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

[Eric Pettersen]

Good to know that there is a workaround for the desperate.:-)  I had a vacation day yesterday, but will get back to the compilation today.

—Eric

> On Feb 14, 2018, at 9:58 AM, Fekete Attila <fekete.attila at science.unideb.hu> wrote:
> 
> Dear Eric,
> 
> I was a bit impatient, so I changed my system-wide language set to en_US, and it works fine. ChimeraX can read any downloaded or locally created pdb file.
> So I'd like to suggest a quick&dirty solution: 
> sudo apt-get install language-pack-en language-pack-en-base manpages
> sudo dpkg-reconfigure locales
> and finally change the primary language to English (System config / Language Support) then apply that System-wide. 
> It's important that you should remove the original language pack!
> 
> 
> Thanks for the support!
> 
> Yours,
> A.
> 
> ----- Eredeti üzenet -----
> Feladó: "Fekete Attila" <fekete.attila at science.unideb.hu>
> Címzett: "Eric Pettersen" <pett at cgl.ucsf.edu>
> Másolatot kap: "chimerax-users" <chimerax-users at cgl.ucsf.edu>
> Elküldött üzenetek: Kedd, 2018. február 13. 7:37:50
> Tárgy: Re: [chimerax-users] open local pdb files "containing no atoms and bonds"
> 
> Dear Eric,
> 
> Thank You so much!
> 
> Yours,
> A.
> 
> ----- 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: Kedd, 2018. február 13. 4:47:56
> Tárgy: Re: [chimerax-users] open local pdb files "containing no atoms and bonds"
> 
> I can reproduce the problem on an Ubuntu system where Hungarian is the primary language at installation.  It may take me awhile to compile ChimeraX on such as system, so you may have to be patient…
> 
> —Eric
> 
>> On Feb 12, 2018, at 12:59 PM, Fekete Attila <fekete.attila at science.unideb.hu> wrote:
>> 
>> 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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>> 
> 
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