[COOT] key binding for difference map peaks

Hi all, this used to work (a while ago) from my-settings.scm for a key binding to get a list of difference map peaks: (add-key-binding "Difference map peaks" "b" (lambda () (difference-map-peaks 2 0 4 2.0 1 1))) but now (and for quite some time) it mentions wrong number of arguments: *(graph

[COOT] large non-native peptide .cif restraints

Hi all, I am increasingly dealing with large macrocycles or cyclized peptides that include unnatural amino acids or modifications. Early on my approach was to treat most of it as the native peptide scaffold, then add a few custom 'LINK' records to capture covalent bonds to some non-native moiety,

Re: [COOT] Glyco module going off script at the B1-4 BMA?

1:10 AM Paul Emsley wrote: > On Tue, 2021-07-13 at 23:59 -0700, Seth Harris wrote: > > > > I have some good resolution (~1.3 A) data with glycosylation that can > pretty clear describe the expected N-linked tree > > of Asn-NAG-NAG-BMA with two MAN off the end and a FUC at

[COOT] real space refine with insertion codes

Hi all, I'm sure this has been asked, but after some searching I can't find hints. Apologies if redundant, but can someone refresh me on how to get Coot to be graceful about residues with insertion codes...particularly during real space refinement. I have a protease structure with very good resolu

[COOT] middle mouse button center versus drag

Hello Paul et al., Click and drag on the middle mouse button is a quick and familiar way to translate around the scene and navigate, generally working well. However, if at the initiation of the click and drag I happen to be near an atom, the fact that I'm holding down the mouse button isn't distin

Re: [COOT] navigating across symmetry mates

AM, Paul Emsley wrote: > On 06/09/2017 18:14, Seth Harris wrote: > >> Hello Paul, Coot users! >> >> In the wonderful pantheon of Coot tools, is there a way to leap between >> equivalent points in symmetry mates with a nice single key shortcut, for >> insta

[COOT] navigating across symmetry mates

Hello Paul, Coot users! In the wonderful pantheon of Coot tools, is there a way to leap between equivalent points in symmetry mates with a nice single key shortcut, for instance? Or could there be? I seem to be getting several cases with 8 copies/asu and while initially one may build a single vers

Re: [COOT] key binding for waters added to mol 0

Thanks Paul, A few follow up notes for how I got that working from your example... On Thu, Jan 9, 2014 at 9:20 PM, Paul Emsley wrote: > On 10/01/14 02:30, Seth Harris wrote: > >> Hi all & Paul, >> >> Sometime back I found or was taught or given this: >>

Re: [COOT] key binding for waters added to mol 0

this > position" button on the right side, then select your PDB file - all > subsequent invocations of the "w" key will add waters to your PDB of > interest instead of putting them in a separate PDB. > Sincerely, > Scott > > > On Jan 9, 2014, at 18:30, Seth Harri

[COOT] key binding for waters added to mol 0

Hi all & Paul, Sometime back I found or was taught or given this: (add-key-binding "Add Water" "w" (lambda () (place-typed-atom-at-pointer "Water"))) (Probably from "Pauls-key-bindings-for-coot"...) I was looking for a quick way while browsing map peaks to add waters that the 'find waters' algo

[COOT] add terminal residue...keep it nearby?

Hi all, I and others have occasionally been plagued by the "Add Terminal Residue" function placing the new residue somewhere distant. While there are various workarounds (reject and try again, do more searches, real space refine or regularize after it's been placed which kind of sucks it over to t

Re: [COOT] Coot - 3D Anaglyph

Ha. Now that's just about where I went running (comments in the other thread on ligand restraints...). See what I mean? Got to watch your step...next run I'll bring my red/green glasses... On Thu, Jan 26, 2012 at 12:06 PM, William G. Scott wrote: > Does coot do red/greed (anaglyph) stereo? All

Re: [COOT] New restraints, same name

Hi all, Working in industry, we do end up with conventions that just give a generic name to whatever small molecule happens to be in that structure, typically LIG or DRG or XXX, e.g.. Makes it easy to navigate solved structures en masse without having to figure out what arbitrary name it has in st

Re: [COOT] script to delete waters below 0.8 e/A^3

l Emsley wrote: > On 03/06/11 23:11, Seth Harris wrote: > >> Hi all, >> >> I often use the Check/Delete waters dialog to delete only those waters >> below 0.8 level in the map. I do this often enough that it is high time to >> find/create a script version, pre

[COOT] script to delete waters below 0.8 e/A^3

Hi all, I often use the Check/Delete waters dialog to delete only those waters below 0.8 level in the map. I do this often enough that it is high time to find/create a script version, preferably even something I could launch from the command line, or barring that maybe could generate a single-clic

[COOT] always on mouse button mode?

Hi all/Paul, I spend a great deal of time stepping through stuctures residue-by-residue (space bar) and rotating the molecule to and fro as a check up. Basically I have the mouse button held down almost constantly. I wondered if it would be simple to have a key binding to toggle in/out of a specia

Re: [COOT] how to set the refinement map

sure the map is already loaded by then). A small thing, but it felt time to get it right! Much gratitude (especially after building up a few new proteins and feeling that tangible time savings from coot's nice tools and keyboard shortcuts!), Seth On Mon, May 10, 2010 at 3:23 PM, Paul Emsley w

[COOT] how to set the refinement map

Hello, After what felt like a reasonable amount of poking about, I can't find how to set the refinement map (yes, I tried 'set-refinement-map') although I did find that "guess-refinement-map" returns a good guess but doesn't seem to stop the "Oops! Must Select Map to fit to!" box from bothering me