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

[hari jayaram]

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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