[ccp4bb] trim back to Cbeta in coot : summary

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CCP4bb <-- 2008 <-- March 2008 <-- 14 March 2008

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Subject: trim back to Cbeta in coot : summary
From: byron delabarre byron {- dot -} ccp4 {- at -} GMAIL {- dot -} COM
Date: 2008-03-14

Hi ccp4'ers:

Thanks for the quick response on the coot side chain trimming issue.

---
I received an email from Patricia Legler to try Chainsaw (a ccp4 program I'm
not familiar with) and clustal to trim sidechains.
----

Paul Emsley tweaked my scheme script which I retweak and present here .
Paul's script didn't work with my version of coot ((I'm using coot
prerelease 0.4), the one I present below takes advantage of the
delete-sidechain-range function to trim back either a single (give start and
finish residue as the same) or range of residues to Cbeta.

Best -

Byron

Coot "trim back sidechain" scheme code:
-----
;; Delete (back to the CB stub) the side change in the range
;; resno-start to resno-end
;;
(define trim-sidechain-range
(lambda (imol chain-id resno-start resno-end)
(delete-sidechain-range imol chain-id resno-start resno-end)))

(let ((menu (coot-menubar-menu "Extensions")))

(add-simple-coot-menu-menuitem
menu "Trim back sidechains"
(lambda ()

(generic-chooser-and-entry
"Choose a molecule to have its sidechains chopped"
"Chain ID: ""A"
(lambda (imol chain-id)
(generic-double-entry "Starting Resno"
"End Resno"
"" "" #f #f " Chop Sidechains "
(lambda (text-1 text-2 dummy)
(let ((resno-1 (string->number text-1))
(resno-2 (string->number text-2)))
(if (and (number? resno-1)
(number? resno-2))
(trim-sidechain-range imol chain-id
resno-1 resno-2))))))))))
-----

--
Byron DeLaBarre, Ph.D.
Structural Biology Group
Millennium Pharmaceuticals
Cambridge, MA

"In Reciprocal Space, I'm a Somebody"

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CCP4bb <-- 2008 <-- March 2008 <-- 14 March 2008

Previous message:
Subject: Announcement: EMBO Practical course on X-ray crystal structure determination
From: Rob Meijers ccp4spamalot {- at -} YAHOO {- dot -} COM
Date: 2008-03-14

Next message:
Subject: Re: Color of heme containing Xtals
From: Dominique BOURGEOIS dominique {- dot -} bourgeois {- at -} IBS {- dot -} FR
Date: 2008-03-14