Re: [ccp4bb]: How to reverse a CA trace?

[Edward Berry <eaberry@lbl.gov>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***



Yong Xiong wrote:
> Hi all, here's a simple question. If we traced the CA in the wrong 
> direction, what is the best way to reverse the main
> chain trace with the pdb file (poly-ala) obtained in the opposite direction?
> 
Maybe not the best, but if you're using O this works-

	s-a-o bckw.pdb model ;;;;;
	 awk '$3~/CA/' bckw.pdb |sort -nrk2 >! forw.pdb
	s-a-i forw.pdb model2
	sam_ren model2 ;;;
	!merge_atoms model2 1 50 model 1 ???
	!lego_auto_MC

Awk gets only the CA's; the relative positions of the other atoms won't
be useful after reversing and can be regenerated with lego_auto commands

sort -nrk2 sorts reversely on atom number which was autogenerated by s-a-o

after reading back in, renumber residues with sam_rename

If one has gone so far as assigning sequence before discovering one's 
mistake, "merge_atoms" merges coords from mol1 and sequence from mol2 and 
puts the result in mol2 (I think- check the syntax before trying it).

Lots of luck,
Ed