[ccp4bb] Coot-0.3

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

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CCP4bb <-- 2007 <-- April 2007 <-- 07 April 2007

Previous message:
Subject: Re: RNA 3D model
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-04-06

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Subject: effect of high salt on protein
From: bputcha bputcha {- at -} UTK {- dot -} EDU
Date: 2007-04-07

Subject: Coot-0.3
From: Paul Emsley emsley {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-07

Dear CCP4bbers,

We are pleased to announce the (slightly delayed) third anniversary
release of coot:

source: http://www.ysbl.york.ac.uk/~emsley/software/coot-0.3.tar.gz
binaries: http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/

Happy Easter.

Paul.

Release 0.3 "Basil Grande"

o Fixed crash on closing Baton Guide Points molecule [Richard
Baxter].

o Fixed crash on manipulating N-terminal backbone angles [Richard
Baxter].

o Concept of "Active Residue" added [Frank von Delft]. Added
trivial functions, (refine-active-residue),
(refine-active-residue-triple) and (autofit-rotamer-active-residue),
so that users can bind them to their own key choices.

o Use "Active Residue" concept to navigate and update "Go To Atom"
parameters [Bob Nolte].

o Skip to next NCS Chain function added [Robert Xu].

o Rationalized hydrogen usage in ligand fitting [Bob Nolte].

o Added template/graph residue matching function.

o Fixed problem of display lists and second GL context
(i.e. side-by-side stereo with density problems).

o Add a function to return all the dictionaries read [JED].

o Added function to find and produce an "interesting things GUI" for
residues with alternate conformations. This is an instance of a
more-general purpose function of any scriptable test on a residue
producing a GUI [John MacLean].

o fit-protein function now refines residues with alternate
conformations [it doesn't rotamer-search the alternate
conformations].

o set-rotate-translate-zone-rotates-about-zone-centre function added
[Martyn Symmons]. Added and Extensions GUI for this too.

o New atoms have a default B factor that can be set by the user
(using set-default-temperature-factor-for-new-atoms).

o Auto-fit rotamer with hydrogens now works better.

o Secondary Structure Restraints buttons are properly set on
generating the dialog.

o No longer try to read various SHELX keywords as atoms when trying
to read a SHELXL .res file [George Sheldrick].

o SHELX log file reader accounts for alternative conformations
[Bernhard Lohkamp].

o findligand ligand fitting gives more useful output [Ingo
Korndoerfer].

o Clear up left-over scraps in mainchain building, freeing memory
[Joel Bard].

o Fixed problem of occupancy changes being ignored [Iain Kerr].

o An unphased mtz file should run REFMAC for 0 cycles to produce
phases [Tadeusz Skarzynski].

o Fixed crash on scripting ligand fitting [Ingo Korndoerfer].

o Added a scripting function to exit coot (coot-real-exit) [Joel
Bard].

o get-symmetry function added to return a list of symops.

o Add Terminal Residue works for just one residue.

o Rigid Body Refinement of a fragment containing residues with
occupancy zero improved, hence "Place Helix Here" may be improved.

o "Same Chain?" test applied to Rotate/Translate and Rigid Body
Refine Zone atom picks [Bob Nolte].

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 07 April 2007

Previous message:
Subject: Re: RNA 3D model
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-04-06

Next message:
Subject: effect of high salt on protein
From: bputcha bputcha {- at -} UTK {- dot -} EDU
Date: 2007-04-07