Re: [ccp4bb] baverage: no tables were found in this file
Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] baverage: no tables were found in this file
This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] baverage: no tables were found in this file
I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical.
Re: [ccp4bb] baverage: no tables were found in this file
Possibility to have file names with the spaces is a curse put on the community by Microsoft, and it will be a big mistake to introduce this to CCP4 (my opinion). I guess there are much more important things new CCP4 GUI should deal with. If CCP4 GUI will start to go this way, file names with spaces will become file names with spaces and multilingual, in some these languages writing is going in the different direction. In my introduction to UNIX, I teach in the beginning of practical protein crystallography my first demand from student is to forget about spaces in the fie names and the life will be much easier. No fix is needed for that, concentrate on more important problems :-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 3, 2014, at 14:47 , Eugene Krissinel eugene.krissi...@stfc.ac.uk wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical.
Re: [ccp4bb] baverage: no tables were found in this file
completely agree with avoiding spaces in paths and file names, but Google Drive is very handy for sharing files, so every once in a while I forget to move a file someone shares with me before running Unix programs on it and get strange errors. Depending on how awake one is at the time finding out the source can be time-consuming...Google should really remove the space! Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 13:47, Eugene Krissinel wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical.
Re: [ccp4bb] baverage: no tables were found in this file
Hi Felix Couldn't agree more, particularly when non-native anglophones have to contend with limiting themselves to ASCII characters in their filenames anyway (e.g. Spanish users have to carefully rename the OSX unnamed folder (carpeta sin título) to something without an accent...) On 3 Jun 2014, at 12:58, Felix Frolow wrote: Possibility to have file names with the spaces is a curse put on the community by Microsoft, and it will be a big mistake to introduce this to CCP4 (my opinion). I guess there are much more important things new CCP4 GUI should deal with. If CCP4 GUI will start to go this way, file names with spaces will become file names with spaces and multilingual, in some these languages writing is going in the different direction. In my introduction to UNIX, I teach in the beginning of practical protein crystallography my first demand from student is to forget about spaces in the fie names and the life will be much easier. No fix is needed for that, concentrate on more important problems :-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 3, 2014, at 14:47 , Eugene Krissinel eugene.krissi...@stfc.ac.uk wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical. Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] baverage: no tables were found in this file
I'm wondering if GUI2 will cope with accents as well as spaces (e.g. in the Spanish carpeta sin título which is the default new folder on Macs)? Discipline. That's what we need... On 3 Jun 2014, at 13:03, Mark J van Raaij wrote: completely agree with avoiding spaces in paths and file names, but Google Drive is very handy for sharing files, so every once in a while I forget to move a file someone shares with me before running Unix programs on it and get strange errors. Depending on how awake one is at the time finding out the source can be time-consuming...Google should really remove the space! Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 13:47, Eugene Krissinel wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical. Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] baverage: no tables were found in this file
Dear Felix, I, too, do not use spaces and file names in Russian :) However, these things are coming nearly for free and automatic with today's development tools, so little effort, if any, is required to adopt them, while the benefits in terms of user friendliness and convenience are not exactly negligible. Many thanks for understanding our situation -- Eugene On 3 Jun 2014, at 12:58, Felix Frolow wrote: Possibility to have file names with the spaces is a curse put on the community by Microsoft, and it will be a big mistake to introduce this to CCP4 (my opinion). I guess there are much more important things new CCP4 GUI should deal with. If CCP4 GUI will start to go this way, file names with spaces will become file names with spaces and multilingual, in some these languages writing is going in the different direction. In my introduction to UNIX, I teach in the beginning of practical protein crystallography my first demand from student is to forget about spaces in the fie names and the life will be much easier. No fix is needed for that, concentrate on more important problems :-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.ilmailto:mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 3, 2014, at 14:47 , Eugene Krissinel eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical. -- Scanned by iCritical.
Re: [ccp4bb] baverage: no tables were found in this file
I thought the addition of ... around file names got round this problem eg This_is_Mine.pdb and That is Yours.pdb Eleanor On 3 June 2014 13:15, Eugene Krissinel eugene.krissi...@stfc.ac.uk wrote: I am afraid that it is us who will need to conform eventually :), same to say about Program Files (x86) and the overall culture in Windows, the system where some 40% () of CCP4 users have chosen to work. Eugene On 3 Jun 2014, at 13:03, Mark J van Raaij wrote: completely agree with avoiding spaces in paths and file names, but Google Drive is very handy for sharing files, so every once in a while I forget to move a file someone shares with me before running Unix programs on it and get strange errors. Depending on how awake one is at the time finding out the source can be time-consuming...Google should really remove the space! Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 13:47, Eugene Krissinel wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical. -- Scanned by iCritical.
