAIL
#3974: Something broke in the PBD look up
-------------------------------------------------+-------------------------
Reporter: Hans-Christian.Reinecker@… | Owner: Eric
| Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------------------+-------------------------
Comment (by Eric Pettersen):
{{{
ChimeraX Is doing exactly what it is supposed to do with SLFN5
partial_threads_domain_43823_cluster_1.pdb. The file contains 12
structures and 13 badly formatted REMARK records (basically comments) that
get ignored. I open it and see:
Is that what you get? Was that the only file in your Robetta results, or
were there others?
--Eric
}}}
[[Image(aligned.png)]]
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3974#comment:5>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
comment:7 by , 5 years ago
In addition to the mail that you got indirectly from ChimeraX-bugs-admin@… (which is the one you responded to), you should have gotten one directly from me (pett@…). The latter should have an image you can see in it. Maybe you need to check your spam folder?
Also, what about my other question -- was the PDB file the only file in your Robetta results?
--Eric
comment:8 by , 5 years ago
Yes, that is what I get now but the same file was imported completely with all the bad remark records a few hours earlier and I was able to create the attached. Please advise on what changed? Cheers, Christian ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Monday, November 23, 2020 12:40 PM To: Hans-Christian Reinecker <Hans-Christian.Reinecker@UTSouthwestern.edu> Cc: ChimeraX-bugs@cgl.ucsf.edu <ChimeraX-bugs@cgl.ucsf.edu> Subject: Re: [ChimeraX] #3974: Something broke in the PBD look up EXTERNAL MAIL ChimeraX Is doing exactly what it is supposed to do with SLFN5 partial_threads_domain_43823_cluster_1.pdb. The file contains 12 structures and 13 badly formatted REMARK records (basically comments) that get ignored. I open it and see: [cid:40C14414-5E47-4D99-83C8-5EC28CF7594C@gateway.sonic.net] Is that what you get? Was that the only file in your Robetta results, or were there others? --Eric CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today.
comment:9 by , 5 years ago
Can I fix that?
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, December 14, 2020 1:09 PM
Cc: Hans-Christian Reinecker <Hans-Christian.Reinecker@UTSouthwestern.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3974: Something broke in the PBD look up
EXTERNAL MAIL
#3974: Something broke in the PBD look up
-------------------------------------------------+-------------------------
Reporter: Hans-Christian.Reinecker@… | Owner: Eric
| Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------------------+-------------------------
Changes (by Hans-Christian.Reinecker@…):
* Attachment "SLFN5 and SLFN13 model-2.jpg" added.
Added by email2trac
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3974>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
comment:10 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | feedback → closed |
Are you certain that there isn't some other output file from Robetta that you used the first time? I have asked around the ChimeraX team just to make sure I wasn't missing something, and no one knows of a way that the file you sent could open with the structures positioned the way you have them in that first image. Sorry I haven't been able to help.
--Eric
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