All - can anyone help me with the syntax of the 'mutate_by_overlap'
scripting command. I need to mutate a CYS to a chemically-modified entity
that I've called CYD. I made a Refmac dictionary entry for this which I
read in it's accepted. I'm using WinCoot so I understand I must use
Python
Hi, is there an easy way to turn off the display of the negative contour
level for a difference map after it has been read in?
I found a function 'set_map_is_difference_map()' to effectively turn on the
negative level, but I couldn't see one to turn it off, maybe something like
Quick question: is there an environment variable in WinCoot which
points to the directory where 'Extensions-Modelling-Monomer from
dictionary' gets its files? This is the '%COOT_PREFIX%/examples'
directory by default. I couldn't see anything relevant in the
documentation (e.g. section 1.5
will try to fix it for next version - 5.7 series.
Garib
On 30 Nov 2011, at 16:08, Ian Tickle wrote:
Note that the _chem_comp and _chem_comp_tor blocks are formatted the
same way if there's only one compound/torsion resp. e.g.:
_chem_comp.id XXX
On 17 January 2012 12:43, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote:
On 17/01/12 08:33, Dayana Nisbar wrote:
How to change the map level from rmsd to sigma?
You can't. Electron density levels should not be expressed in terms of
sigma. Sigma refers to probability distributions - and an
On 24 January 2012 17:53, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote:
Now that Coot uses the restraints dictionary to render ligands it has become
apparent that the method of doing so is problematic for typical working
situations.
Say for example your read in
complex-XYZ00123456.pdb in
I just spotted one minor infelicity: when it starts it pops up a
window Fix Nomenclature Errors (which is very nice). However if I
close this it still remains visible but inactive. The same thing
happens if I open other dialogs, so eventually I can cover the screen
with inactive dialogs!
this is
experimental phasing so we don't (at this stage) have any coordinates beyond
the substructure. Including the shelxe chain tracing is on the cards, but
this takes a little while and we're trying to pack a lot into a short time.
Many thanks,
Graeme
-Original Message-
From: Ian
Hi Graeme
This has nothing to do with Randy's 1986 paper on minimally-biased map
coefficients from partial structures (which I assume is the one you're
referring to) since as you said yourself these are experimental, not
partial structure, phases. Rather, this is Blow Crick's (1959)
result
Paul, I'm having trouble accessing the md5sums on
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/ ,
though the tar.gzs themselves seem to be OK. I get source file could not
be read. on all of them. Could you check it out?
Cheers
-- Ian
On 10 December 2013 11:47, Paul
On 27 March 2015 at 19:16, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote:
There might be a python version of these available from the Molprobity
server. It should be straightforward for them to make it if not.
OK after some digging in the MP distribution (i.e. find/xargs/grep) I found
that if
Hello All
I'm trying to read the script from multichart into WinCoot. I do:
multichart-coot reduce.pdb reduce.scm
but when I select Calculate - Run Script absolutely nothing happens,
there's no error message on the console, nothing.
I'm assuming this is because WinCoot doesn't recognise
-centered. If I forget to do that it's very easy to miss bumps (and I
don't have a great deal of faith in MP's concept of what constitutes a
bump)!
Cheers
-- Ian
On 30 June 2015 at 14:33, Ian Tickle ianj...@gmail.com wrote:
Hello All
I guess this is really a question about MolProbity
no program from
integration to structure solution did not recognised. It appeared in
structure refinement in wrong bond distances.
Worth of checking.
Jan
On 07/01/2015 10:58 AM, Ian Tickle wrote:
Paul, as an aside to this, would it be possible to have it so that if the
relevant boxes
Hello All
I guess this is really a question about MolProbity (and possibly about
autoBuster) but I assume that most Coot users will be using the MolProbity
validation tools.
I am in the process of depositing 4 structures of the same protein
(different ligands) and I noticed that MP seems to be
Thanks Paul, (and for the swift response!).
-- Ian
On 24 May 2015 at 17:16, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote:
On 24/05/2015 16:57, Ian Tickle wrote:
Hello, does anyone know how to simultaneously display negative positive
contours for a neutron 2Fo-Fc map?
For example
Hello, does anyone know how to simultaneously display negative positive
contours for a neutron 2Fo-Fc map?
For example, as in Fig. 2 here:
Correction: maps are produced by Refmac & FFT. Original references are:
Read, R.J.: Acta Cryst. A42 (1986) 140-149 for map coefficients, and type
'FFT' in Wikipedia for FFT algorithm & references.
Cheers
-- Ian
On 19 April 2018 at 13:57, Ian Tickle <ianj...@gmail.com> wrote:
Fast Fourier Transform Algorithm*
<https://carma.newcastle.edu.au/jon/Preprints/Talks/CARMA-CE/FFT.pdf> (PDF).
*Mikrochimica Acta*. *III*. Vienna, Austria. pp. 33–45.
Cheers
-- Ian
On 19 April 2018 at 14:18, Ian Tickle <ianj...@gmail.com> wrote:
>
> Correction: maps are produc
Hi, first maps are produced by Refmac, not Coot, and second it shouldn't be
called sigma because it's not an uncertainty, it's a root-mean-square
deviation from the mean. The equation for the RMSD can be found in any
basic text on statistics, e.g. just type 'RMSD' in Wikipedia.
Cheers
-- Ian
, for example, this map
> is contoured at 3 sigma, this is a wrong statement?
>
> Cheers,
>
> On Thu, Apr 19, 2018 at 2:57 PM, Ian Tickle <ianj...@gmail.com> wrote:
>
>>
>> Hi, first maps are produced by Refmac, not Coot, and second it shouldn't
>> be called sigma because
On 19 April 2018 at 17:03, Marcin Wojdyr wrote:
I think he means the numbers that coot displays, e.g.
> map 1 level = 1.56 e/A^3 (3.50 rmsd)
>
> So the answer to the question if the relation between the two numbers
> is linear is yes.
>
OK I see, Mohamed means the electron
8 at 17:44, Edward A. Berry <ber...@upstate.edu> wrote:
>
>
> On 04/19/2018 08:57 AM, Ian Tickle wrote:
>
>>
>> Hi, first maps are produced by Refmac, not Coot, and second it shouldn't
>> be called sigma because it's not an uncertainty, it's a root-mean-square
>
with the unit
> e/A^3, and I seem to remember Paul's recommendation to use this unit,
> rather than the rmsd, which is displayed in brackets.
>
> Cheers,
> Tim
>
> On Mon, 2 May 2022 09:48:30 +0100 Ian Tickle wrote:
>
> > Hi Tim
> >
> > F000 is customarily not in
Hi Tim
F000 is customarily not included in MX electron density for the reason you
mention. This doesn't matter because the contour levels are completely
arbitrary anyway, i.e. you choose a level that shows the features you
expect to see. This can be misleading of course since there may be
Hi Tim
I would say that it's not the displayed map density value in whatever units
that's arbitrary: it's completely defined as the true density on an
absolute scale minus the F000 contribution ('b' below) and optionally
divided by the RMS. It's just that we don't have a good estimate of F000
All, could this behaviour be due to different line terminators
(DOS/Linux/Mac)? I've had that problem before, though not in this
particular context.
-- Ian
On Fri, 24 Mar 2023 at 10:00, Martin Moche <
9c00cd8c651b-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear Clemens and colleagues,
>
> I
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