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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users