Dear Eric,
Many thanks for your response!
Here are my answers:
1.) Yes, absolutely, billion times, I'm a Chimera fan, so Chimera 1.11.2 is able to open anything perfectly.
2.) I checked. I can open the downloaded mmCIF (yeeeah!), but not the pdb :( .
3.) see below, do you think my problem is in connection with the language of my system? I tried to change locales to en_US.utf8 but it's not working yet I have to go a bit deeper...
Yours,
A.
/home/feketea/>locale
LANG=hu_HU.UTF-8
LANGUAGE=hu:en
LC_CTYPE="hu_HU.UTF-8"
LC_NUMERIC=hu_HU.UTF-8
LC_TIME=hu_HU.UTF-8
LC_COLLATE="hu_HU.UTF-8"
LC_MONETARY=hu_HU.UTF-8
LC_MESSAGES="hu_HU.UTF-8"
LC_PAPER=hu_HU.UTF-8
LC_NAME=hu_HU.UTF-8
LC_ADDRESS=hu_HU.UTF-8
LC_TELEPHONE=hu_HU.UTF-8
LC_MEASUREMENT=hu_HU.UTF-8
LC_IDENTIFICATION=hu_HU.UTF-8
LC_ALL=
----- Eredeti üzenet -----
Feladó: "Eric Pettersen" <
pett@cgl.ucsf.edu>
Címzett: "Fekete Attila" <
fekete.attila@science.unideb.hu>
Másolatot kap: "chimerax-users" <
chimerax-users@cgl.ucsf.edu>
Elküldött üzenetek: Hétfő, 2018. február 12. 19:32:56
Tárgy: Re: [chimerax-users] open local pdb files "containing no atoms and bonds"
Hi Attila,
We have had this problem reported by another Ubuntu user and so far have been unable to reproduce it. I have a few questions:
1) Do these files open in regular Chimera?
2) Did you actually try opening downloaded mmCIF files, or only PDB files? If not, could you try with a downloaded mmCIF file (and what happens)?
3) In a terminal window, what output do you get from the “locale” command?
—Eric
Eric Pettersen
UCSF Computer Graphics Lab
On Feb 12, 2018, at 12:11 AM, Fekete Attila <fekete.attila@science.unideb.hu> wrote:
Dear Colleagues,
I have tried to open several local *.pdb files, but in each case I got the error: "Opened PDB data containing 0 atoms, 0 bonds and 0 coordinate sets", and a series of warnings (for each lines of the files) and ChimeraX doesn't show the structure.
I have also tried different versions of ChimeraX (0.1/0.5 and even alpha releases, recently I'm using 0.5 under Ubuntu 16.04).
I can open any online files (*pdb,*mmCIF) from the RCSB database, however if I download the same file, I got the above mentioned error message, so I have absolutely no clue to resolve the problem because I suppose this isn't related to pdb format issues but a bug can be somewhere in the softwere.
I am really impressed by the visualization capabilities of ChimeraX so please help me if you can.
Yours,
Attila
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