[ccp4bb] Missing space group in ?.mtz file
Dear colleagues, I have a ?.mtz file from integration with missing info about the space group in the SYMINFO. I tried to modify the file with combat and mtzutils, but it always ends up in reading the original file with this message: Failed to find spacegroup in SYMINFO! MTZUTILS: Fatal error in ccp4spg_register_by_symops MTZUTILS: Fatal error in ccp4spg_register_by_symops Here is report from mtzdump: Failed to find spacegroup in SYMINFO! MTZDUMP: Fatal error in ccp4spg_register_by_symops I know the correct space group, but I do not know how to supply the .mtz file. Any suggestion, please? Thanks for all of them. Best Regards, Petr Petr Kolenko [EMAIL PROTECTED]
Re: [ccp4bb] Missing space group in ?.mtz file
When all else fails you can dump the file as an ASCII format using mtztona4, edit that file to correct the spacegroup and reconvert it to mtz using na4tomtz. Eleanor Petr Kolenko wrote: Dear colleagues, I have a ?.mtz file from integration with missing info about the space group in the SYMINFO. I tried to modify the file with combat and mtzutils, but it always ends up in reading the original file with this message: Failed to find spacegroup in SYMINFO! MTZUTILS: Fatal error in ccp4spg_register_by_symops MTZUTILS: Fatal error in ccp4spg_register_by_symops Here is report from mtzdump: Failed to find spacegroup in SYMINFO! MTZDUMP: Fatal error in ccp4spg_register_by_symops I know the correct space group, but I do not know how to supply the .mtz file. Any suggestion, please? Thanks for all of them. Best Regards, Petr Petr Kolenko [EMAIL PROTECTED]
Re: [ccp4bb] Missing space group in ?.mtz file
Unfortunately, it also failed: Failed to find spacegroup in SYMINFO! MTZTONA4: Fatal error in ccp4spg_register_by_symops Does anybody know how to fix it? Petr
Re: [ccp4bb] Missing space group in ?.mtz file
what happens if you type: env | grep SYMINFO Does it show the path? Either Solve or CCP4? On Tue, Jul 8, 2008 at 10:15 AM, Petr Kolenko [EMAIL PROTECTED] wrote: Unfortunately, it also failed: Failed to find spacegroup in SYMINFO! MTZTONA4: Fatal error in ccp4spg_register_by_symops Does anybody know how to fix it? Petr -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] Missing space group in ?.mtz file
Dobre den, If all else fails, use a text editor! I use emacs for this ... Most of the file will look like garbage, but the header at the end of the file can be edited. Be very very careful not to change the number of characters just do replacements. Send the file to me if you want (and tell me the correct space group!). Of course, the standard reply is I wouldn't start from here Martyn On Tue, 2008-07-08 at 11:15 +0200, Petr Kolenko wrote: Unfortunately, it also failed: Failed to find spacegroup in SYMINFO! MTZTONA4: Fatal error in ccp4spg_register_by_symops Does anybody know how to fix it? Petr -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] Missing space group in ?.mtz file
env | grep SYMINFO shows nothing. But there was a Logical Name: SYMINFO Filename: /protein/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib line in logfile of all runs. Is it what you mean? Petr Partha Chakrabarti wrote: what happens if you type: env | grep SYMINFO Does it show the path? Either Solve or CCP4? On Tue, Jul 8, 2008 at 10:15 AM, Petr Kolenko [EMAIL PROTECTED] wrote: Unfortunately, it also failed: Failed to find spacegroup in SYMINFO! MTZTONA4: Fatal error in ccp4spg_register_by_symops Does anybody know how to fix it? Petr
Re: [ccp4bb] Missing space group in ?.mtz file
Dear Petr In your $CCP4/src/dev_tools_ directory there is a small utility named readmtz.cpp which I created for use in a situation like this. You will need to compile it by typing g++ -o readmtz readmtz.cpp Then type ./readmtz filename.mtz The data will be written out as an ascii file called output.txt. You can read this back in using the CCP4 program F2MTZ, which allows you to supply the spacegroup. Norman Norman Stein CCP4 Daresbury Laboratory -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Petr Kolenko Sent: 08 July 2008 09:54 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Missing space group in ?.mtz file Dear colleagues, I have a ?.mtz file from integration with missing info about the space group in the SYMINFO. I tried to modify the file with combat and mtzutils, but it always ends up in reading the original file with this message: Failed to find spacegroup in SYMINFO! MTZUTILS: Fatal error in ccp4spg_register_by_symops MTZUTILS: Fatal error in ccp4spg_register_by_symops Here is report from mtzdump: Failed to find spacegroup in SYMINFO! MTZDUMP: Fatal error in ccp4spg_register_by_symops I know the correct space group, but I do not know how to supply the .mtz file. Any suggestion, please? Thanks for all of them. Best Regards, Petr Petr Kolenko [EMAIL PROTECTED]
Re: [ccp4bb] Missing space group in ?.mtz file
Dear colleagues, manual editing suggested by Martyn Winn worked and I can process the data further now. I was not able to process the file with readmtz, most probably because of my low experience with this. Thanks to all of you, for discussion and goodwill to help me. Best Regards, Petr Petr Kolenko [EMAIL PROTECTED] Martyn Winn wrote: Dobre den, If all else fails, use a text editor! I use emacs for this ... Most of the file will look like garbage, but the header at the end of the file can be edited. Be very very careful not to change the number of characters just do replacements. Send the file to me if you want (and tell me the correct space group!). Of course, the standard reply is I wouldn't start from here Martyn On Tue, 2008-07-08 at 11:15 +0200, Petr Kolenko wrote: Unfortunately, it also failed: Failed to find spacegroup in SYMINFO! MTZTONA4: Fatal error in ccp4spg_register_by_symops Does anybody know how to fix it? Petr