Re: [ccp4bb] baverage: no tables were found in this file
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Eleanor, yes, it does. At least on Linux and OpenBSD (i.e. 'real' UNIX) typing # mkdir dir with spaces # cd dir\ with\ spaces/ # touch file with spaces # echo Some text file\ with\ spaces causes no problems at all. Changing code reliably to include accents, though, might be much more work than enclosing words with double quotes. Best, Tim On 06/03/2014 02:23 PM, Eleanor Dodson wrote: I thought the addition of ... around file names got round this problem eg This_is_Mine.pdb and That is Yours.pdb Eleanor On 3 June 2014 13:15, Eugene Krissinel eugene.krissi...@stfc.ac.uk wrote: I am afraid that it is us who will need to conform eventually :), same to say about Program Files (x86) and the overall culture in Windows, the system where some 40% () of CCP4 users have chosen to work. Eugene On 3 Jun 2014, at 13:03, Mark J van Raaij wrote: completely agree with avoiding spaces in paths and file names, but Google Drive is very handy for sharing files, so every once in a while I forget to move a file someone shares with me before running Unix programs on it and get strange errors. Depending on how awake one is at the time finding out the source can be time-consuming...Google should really remove the space! Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 13:47, Eugene Krissinel wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical. -- Scanned by iCritical. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTjb8eUxlJ7aRr7hoRApyPAKCGq/1XweO13d57W9vaho+DoXLHSgCeJXYW 7mc+g+F1Win65zZc8+nLN6I= =U7dS -END PGP SIGNATURE-
Re: [ccp4bb] baverage: no tables were found in this file
This may not work if a program implements its own algorithm for parsing command line parameters Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Tim Gruene t...@shelx.uni-ac.gwdg.de /divdivDate:06/03/2014 8:27 AM (GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: Re: [ccp4bb] baverage: no tables were found in this file /divdiv /div-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Eleanor, yes, it does. At least on Linux and OpenBSD (i.e. 'real' UNIX) typing # mkdir dir with spaces # cd dir\ with\ spaces/ # touch file with spaces # echo Some text file\ with\ spaces causes no problems at all. Changing code reliably to include accents, though, might be much more work than enclosing words with double quotes. Best, Tim On 06/03/2014 02:23 PM, Eleanor Dodson wrote: I thought the addition of ... around file names got round this problem eg This_is_Mine.pdb and That is Yours.pdb Eleanor On 3 June 2014 13:15, Eugene Krissinel eugene.krissi...@stfc.ac.uk wrote: I am afraid that it is us who will need to conform eventually :), same to say about Program Files (x86) and the overall culture in Windows, the system where some 40% () of CCP4 users have chosen to work. Eugene On 3 Jun 2014, at 13:03, Mark J van Raaij wrote: completely agree with avoiding spaces in paths and file names, but Google Drive is very handy for sharing files, so every once in a while I forget to move a file someone shares with me before running Unix programs on it and get strange errors. Depending on how awake one is at the time finding out the source can be time-consuming...Google should really remove the space! Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 13:47, Eugene Krissinel wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical. -- Scanned by iCritical. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTjb8eUxlJ7aRr7hoRApyPAKCGq/1XweO13d57W9vaho+DoXLHSgCeJXYW 7mc+g+F1Win65zZc8+nLN6I= =U7dS -END PGP SIGNATURE-
Re: [ccp4bb] baverage: no tables were found in this file
Would a no-space symlink resolve this? Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Mark J van Raaij mjvanra...@cnb.csic.es /divdivDate:06/03/2014 8:03 AM (GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: Re: [ccp4bb] baverage: no tables were found in this file /divdiv /divcompletely agree with avoiding spaces in paths and file names, but Google Drive is very handy for sharing files, so every once in a while I forget to move a file someone shares with me before running Unix programs on it and get strange errors. Depending on how awake one is at the time finding out the source can be time-consuming...Google should really remove the space! Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 13:47, Eugene Krissinel wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical.
Re: [ccp4bb] baverage: no tables were found in this file
Thank you guys! Fix it already! It is the problem that a space was put into my file paths. When I move the files to other place as you guys said, it works! Bing From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eugene Krissinel [eugene.krissi...@stfc.ac.uk] Sent: Tuesday, June 03, 2014 8:49 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] baverage: no tables were found in this file Positive I'd imagine -- Eugene On 3 Jun 2014, at 13:48, Ed Pozharski wrote: Would a no-space symlink resolve this? Sent on a Sprint Samsung Galaxy S® III Original message From: Mark J van Raaij Date:06/03/2014 8:03 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] baverage: no tables were found in this file completely agree with avoiding spaces in paths and file names, but Google Drive is very handy for sharing files, so every once in a while I forget to move a file someone shares with me before running Unix programs on it and get strange errors. Depending on how awake one is at the time finding out the source can be time-consuming...Google should really remove the space! Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 13:47, Eugene Krissinel wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical. -- Scanned by iCritical.
[ccp4bb] baverage: no tables were found in this file
Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing
