the command line execution does not do anything while ccp4i gives the "garbage on line" error. i have copied both the log files.
Thanks
Raj
[w0054963w:~/Desktop/a] sssraj% top3d 1cs6A.pdb mL1.pdb
----------------------------------------------------------------------
TOP -- Internet version
for automatic structure comparisons
----------------------------------------------------------------------
Mol1 PDB file name: 1cs6A.pdb
Mol2 PDB file name: mL1.pdb
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
###############################################################
###############################################################
###############################################################
### CCP4 6.0: TOP version 6.0 : 06/03/06##
###############################################################
User: sssraj Run date: 25/ 8/2006 Run time: 14:38:07
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
as well as any specific reference in the program write-up.
<!--SUMMARY_END--></FONT></B>
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=
Program: TOP --- Version 6.5 (Internet) Sep 1999
Author: Guoguang Lu, Ph.D
Address: Department of Molecular Biophysics
Lund University
Box 124, 221 00, Lund, Sweden
E-mail: [EMAIL PROTECTED]
ftp: ftp://bioinfo1.mbfys.lu.se/pub/guoguang/top.tar.Z
WWW: http://bioinfo1.mbfys.lu.se/TOP
Date: Dec 1991, BMC, Uppsala, Sweden (V1,V2)
Sep 1995, Purdue Univ, USA (V3,V4)
Jul 1996, Karolinska Inst., Sweden (V5,V6)
Sep 1999, Lund University (V6.5 for g77)
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=
FORMATTED UNKNOWN file opened on unit 13
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: CHAR.CHA, Filename: CHAR.CHA
<!--SUMMARY_END--></FONT></B>
FORMATTED UNKNOWN file opened on unit 14
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: SEQ.CHA, Filename: SEQ.CHA
<!--SUMMARY_END--></FONT></B>
Automatic mode of the program:
Least matching rate for the two molecules 0.33
Least second matching rate 0.90
FORMATTED OLD file opened on unit 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: 1cs6A.pdb, Filename: 1cs6A.pdb
<!--SUMMARY_END--></FONT></B>
TITLE N-TERMINAL FRAGMENT OF AXONIN-1 FROM CHICKEN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: AXONIN-1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: IG1-4;
COMPND 5 ENGINEERED: YES
FORMATTED OLD file opened on unit 29
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: 1cs6A.pdb, Filename: 1cs6A.pdb
<!--SUMMARY_END--></FONT></B>
FORMATTED OLD file opened on unit 11
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: 1cs6A.pdb, Filename: 1cs6A.pdb
<!--SUMMARY_END--></FONT></B>
FORMATTED UNKNOWN file opened on unit 8
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: 1cs6A.sec, Filename: 1cs6A.sec
<!--SUMMARY_END--></FONT></B>
FORMATTED SCRATCH file opened on unit 12
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: TOPPTMP1, Filename: TOPPTMP1
<!--SUMMARY_END--></FONT></B>
Segmentation fault (core dumped)
[w0054963w:~/Desktop/a] sssraj%
###############################################################
###############################################################
###############################################################
### CCP4 6.0: LSQKAB version 6.0 : 06/09/05##
###############################################################
User: sssraj Run date: 25/ 8/2006 Run time: 14:36:16
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
as well as any specific reference in the program write-up.
Data line--- title [No title given]
Data line--- fit res CA to
LSQKAB: ***** GARBAGE ON LINE ****
Times: User: 0.0s System: 0.0s Elapsed: 0:00
</pre>
</html>
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<pre>
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: lsqkab XYZIN2 /Users/sssraj/Desktop/a/1cs6A.pdb XYZIN1 /Users/sssraj/Desktop/a/mL1.pdb XYZOUT /Users/sssraj/Desktop/a/1cs6A_lsq1.pdb
has failed with error message
LSQKAB: ***** GARBAGE ON LINE ****
***************************************************************************
#CCP4I TERMINATION STATUS 0 " LSQKAB: ***** GARBAGE ON LINE ****"
#CCP4I TERMINATION TIME 25 Aug 2006 14:36:16
#CCP4I MESSAGE Task failed
"Stein, ND (Norman)" <[EMAIL PROTECTED]> wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
The "garbage on line" error message originates from the LSQKAB program rather than TOPP. (The superpose molecules task in ccp4i calls LSQKAB as well as TOPP.) If you can send me your log file and input files, I will investigate.
The basic TOPP program used by ccp4i should work on both Windows and Unix based systems. The top3d and topsearch scripts mentioned in the TOPP documentation only work on unix based systems.
Norman Stein
CCP4
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