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