[sharp-discuss] Problem with pir file in new version

Clemens Vonrhein vonrhein at globalphasing.com
Wed Dec 14 21:13:07 GMT 2005


Dear Hari,

could you resend the pir file (so that everything is preserved
... even control characters etc). One thing you could do: create the
file new and cut and paste the sequence again ... maybe there is a
funny character lurking around somewhere.

Are you running the new SHARP/autoSHARP on the exactly same machine as
before (any recent upgrades)? Is it the exactly same PIR file? Is it
sitting on exactly the same disk (local, SAMBA, NFS)?

We don't have problems with reading PIR files - so I guess something
must have changed on your side.

Cheers

Clemens

On Wed, Dec 14, 2005 at 03:52:31PM -0500, hari jayaram wrote:
> Hello,
> We are trying to use a pir file for lysozyme that worked real well with
> autosharp with the old version of Sharp/autosharp/sushi. Somehow the new
> version complains about the pir file
> 
> The error log is attached below , but the offending line is
> 
> ERROR   : second line of sequence file wrong: the second line of your
> sequence
>            file /home/oprian/lysozyme/14_autoSHARP/autoSHARP.0/cmsharp.pir
> should
>            be empty - please check the format description in the
> documentation,
>            correct this and re-start
> 
> The pir file is pretty ok and considering it worked just great for the
> autosharp with build in the old version . I am wondering why this error has
> cropped up
> Both the pir and error log are attached below.
> Any help troubleshooting this error will be greatly appreciated.
> Thanks
> Hari Jayaram
> Brandeis University
> 
> #############
> cmsharp.pir
> #############
> >1VDS:A LYSOZYME C
> 
> KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
> RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
> QAWIRGCRL*
> 
> ##############################
> logfile
> ##############################
> Checking supplied information
> (start: Wed Dec 14 15:35:51 EST 2005)
> 
>  Copyright (C) 1999-2003 Clemens Vonrhein and the
>                          Buster Development Group.
> 
>                All rights reserved.
> 
>     Use of this program implies acceptance of conditions
>     given in the SHARP licence agreement.
> 
>     (please reload this document from time to time!)
> 
>   Title : autoSHARP run
> 
> 1. General
> (explanation)
> 
>  NOTE    : The Speed/Accuracy rate is set to 5 (where "1" is pure speed and
> "5"
>            is pure accuracy)
> 
>  ERROR   : second line of sequence file wrong: the second line of your
> sequence
>            file /home/oprian/lysozyme/14_autoSHARP/autoSHARP.0/cmsharp.pir
> should
>            be empty - please check the format description in the
> documentation,
>            correct this and re-start
> 
> 
> 
>  NOTE    : sequence file contains a single monomer - leaving it to autoSHARP
> to
>            determine the most likely number of molecules later
> 
> 
> 
>  NOTE    : molecular weight from sequence file = 14295.2
> 
> 
> 
>  NOTE    : no of amino acid residues from sequence file = 129
> 
> 
> 
>  NOTE    : apparently you are using CCP4 [1] version 5.0.2 -
>            the supported CCP4 versions are: 4.2.2 5.0.2 (with the latest
> patches
>            applied from the official CCP4 problems page)
> 
> 2. Checking each dataset
> (explanation)
>    2.1 native dataset (w1)
> 
>       2.1.1 general
> 
> 
>  NOTE    : everything ok
> 
>    2.2 derivative 1 (w2)
> 
>       2.2.1 general
> 
>       2.2.2 Wavelength analysis for heavy atom Gd (see also [2])
> 
>  NOTE    : f'/f" edges for element Gd are
> 
>             lambda     f'       f"
>            --------------------------
>             1.480 -10.0463  12.9409
>             1.562 -12.6408  12.2762
>             1.710 -18.0106  10.5868
> 
> 
> 
>  NOTE    : f'/f" edges for element Gd close to 1.5418 Å are
> 
>             lambda     f'       f"
>            --------------------------
>             1.563 -16.9391  12.2938
> 
> 
> 
>  NOTE    : calculated wavelengths closest to given f'/f" values of ( -9.2420
> ,
>            11.9460) are
> 
>              ~ 1.48120 Å (based on f')
>              ~ 1.40420 Å (based on f")
>              ~ 1.47620 Å (based on f' and f")
> 
>              ~ 1.47870 Å (most likely) - you specified    1.5418 Å
> 
> 
>       2.2.3 Scattering factor analysis for heavy atom Gd
> 
> 
>  NOTE    : everything ok
> 
> 3. Summary
> (explanation)
> 
>  NOTE    : The following files will be used (from your datafiles directory):
> 
>            -rw-rw-r--    1 oprian   oprian    1546912 Dec  6 14:34
> lyso_all_merged_and_scaled_scaleit1.mtz
>            -rw-rw-r--    1 oprian   oprian        164 Dec 14 15:32
> cmsharp.pir
> 
> 
> 
>  NOTE    : A total of 1 errors were found: you will have to correct these
>            before you can run this job.
> 
> 
> 
>  NOTE    : Since there were errors in the input we will NOT start the
>            job!
> 
> 4. References
> [1]    Collaborative Computational Project, Number 4 (1994). The CCP4 Suite:
> Programs for Protein Crystallography. Acta Cryst. D50. 760-763.
> [2]    Merritt, E. A. X-ray Absorption Edges
> 
> 
>        directory listing
> 
> (stop: Wed Dec 14 15:36:08 EST 2005)
> Buster Development Group

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> sharp-discuss at globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss


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* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
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*  Cambridge CB3 0AX, UK
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