[ccp4bb] New validation program...

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CCP4bb <-- 2007 <-- September 2007 <-- 03 September 2007

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From: Adnane Achour Adnane {- dot -} Achour {- at -} KI {- dot -} SE
Date: 2007-09-03

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Subject: Shelx install in ccp4iv6.0.2
From: Xue-Yuan Pei xyp20 {- at -} MOLE {- dot -} BIO {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-09-03

Subject: New validation program...
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-03

Hi!

I've just written a new validation program which validates the sequence
of a coordinate model to detect register errors caused by extra or
missing residues in the chain trace.

This was inspired by a recent message from the Richardsons, about
something similar in molprobity (I think, I can't find it any more). I
realised I already had all the code to do this in buccaneer. However,
the approach to sequencing implemented in buccaneer is sufficiently
different to anything used elsewhere that it should provide an
independent check.

It may be run with phases from experimental phasing, or it can calculate
its own phases using a side-chain-omit process. In this case it can be
used after molecular replacement, or to validate structures in the PDB.

The software includes a GUI and auto-installer script, and is available
for Linux/x86, Mac/x86 and Mac/ppc. You can download it from here:
http://www.ysbl.york.ac.uk/~cowtan/sequins/sequins.html
The installer will create a new task in the 'Validation and Depostition'
menu, labelled 'Sequence validation'.

I've attached a screenshot of the GUI. Below is sample output, showing a
case in which there is a 30 residue register shift in the model. Note
the '+' and '-' in the modified sequence, and the warning message below.

###############################################################
###############################################################
###############################################################
### CCP4 6.0: csequins version 0.0.1 : 29/08/07##
###############################################################
User: cowtan Run date: 3/ 9/2007 Run time: 11:44:05

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.

Copyright 2007 Kevin Cowtan and University of York. All rights reserved.

Please reference:
Cowtan K. (2006) Acta Cryst. D62, 1002-1011.

pdbin-ref /home/cowtan/test/reference-1tqw.pdb
mtzin-ref /home/cowtan/test/reference-1tqw.mtz
colin-ref-fo /*/*/[FP.F_sigF.F,FP.F_sigF.sigF]
colin-ref-hl /*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D]
mtzin-wrk modified.mtz
colin-wrk-fo /*/*/[FP,SIGFP]
pdbin-wrk modified.pdb
correlation-mode

------------------------------------------------------------------------

CHAIN: A
Original:
MKTRADLFAFFDAHGVDHKTLDHPPVFRVEEGLEIKAAMPGGHTKNLFLKAKGQLWLISALGETTIDLKKLHHVIGSGRLASFGPQEMMLETLGVTPGSVTAFGLINDTEKRVRFVLDKALADSDPVNFHPLKNDATTAVSQAGLRRFLAALGVEPMIVDFAAMEVVG
Modified:
??TRADLFAFFDAHGVDHKTLDHPPVFRVEEGLEIKAAMPGGHTKNLFLK+AKGQLWLISALGETTIDLKKLHHVIGSGRLASFGP-MMLETLGVTPGSVTAFGLINDTEKRVRFVLDKALADSDPVNFHPLKNDATTAVSQAGLRRFLAALGVEPMIVDFAAMEVV?
Confidence: 0.999992

WARNING: The supplied data suggests a partial sequence register error.

------------------------------------------------------------------------

Times: User: 36.9s System: 0.1s Elapsed: 0:38

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CCP4bb <-- 2007 <-- September 2007 <-- 03 September 2007

Next message:
Subject: Shelx install in ccp4iv6.0.2
From: Xue-Yuan Pei xyp20 {- at -} MOLE {- dot -} BIO {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-09-03