Opened 8 years ago

Closed 13 months ago

#996 closed defect (fixed)

Issue reading PDB files

Reported by: carlo.camilloni@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen)

Dear Developers 

I noticed that while ChimeraX can correctly import PDB files from RCSB, when trying to read PDB files locally, like those generated by MODELLER or other common programs it gives warnings and doesn’t open them. A work around is for example saving the same PDB in CIF using pymol and then ChimeraX can open it correctly.

Best,
Carlo
_______

Department of Biosciences
University of Milano
Via Celoria 26 - 20133 Milano, Italy

www: sites.unimi.it/camilloni <http://sites.unimi.it/camilloni>
www: bioscienze.bio <http://bioscienzebio.unimi.it/>



Attachments (4)

GLTb.B99990001.pdb (289.7 KB ) - added by carlo.camilloni@… 8 years ago.
Added by email2trac
untitled-part.html (208 bytes ) - added by carlo.camilloni@… 8 years ago.
Added by email2trac
Screen Shot 2018-01-15 at 09.19.15.png (256.1 KB ) - added by carlo.camilloni@… 8 years ago.
Added by email2trac
untitled-part-1.html (6.5 KB ) - added by carlo.camilloni@… 8 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (9)

comment:1 by Eric Pettersen, 8 years ago

Component: UnassignedInput/Output
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted

Hi Carlo,

ChimeraX *should* be able to read the same files as regular Chimera -- the code is very, very similar. Can you provide an example file or two that ChimeraX is having trouble with? Thanks!

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:2 by Eric Pettersen, 8 years ago

Status: acceptedfeedback

in reply to:  3 ; comment:3 by carlo.camilloni@…, 8 years ago

Hi Eric

Sorry for the late reply. This is a PDB file and a screenshot on Ubuntu 17.10.
The same currently works well on my macbook.

Cheers,
Carlo



 
_______

Department of Biosciences
University of Milano
Via Celoria 26 - 20133 Milano, Italy

www: sites.unimi.it/camilloni <http://sites.unimi.it/camilloni>
www: bioscienze.bio <http://bioscienzebio.unimi.it/>



GLTb.B99990001.pdb

untitled-part.html

Added by email2trac

untitled-part-1.html

by carlo.camilloni@…, 8 years ago

Attachment: GLTb.B99990001.pdb added

Added by email2trac

by carlo.camilloni@…, 8 years ago

Attachment: untitled-part.html added

Added by email2trac

by carlo.camilloni@…, 8 years ago

Added by email2trac

by carlo.camilloni@…, 8 years ago

Attachment: untitled-part-1.html added

Added by email2trac

comment:4 by Eric Pettersen, 8 years ago

Using the latest daily build of ChimeraX on Ubuntu 16.04, I can open the file you attached without any errors, and it successfully displays the structure. Maybe you need to get a newer version of ChimeraX? I'm not certain that will help because I don't recall any older versions having the problems you're having... Nonetheless, it's best to work with the latest version since that will help me debug the problem. Also, I opened the file by using the File->Open menu and browsing to it. How did you open it?

--Eric

comment:5 by Eric Pettersen, 13 months ago

Description: modified (diff)
Resolution: fixed
Status: feedbackclosed
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