PDB Deposition Question
Hi all - I refined a structure using Phenix 1.4-3 and now I need to submit it to the PDB. When I try to run sfcheck on the .mtz that Phenix generated, sfcheck can't read the file. I also tried to convert the .mtz to .cns using phenix.reflection_file_converter. This time, sfcheck could "not find IOBS or FOBS in your file". Any advice would be greatly appreciated. -Alex
Hi Alex, it is strange... How you obtained the MTZ file? Can you send the output of this command: phenix.mtz.dump data.mtz ? Are you sure you use the MTZ file with the data and not the one containing map coefficients? Pavel.
Hi all - I refined a structure using Phenix 1.4-3 and now I need to submit it to the PDB. When I try to run sfcheck on the .mtz that Phenix generated, sfcheck can't read the file. I also tried to convert the .mtz to .cns using phenix.reflection_file_converter. This time, sfcheck could "not find IOBS or FOBS in your file". Any advice would be greatly appreciated.
Are you using the maps mtz file or the mtz with all data? ________________________________________ From: Pavel Afonine [[email protected]] Sent: Monday, May 24, 2010 11:11 PM To: PHENIX user mailing list Subject: Re: [phenixbb] PDB Deposition Question Hi Alex, it is strange... How you obtained the MTZ file? Can you send the output of this command: phenix.mtz.dump data.mtz ? Are you sure you use the MTZ file with the data and not the one containing map coefficients? Pavel.
Hi all - I refined a structure using Phenix 1.4-3 and now I need to submit it to the PDB. When I try to run sfcheck on the .mtz that Phenix generated, sfcheck can't read the file. I also tried to convert the .mtz to .cns using phenix.reflection_file_converter. This time, sfcheck could "not find IOBS or FOBS in your file". Any advice would be greatly appreciated.
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Thanks for all the replies - it turns out I was using the .mtz file
with the map coefficients. Things are going smoothly now!
On Mon, May 24, 2010 at 8:16 PM, Mayer, Mark (NIH/NICHD) [E]
Are you using the maps mtz file or the mtz with all data? ________________________________________ From: Pavel Afonine [[email protected]] Sent: Monday, May 24, 2010 11:11 PM To: PHENIX user mailing list Subject: Re: [phenixbb] PDB Deposition Question
Hi Alex,
it is strange... How you obtained the MTZ file? Can you send the output of this command:
phenix.mtz.dump data.mtz
?
Are you sure you use the MTZ file with the data and not the one containing map coefficients?
Pavel.
Hi all - I refined a structure using Phenix 1.4-3 and now I need to submit it to the PDB. When I try to run sfcheck on the .mtz that Phenix generated, sfcheck can't read the file. I also tried to convert the .mtz to .cns using phenix.reflection_file_converter. This time, sfcheck could "not find IOBS or FOBS in your file". Any advice would be greatly appreciated.
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
From the validation server upload page: Running the ADIT Validation Server Please note that SFCHECK can only be run on structure factor files in mmCIF format. Alexander Hirschi wrote:
Hi all - I refined a structure using Phenix 1.4-3 and now I need to submit it to the PDB. When I try to run sfcheck on the .mtz that Phenix generated, sfcheck can't read the file. I also tried to convert the .mtz to .cns using phenix.reflection_file_converter. This time, sfcheck could "not find IOBS or FOBS in your file". Any advice would be greatly appreciated.
-Alex _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (4)
-
Alexander Hirschi -
Edward A. Berry -
Mayer, Mark (NIH/NICHD) [E] -
Pavel Afonine