Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

Re: [ccp4bb] OMIT map from Sfcheck
 

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2008 <-- April 2008 <-- 04 April 2008
Previous message:
Subject: Re: fixing position in the refinement: Shelx, refmac5
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-04-04 		Next message:
Subject: Opening for a X-ray facility/computing manager
From: Remy Loris reloris {- at -} VUB {- dot -} AC {- dot -} BE
Date: 2008-04-04


Subject: Re: OMIT map from Sfcheck
From: Jovine Luca luca {- dot -} jovine {- at -} KI {- dot -} SE
Date: 2008-04-04
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)
>
> 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: 50000 - <= !!!

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: 100000 -

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: luca.jovine@ki.se
W3: http://ki.se
------------------------------------------------
ProteinCrystallography.org: Copyright 2006-2008 by Quid United Ltd