Re: [ccp4bb] OMIT map from Sfcheck
On 7 Apr 2008, at 21:28, Michael Giffin wrote: my model has 1600 atoms. the memory allocation for the linux (worked) and OS X (failed) binaries is the same: Sol_ Sol_ - Sol_ --- SFCHECK --- /Vers 7.2.02; 01.10.2006/ - Sol_ Memory: 30 Mb N_atom_max: 5 - Sol_ - Sol_ compiling from source or downloading the mac intel binary worked with no errors. Hi Mike, Then I guess the reason must be that some other OS X-specific issue was fixed between sfcheck versions 7.2.02 and 7.02.4; but, in any case, this message from the program's author points to the location of the latest version: Begin forwarded message: From: Alexei Vagin [EMAIL PROTECTED] Date: 4 April 2008 11:33:56 GMT+02:00 To: Jovine Luca [EMAIL PROTECTED] Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] OMIT map from Sfcheck Please try to use sfcheck binaries or source code from my home page: http://www.ysbl.york.ac.uk/~alexei/sfcheck.html Regards Alexei Hopefully updating to this will fix your problem! Good luck, Luca
Re: [ccp4bb] OMIT map from Sfcheck
my model has 1600 atoms. the memory allocation for the linux (worked) and OS X (failed) binaries is the same: Sol_ Sol_ - Sol_ --- SFCHECK --- /Vers 7.2.02; 01.10.2006/ - Sol_ Memory: 30 Mb N_atom_max: 5 - Sol_ - Sol_ compiling from source or downloading the mac intel binary worked with no errors. Thanks, Mike On Fri, Apr 4, 2008 at 1:58 AM, Jovine Luca [EMAIL PROTECTED] wrote: On 4 Apr 2008, at 01:36, Michael Giffin wrote: i get the same error on OS X 10.5.2 and 10.4.11: sfcheck -f refmac2.mtz -m refmac2.pdb -out y -nomit 2 -map the error: Open failed: Unit: 11, File: sfcheck_scr.dat (logical: sfcheck_scr.dat) BFONT COLOR=#FF!--SUMMARY_BEGIN-- Last system error message: Bad file descriptor CCP4: Open failed: File: sfcheck_scr.dat CCP4: Open failed: File: sfcheck_scr.dat the binary file sfcheck_scr.dat exists. Hi Mike, I encountered the same exact issue under OS X not long ago, and it turned out to be caused by memory/atom limitations of Fink's sfcheck (I assume that's what you are using?): Sol_ --- SFCHECK --- /Vers 7.2.02; 01.10.2006/ - Sol_ Memory: 30 Mb N_atom_max: 5 - = !!! so that using the sfcheck binary included with BALBES: Sol_ --- SFCHECK --- /Vers 7.02.4; 02.05.2007/ - Sol_ Memory: 60 Mb N_atom_max: 10 - solved the problem. How many atoms are you playing with? HTH, Luca Luca Jovine, Ph.D. Karolinska Institutet Department of Biosciences and Nutrition Hälsovägen 7, S-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290 E-mail: [EMAIL PROTECTED] W3: http://ki.se
[ccp4bb] OMIT map from Sfcheck
Dear, I'm intending to make an OMIT map using Sfcheck (ccp4i 6.0.2, Mac OS X Tiger, PPC). However, the program terminates with: has failed with error message 1525-005 1525-005 1525-005 1525-005 1525-005 1525-005 When using 'command line' from a script (with '-nomit 2 -map -origin - out y') I got: Last system error message: No such file or directory CCP4: Open failed: File: /Users/kristof/data/11mer/data2/ sfcheck_scr.dat Does anyone know this problem please..? Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
