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[ccp4bb]: converting Xplor to PDB coordinate files
- Subject: [ccp4bb]: converting Xplor to PDB coordinate files
- From: Edward Berry <eaberry@lbl.gov>
- Date: Thu, 10 Feb 2000 14:57:04 -0800
- CC: ccp4 <ccp4bb@dl.ac.uk>
- Organization: Lawrence Berkeley National Laboratory
- References: <37FE68FA.FAB7A246@lnls.br>
- Sender: owner-ccp4bb@dl.ac.uk
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Is it the case that PDBSET keyword ELEMENT no longer works after v 3.3?
If so, how do people convert Xplor/CNSv0.1 files to standard
pdb format for sfall? My irons are all changing to flourines!
(OK, it wouldn't kill me to edit manually, but automation is nice)
Ed
Test program:
==============================================================================
cat >! xplor.pdb << eof
ATOM 15780 FE HEM 1 23.137 134.086 77.947 1.00 38.60 KKKK
ATOM 15823 FE HEM 2 21.814 113.455 76.862 1.00 30.84 KKKK
ATOM 15866 FE HEM 3 4.083 160.313 66.059 1.00 45.47 KKKK
ATOM 15909 FE1 FES 4 51.605 169.442 89.490 0.60150.00 KKKK
ATOM 15910 FE2 FES 4 51.424 168.079 91.793 0.60150.00 KKKK
ATOM 15911 S1 FES 4 53.286 168.745 90.770 0.60148.20 KKKK
ATOM 15912 S2 FES 4 49.815 169.251 90.802 0.60150.00 KKKK
eof
pdbset xyzin xplor.pdb xyzout brk.pdb << eof-1
ELEMENT FE
eof-1
cat brk.pdb
output (correct) with pdbset from ccp4 version 3.3:
===============================================================================
1##########################################################
##########################################################
##########################################################
### CCP PROGRAM SUITE: PDBSET VERSION 3.3: 11/03/97##
##########################################################
User: berry Run date: 2/10/ 0 Run time:13:06:39
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.
FORMATTED OLD file opened on unit 1
Logical name: XYZIN, Full name: xplor.pdb
FORMATTED UNKNOWN file opened on unit 2
Logical name: XYZOUT, Full name: brk.pdb
Data line--- ELEMENT FE
Hydrogen atoms will be kept
Left-justify atoms of element FE
7 atoms copied
Coordinate limits in output file:
Minimum Maximum Centre Range
On X : 4.08 53.29 28.68 49.20
On Y : 113.46 169.44 141.45 55.99
On Z : 66.06 91.79 78.93 25.73
PDBSET: === Normal completion PDBSET ===
Times: User: 0.1s System: 0.0s Elapsed: 0:00
sb5 84% cat brk.pdb
ATOM 1 FE HEM 1 23.137 134.086 77.947 1.00 38.60
ATOM 2 FE HEM 2 21.814 113.455 76.862 1.00 30.84
ATOM 3 FE HEM 3 4.083 160.313 66.059 1.00 45.47
ATOM 4 FE1 FES 4 51.605 169.442 89.490 0.60150.00
ATOM 5 FE2 FES 4 51.424 168.079 91.793 0.60150.00
ATOM 6 S1 FES 4 53.286 168.745 90.770 0.60148.20
ATOM 7 S2 FES 4 49.815 169.251 90.802 0.60150.00
===============================================================================
output with pdbset from ccp4 version 4.0 (or 3.5):
1##########################################################
##########################################################
##########################################################
### CCP PROGRAM SUITE: PDBSET VERSION 4.0: 09/12/99##
##########################################################
User: berry Run date: 2/10/00 Run time:13:01:52
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>
FORMATTED OLD file opened on unit 7
Logical name: XYZIN, Full name: xplor.pdb
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
$TEXT:Warning: $$ comment $$
WARNING: NO CRYST CARDS READ FROM XYZIN
$$
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
$TEXT:Warning: $$ comment $$
WARNING: NO SCALE CARDS READ FROM XYZIN
$$
<!--SUMMARY_END--></FONT></B>
FORMATTED UNKNOWN file opened on unit 8
Logical name: XYZOUT, Full name: brk.pdb
Data line--- ELEMENT FE
Hydrogen atoms will be kept
Left-justify atoms of element FE
7 atoms copied
Coordinate limits in output file:
Minimum Maximum Centre Range
On X : 4.08 53.29 28.68 49.20
On Y : 113.46 169.44 141.45 55.99
On Z : 66.06 91.79 78.93 25.73
Number of chains in input file = 1
Original chain IDs: KKKK
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
PDBSET: === Normal completion PDBSET ===
Times: User: 0.1s System: 0.0s Elapsed: 0:00
</pre>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
</html>
<!--SUMMARY_END--></FONT></B>
sb5 82%
sb5 82% cat brk.pdb
ATOM 15780 FE HEM K 1 23.137 134.086 77.947 1.00 38.60 KKKK F
ATOM 15823 FE HEM K 2 21.814 113.455 76.862 1.00 30.84 KKKK F
ATOM 15866 FE HEM K 3 4.083 160.313 66.059 1.00 45.47 KKKK F
ATOM 15909 FE1 FES K 4 51.605 169.442 89.490 0.60150.00 KKKK F
ATOM 15910 FE2 FES K 4 51.424 168.079 91.793 0.60150.00 KKKK F
ATOM 15911 S1 FES K 4 53.286 168.745 90.770 0.60148.20 KKKK S
ATOM 15912 S2 FES K 4 49.815 169.251 90.802 0.60150.00 KKKK S
END