syntex for 'patch' card

JAMES.R.KIEFER at monsanto.com JAMES.R.KIEFER at monsanto.com
Thu Mar 25 11:25:30 EST 1999


     
        Satya,

        For whatever reason, you are not able to perform complex atom selections
        in X-PLOR during patching.  [You cannot define BOTH the segid and the 
        residue number.]  I am aware of two options for dealing with this:

        1.  Renumber each molecule in the asym unit so that each residue has a 
        unique number.  Mol1 might be resid 1-300, mol2 could be 1001-1300, etc.
        In this case, use the first syntax that you proposed, just repeat it for
        each set of disulfides to form.

        2.  Run 4 separate topology generation routines, and then read in the
        four topology files and four pdb files when you start your refinement.
        For this option to work, each molecule will need to have its own segid.
        Again, you should use your first example for syntax of the patch 
        statement.  NOTE: correct X-PLOR syntax for segid puts the id in quotes:

        (segid "mol1" and resid 2:36)

        This will be important for setting up your NCS restraints if you use 
        them.

        Good luck,

        Jim

        james.r.kiefer at monsanto.com

______________________________ Reply Separator _________________________________
Subject: syntex for 'patch' card
Author:  BIOSCI-REQUEST at net.bio.net at INTERNET
Date:    03/24/1999 7:41 PM


Dear Everybody,
               I am refining a MR model ( four molecule in the asymmetric 
unit e.g. A,B,C and D ) by X-PLOR (Version 3.851). There are two di-sulfide 
bridges in each chain.
What is the correct syntex for 'patch' card ?
     
******************************************************************************
     
 (===>)                                               (*Create S-S bridges.*)
  patch disu
    reference=1=( resid 23 )
    reference=2=( resid 55 )
  end
  patch disu
    reference=1=( resid 125 )
    reference=2=( resid 144 )
  end
*****************************************************************************
     
     
 (===>)                                               (*Create S-S bridges.*)
  patch disu
    reference=1=( segid A and resid 23 ) 
    reference=2=( segid A and resid 55 )
  end
  patch disu
    reference=1=( segid A and resid 125 ) 
    reference=2=( segid A and resid 144 )
  end
***************************************************************************
     
I am just started learning X-plor, please help me. 
Thanks in advance.
Satya
     



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