[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[ccp4bb]: converting Xplor to PDB coordinate files

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

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