science PDB file is not processed correctly after extraction

[Sasa Paporovic]

The affected archiv will be attached.

When I open the archiv

pdb163d.ent.gz

with file roller, I get the compressed file shown in file-roller GUI,

When I open it within the file-roller GUI with rasmol or jmol all works correct and the protein structure is shown.

So, far so good.

When I extract the compressed file to the filesystem, close file-roller, because it is no longer needed.

When I ttry then to open the file

pdb163d.ent

with rasmol or jmol it is not possible. The file is not anymore a appopriate format for those programs.

Steps to reproduce:

1.Install rasmol and jmol (oneof them may be enough)
2.Donwlaod the file

pdb163d.ent.gz

from here,
3.Extract the file to the filesytem with file-roller
4.Try to open the file with right mouse click - > open with... -> choose rasmol or jmol as your choice
5.See only a black visualisation or in jmol an error message(file not found exception)

ProblemType: Bug
DistroRelease: Ubuntu 12.10
Package: file-roller 3.6.1.1-0ubuntu1.1
ProcVersionSignature: Ubuntu 3.5.0-27.45-generic 3.5.7.7
Uname: Linux 3.5.0-27-generic x86_64
NonfreeKernelModules: fglrx
ApportVersion: 2.6.1-0ubuntu10
Architecture: amd64
Date: Sun Mar 24 19:33:18 2013
ExecutablePath: /usr/bin/file-roller
InstallationDate: Installed on 2013-01-13 (70 days ago)
InstallationMedia: Ubuntu 12.10 "Quantal Quetzal" - Release amd64 (20121017.5)
MarkForUpload: True
ProcEnviron:
 PATH=(custom, no username)
 XDG_RUNTIME_DIR=<set>
 LANG=de_DE.UTF-8
 SHELL=/bin/bash
SourcePackage: file-roller
UpgradeStatus: No upgrade log present (probably fresh install)

[Michael Banck (mbanck)]

I tried to reproduce this problem in Debian stable, and I cannot reproduce it all.

If I manually gunzip the file and open it with jmol, it displays fine. If I extract it with file-roller and open it in jmol, it displays fine as well.

 Are you sure this is not a file-roller issue? Or maybe it is a Ubuntu-specific issue.

[Sasa Paporovic (melchiaros)]

Hi Michael,

have you checked if the version of jmol on Debian stable as I have used here for quantal:

http://packages.ubuntu.com/search?keywords=jmol&searchon=names&suite=all&section=all

jmol12.2.32+dfsg-1

Well, I was and I am not sure that this here could be a file-roller issue. Caused by this I have opened the bug for file-roller, jmoler and rasmol all together. But when you can confirm that the jmol version on Debian is the same as I have used here, we could set the jmol status to invalid.

[Georges Khaznadar (georgesk)]

I downloaded a similar file from ftp://ftp.pdbj.org/pub/pdb/data/structures/all/pdb/pdb163l.ent.gz
...
and with the current version of file-roller and jmol, I could not reproduce this bug.
So I consider it as non-reproducible, and will close it.