open local pdb files "containing no atoms and bonds"
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
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@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
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@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. 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@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
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
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
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@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@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
Dear Eric, Thank You so much! Yours, A. ----- 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: 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@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@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
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@science.unideb.hu> Címzett: "Eric Pettersen" <pett@cgl.ucsf.edu> Másolatot kap: "chimerax-users" <chimerax-users@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@cgl.ucsf.edu> Címzett: "Fekete Attila" <fekete.attila@science.unideb.hu> Másolatot kap: "chimerax-users" <chimerax-users@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@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@science.unideb.hu> Címzett: "Eric Pettersen" <pett@cgl.ucsf.edu> Másolatot kap: "chimerax-users" <chimerax-users@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@cgl.ucsf.edu> Címzett: "Fekete Attila" <fekete.attila@science.unideb.hu> Másolatot kap: "chimerax-users" <chimerax-users@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@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Okay, this problem is fixed in the current daily build. The problem was that with the locale set to Hungarian, it was looking for floating point numbers where the decimal point was a ‘,’ instead of a ‘.’. —Eric
On Feb 14, 2018, at 10:07 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
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@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@science.unideb.hu> Címzett: "Eric Pettersen" <pett@cgl.ucsf.edu> Másolatot kap: "chimerax-users" <chimerax-users@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@cgl.ucsf.edu> Címzett: "Fekete Attila" <fekete.attila@science.unideb.hu> Másolatot kap: "chimerax-users" <chimerax-users@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@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@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
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Fekete Attila