[ccp4bb] FW: Refmac5: Open failed: Unit: 7, File: /tmp/refmac-nm temp1.21850 new.crd

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

Previous message:
Subject: Offtopic - In vitro protein interaction analysis using Diazirine crosslinkers.
From: Rohan Agashe rohan {- dot -} agashe {- at -} GMAIL {- dot -} COM
Date: 2009-11-04

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From: Jan Dohnalek dohnalek007 {- at -} GMAIL {- dot -} COM
Date: 2009-11-04

Subject: FW: Refmac5: Open failed: Unit: 7, File: /tmp/refmac-nm temp1.21850 new.crd
From: "Czerminski, Ryszard" Ryszard {- dot -} Czerminski {- at -} ASTRAZENECA {- dot -} COM
Date: 2009-11-04

> Hello,
>
> I am working with refmac-nm code derived from refmac5
> and I am encountering an error below
> [...]
> Open failed: Unit: 7, File: /tmp/refmac-nm_temp1.21850_new.crd (logical: /tmp/refmac-nm_temp1.21850_new.crd)
>
> Refmac_5.2.0019: Open failed: File: /tmp/refmac-nm_temp1.21850_new.crd
> [...]
>
> It is apparently very similar to bug#1004 reported on 14/01/2005 (see below) for which proposed solution was to make sure that
> there is CRYST1 line in the PDB file. In my case this line is present in the PDB file, but I am still getting this error.
>
> Any other possible reasons for this problem?
>
> Any help will be appreciated.
>
> Best regards,
> Ryszard
>
>
> Ryszard Czerminski
> AstraZeneca Pharmaceuticals LP
> 35 Gatehouse Drive
> Waltham, MA 02451
> USA
> 781-839-4304
> ryszard.czerminski@astrazeneca.com
>
> Refmac fails to open temporary file when generating new dictionary from PDB file
> Date : 14/01/2005
> CCP4 Version : 5.0.2 and earlier
> System : all
> Level : minor
> Status : workaround
> Bugzilla number : #1004
>
> Refmac may fail with an error message of the form:
>
> Open failed: Unit: 7, File: /scratch/rb84480/refmac5_temp1.36145_new.crd
> (logical: /scratch/rb84480/refmac5_temp1.36145_new.crd)
>
> Last system error message: No such file or directory
> Refmac_5.2.0005: Open failed: File: /scratch/rb84480/refmac5_temp1.36145_new.crd
>
> This can happen when the input PDB file doesn't contain cell or spacegroup information - this information is now compulsory and should be supplied on the CRYST1 line in the PDB file.
>
> To confirm whether this is the case check the Refmac output for a line of the form:
>
> ===> Warning: Input coordinate file does not have CRYST card
>
> If so then the workaround is to make sure that you add the cell and spacegroup information into the file. In future versions of Refmac the absence of this information will be a fatal error.
>
>

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CCP4bb navigation
CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Offtopic - In vitro protein interaction analysis using Diazirine crosslinkers.
From: Rohan Agashe rohan {- dot -} agashe {- at -} GMAIL {- dot -} COM
Date: 2009-11-04 Next message:
Subject: Special position refinement
From: Jan Dohnalek dohnalek007 {- at -} GMAIL {- dot -} COM
Date: 2009-11-04