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

[Fekete Attila]

Dear Elaine,

Thanks for your answer. As I mentioned earlier, I don't think that it would be a format related error. Pdb files have a very strict format, however most of my pdb files were generated with Gromacs, but I got the same error when I tried to open files downloaded from the rcsb.org without any editing, just download and open , nothing else.

Yours,
A.

----- Eredeti üzenet -----
Feladó: "Elaine Meng" <meng 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. 18:39:07
Tárgy: Re: [chimerax-users] open local pdb files "containing no atoms and bonds"

Dear Attila,
We would need you to send an example PDB file that has the problem.  

I open local PDB files all the time in ChimeraX without problems. It should really be exactly the same as if you fetch a PDB from RCSB directly (e.g. ChimeraX command: open 2gbp format pdb) because that file is saved locally and opened.

Maybe there is something strange about the way you are saving it? E.g. it should be plain text, not a Word document, rich text, or anything like that.  You could also look at your local files with your favorite text-editor and make sure they are not empty.  I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> 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