Re: [ccp4bb] OMIT map from Sfcheck

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Help with Superpose results
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-04-07

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Date: 2008-04-07

Subject: Re: OMIT map from Sfcheck
From: Michael Giffin mijogiffin {- at -} GMAIL {- dot -} COM
Date: 2008-04-07

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: 50000 -
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 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)
> >
> > 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
> ------------------------------------------------
>

CCP4bb navigation
CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: Help with Superpose results
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-04-07 Next message:
Subject: Crystallization and cryo with Li at high concentration!
From: Lijun Liu liulj {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-04-07