[ccp4bb] CNS v1.2 and unwanted introduction of OXT

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: MTZ to Shel-X?
From: Martyn Winn m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-03-05

Next message:
Subject: Re: protease cleavage sites
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2007-03-05

Subject: CNS v1.2 and unwanted introduction of OXT
From: "Fred {- dot -} Vellieux" vellieux {- at -} IBS {- dot -} FR
Date: 2007-03-05

Dear CCP4BB,

Sorry about the non-ccp4 question, it has to do with CNS v1.2 and
(perhaps) Coot.

Also, can you avoid "hilarious" replies such as "go build a better
model" or "provide us with the data and current model, we will build and
refine and publish it for you" (no harm meant there, this is not targetted
at anyone).

Please note that I have also posted to cnsbb in order to get more replies.

Help is really needed since I do not know why I get these extra OXT atoms
introduced in the model.

Please read on further:

Date: Mon, 5 Mar 2007 13:34:54 +0100 (CET)
From: Fred. Vellieux
To: cnsbb@yahoogroups.com
Subject: CNS v1.2 and unwanted introduction of OXT

Hello all,

I am a newbie wrt Coot and CNS v1.2

I have reconstructed a model using Coot and wish to refine it (until now I
was using CNS v1.1).

The generate step gives me a PDB file that contains:

REMARK coordinates built for atom: SUB1 HIS 115 OXT
REMARK coordinates built for atom: SUB1 LEU 116 OXT
REMARK coordinates built for atom: SU11 THR 3422 OXT
REMARK coordinates built for atom: SU11 LEU 3426 OXT

Until now (with CNS v1.1 or the previous round of refinement using
v1.2) this introduction of erroneous OXT atoms never happened.

Does anyone have an idea of how to prevent it? There are certainly OXT
atoms present at the end of each chain but I do not want to have these
extra OXT atoms for refinement (they probably have unwanted effects).
In particular HIS 115 is connected to LEU 116 and this is followed by a
gap, an area where there is no density. CNS v1.2 recognises the gap.

Any help there would be most welcome. I definitely want CNS not to
introduce these 4 OXT atoms.

Fred.

--

Fred. Vellieux, esq.

=================================
IBS J.-P. Ebel CEA CNRS UJF / LBM
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: (+33) (0) 438789605
Fax: (+33) (0) 438785494
=================================

--

Fred. Vellieux, esq.

=================================
IBS J.-P. Ebel CEA CNRS UJF / LBM
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: (+33) (0) 438789605
Fax: (+33) (0) 438785494
=================================

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: MTZ to Shel-X?
From: Martyn Winn m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-03-05

Next message:
Subject: Re: protease cleavage sites
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2007-03-05