On Friday, March 22, 2013 02:57:07 pm Tim Gruene wrote:
> Salut Xavier,
>
> (i) you have to give the explicit residue range when changing the chain
> ID. The 'whole chain' does not work.
> (ii) Renumber the downstream end by adding one, and add the residue
> (iii) Under Edit->Preferences->Others->Fonts you can choose "Larger"
> (iv) I don't know
(iv) Click on the delete icon in the toold bar,
then click on one atom of the alternate conformer you want to get rid of.
>
> Best,
> Tim
>
> On 03/22/2013 04:16 PM, "F.Xavier Gomis-RĂ¼th" wrote:
> > Dear Paul & The Cooters,
> > some questions:
> > (i) Is it possible to tell the program in a rather straightforward manner to
> > connect two chains within a model
> > that have different chain identifiers? This is very useful when rebuilding
> > models created by automatic tracing
> > programs. I also found that manual renaming of a chain to match another letter
> > doesn't work if this letter is already
> > taken by another chain.
> > (ii) If I understood it correctly, the program only adds residues to termini.
> > How do I "insert" a residue between two
> > residues of a chain with correlative numbering?
> > (iii) Can I put larger larger labels and numbers? Specially when working in
> > Zalman stereo mode, the numbers are really small...
> > (iv) How do I remove alternate conformations without deleting the residue and
> > inserting a new one manually?
> > Thanks a lot in advance,
> > Xavier
> >
> >
> > On 8/3/13 3:20 PM, Paul Emsley wrote:
> >> On 07/03/13 12:27, Dave wrote:
> >>> Hi -
> >>>
> >>> I'm working on a mammalian derived crystal. In a few chains where I can see
> >>> the N-terminus, it appears that they are acetylated. I looked for previous
> >>> discussion on how to deal with this, and I was wondering how exactly to deal
> >>> with this in coot as of 2013.
> >>>
> >>> Thus far, I added an ala to the n-terminus, then used
> >>> extensions>modelling>replace residue
> >>> to mutate to ACE
> >>
> >> That sounds fine.
> >>>
> >>> I'm running coot 0.7 stable release sept 2012.
> >>>
> >>> I'm not seeing a bond between the original N-term N atom and the C of he
> >>> acetyl group
> >>
> >> Coot won't link het groups that are non-polymers. Maybe there should be an
> >> exception for ACE.
> >>
> >>>
> >>> Real Space Refine Zone and Regularize Zone do not like the setup.
> >>
> >> quite right.
> >>
> >>> I'm sure I need to define some things, but haven't dealt with this before, as
> >>> for things like this, I used to switch to xfit.
> >>
> >> :-(
> >>
> >> I suspect that you need to not tell coot that ACE is a non-polymer - you can
> >> do that by either copying and hand-editing the cif file or using Edit ->
> >> Restraints -> ACE -> then change "non-polymer" to "L-peptide", Apply.
> >>
> >> Then I would do a sphere refine.
> >>
> >>>
> >>> Would it be better to ask at CCP4?
> >>>
> >>
> >> :-(
> >>
> >>
> >> Paul.
> >>
> >
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
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