Re: [COOT] Disulphide sphere refinement fails in COOT when PDB file comes from BUSTER?

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

Re: [COOT] absolute map levels

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

Re: [COOT] absolute map levels

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

Re: [COOT] absolute map levels

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

Re: [COOT] Calculating sigma value

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 >

Re: [COOT] Calculating sigma value

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

Re: [COOT] Calculating sigma value

, 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

Re: [COOT] Calculating sigma value

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

Re: [COOT] Calculating sigma value

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:

Re: [COOT] Calculating sigma value

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

Re: [COOT] CHO H-bonds.

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

Re: [COOT] CHO H-bonds.

-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

[COOT] CHO H-bonds.

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

Re: [COOT] Negative positive contours for neutron map.

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

[COOT] Negative positive contours for neutron map.

Hello, does anyone know how to simultaneously display negative positive contours for a neutron 2Fo-Fc map? For example, as in Fig. 2 here:

Re: [COOT] Reading multichart script into WInCoot.

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

[COOT] Reading multichart script into WInCoot.

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

Re: [COOT] Selecting columns from MTZ file

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

Re: [COOT] --auto column labels

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

Re: [COOT] --auto column labels

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

Re: [COOT] Version 7 not repainting screen after initial load.

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!  

Re: [COOT] New restraints, same name

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

Re: [COOT] map level

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

Re: [COOT] reading chiral restraints from grade's cif files

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

[COOT] Environment variable for 'examples' directory?

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

[COOT] How to turn off display of negative contour level?

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

[COOT] Syntax of mutate_by_overlap.

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