[chimerax-users] open local pdb files "containing no atoms and bonds"

[Fekete Attila]

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 at cgl.ucsf.edu>
Címzett: "Fekete Attila" <fekete.attila at science.unideb.hu>
Másolatot kap: "chimerax-users" <chimerax-users at 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 at 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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