Re: [ccp4bb] OMIT map from Sfcheck

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From: Remy Loris reloris {- at -} VUB {- dot -} AC {- dot -} BE
Date: 2008-04-04

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From: "Navraj S {- dot -} Pannu" raj {- at -} CHEM {- dot -} LEIDENUNIV {- dot -} NL
Date: 2008-04-04

Subject: Re: OMIT map from Sfcheck
From: Alexei Vagin alexei {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-04-04

Please try to use sfcheck binaries or source code from my home page:

http://www.ysbl.york.ac.uk/~alexei/sfcheck.html

Regards
Alexei

On 4 Apr 2008, at 09:58, 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
> ------------------------------------------------
>
>

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CCP4bb <-- 2008 <-- April 2008 <-- 04 April 2008

Previous message:
Subject: Opening for a X-ray facility/computing manager
From: Remy Loris reloris {- at -} VUB {- dot -} AC {- dot -} BE
Date: 2008-04-04 Next message:
Subject: Post doctoral postion in computational methods development, Leiden, NL
From: "Navraj S {- dot -} Pannu" raj {- at -} CHEM {- dot -} LEIDENUNIV {- dot -} NL
Date: 2008-04-04