On 30 January 2012 14:47, Phil Evans wrote:
> Can someone explain Extensions->Modelling->DB Loop or point to documentation
> (I've tried Google)? What are "Number of residues for basis"?
>
> Phil
Assume we have a missing loop that we would like to get built. The
conformation of the newly built l
I would like to second to most of Steven's, Seth's and Garib's points
and would welcome a change that would enable us to use the same three
letter code for different ligands within one coot session.
Renaming ligands in pdb and cif files is a good workaround, however it
is not more than a workaroun
Have you tried loading both the pdb and cif files for the custom residue?
As far as I remember, custom ligands need both to be used in mutation
-- but I rarely do that so I might be wrong... You can always revert
to mutating "by hand": load pdb and cif, delete old residue, merge in
new one, renumb
On 26 December 2011 03:25, Dialing Pretty wrote:
> Dear All,
>
> You see the part labelled "D and "LARGE" in the attached image is the part
> for the last residue in a chain, however it localizes in the red part. If I
> can change the part labelled "D" and "LARGE" into the part labelled "F", the
>
On 20 December 2011 16:37, Paul Emsley wrote:
> Hi JED,
>
>
> On 09/12/11 13:29, Judit Debreczeni wrote:
>>
>> I used to use delete-residue-with-altconf in an extension, looping
>> over a subset of residues returned by residues-with-alt-confs.
>>
>> As de
I used to use delete-residue-with-altconf in an extension, looping
over a subset of residues returned by residues-with-alt-confs.
As delete-residue-with-altconf no longer exists, I use
delete-residue-with-full-spec instead, which requires an imodel.
Unfortunately, residues-with-alt-confs does not
>>> Anyway, it's something that I should fix. I'll add it for 0.7.
>
> revision 3793.
>
That seems to work, thanks.
It seems, however, that the restraints editor fails to display/edit
planar restraints if one of the planar groups has more than 25 atoms,
which some molecules can be "contrary" en
On 30 November 2011 15:06, Paul Emsley wrote:
> On 30/11/11 10:52, Judit Debreczeni wrote:
>>
>> Grade (from Global Phasing) produces cif files with non-loop_
>> descriptions of chiral restraints, e.g.:
>>
>> _chem_comp_chir.comp_id INH
>> _
Grade (from Global Phasing) produces cif files with non-loop_
descriptions of chiral restraints, e.g.:
_chem_comp_chir.comp_id INH
_chem_comp_chir.id chir_01
_chem_comp_chir.atom_id_centre C1
_chem_comp_chir.atom_id_1C
_chem_comp_chir.atom_id_2C2
_chem_comp
Modern coots come with tutorial data. You can load them by:
Extensions->Load tutorial model and data
2011/11/18 herohonan :
> Hello:
> http://www.biop.ox.ac.uk/coot/
> This website is about the "coot". You can download the software and the
> tutorial here. And there are many other useful
> info
On 9 November 2011 20:04, Francis E Reyes wrote:
> Hi all
>
> It seems that converting a small molecule refined (shelx) with openbabel to
> pdb results in a slew of CONECT records which Coot doesn't recognize. As a
> result I've got a bunch of unbonded atoms for my ligand. Anyone have a
> solut
On 17 October 2011 21:24, Alejandro Buschiazzo wrote:
> Hi,
>
> I wonder how should I go about changing the range of the B-factor ramp for
> coloring atoms, at will, in order to have a full range of colors even when
> my pseudo-B factors go from, say, 0 to 1 (default settings in this case
> disp
On 4 October 2011 00:41, Paul Emsley wrote:
> On 30/09/11 19:58, Judit Debreczeni wrote:
>>
>> 1. Displaying ball-and-stick representation of a residue turns dashed
>> lines representing LINKs ball-and-stick style for other (unrelated)
>> residues.
>
> Driver bug,
0.7-pre-1 (revision 3669) [with guile 1.8.7 embedded] [with python
2.6.0 embedded] crashes when trying to read 1x8b-sf.cif, freshly
downloaded from the PDB, on fedora12, fedora12 build.
Earlier versions detected that this file was lacking cell, symmetry
and phase info and failed more gracefully.
1. Displaying ball-and-stick representation of a residue turns dashed
lines representing LINKs ball-and-stick style for other (unrelated)
residues.
2. Ball-and-stick representations are undisplayed and can no longer be
turned on using the display manager if the stereo status is changed
(e.g. to ha
> You can use (pythonic):
>
> set_molecule_name(imol, name_str)
>
> [Note: I recall some warning that you are encouraged not to use this on
> maps; not sure why]
>
Perhaps because it only works on model molecules and not on map molecules?
> (Python scripting option verendus est)
>
> In python script, it appears that show_select_map_dialog simply shows
> the dialog and quits. I am trying to set up a method that would do
> certain things depending on the choice of map. So I use
> show_select_map_dialog, but it appears that it does n
> Does anyone have a script to assign a key to step the map number connected to
> the scroll wheel? The scheme commands exist and I thought someone may have
> done this already. It seems like an obvious shortcut.
>
> Thanks, Mark
If you mean stepping to another map and making that scrollable,
> Hi all,
>
> I am running Coot 0.6.2-pre-1(revision 2816). The OS is Open Suse 11.1.
> Every time I try to open a SHELX refined pdb file with ANISOU cards I get
> this error
>
> ERROR 14 READ: Unmatch in different records for the same atom
>
> Then it lists the line number of the first ANISOU card
2010/1/15 Tatsuya KAMINISHI :
> Hi Paul,
>
> Thank you for your reply. But I would like to use this function quite often,
> and python/guile scripting could be helpful.
> In fact, the following guile one-liner I made based on Judit's suggestion
> still doesn't work for me:
>
> (rigid-body-refine-by
2009/11/13 Ben Eisenbraun :
> Hello Cooters,
>
> I'm trying to add a keyboard shortcut for Rotate/Translate Zone. I
> stumbled around a bit and decided on:
>
> (add-key-binding "Rotate-Translate Zone" "r" (do-rot-trans-setup 1))
>
> But it doesn't quite work. I get this error:
>
> ((safe_scheme_c
2009/9/9 Arnaud Basle :
> Hi,
>
> I have a peptide structure at 0.92A and for the latest stage of refinement I
> would like to real space refine a Met residue including hydrogens. The H are
> flying away from their original position and density.
>
> I am using shelxl for refinement (.res and .ins f
2009/7/31 Paul Emsley :
> Alex Theodossis wrote:
>
>>
>> Is it is possible to configure the Probe output in Coot not to display
>> contact dots between atoms of the same residue?
>>
>
> I don't see how to do that in probe, so I guess not. If you can persuade the
> authors/maintainers of probe to cr
2009/6/5 hari jayaram :
> Hi I have a very low resolution map in which I can barely see side chains .
> I want to set to zero occupancy many residues and residue side-chains before
> I do a refinement.
>
> Currently I am using the Residue-Info menu item to set each occupancy to
> zero residue by re
> Hello Everyone
>
> Where does coot get monomers from?
> Is it my ccp4 distribution? Or the coot distribution (It's a kind of old
> coot)
>
> I'd like to use get monomer for a ligand I've created a dictionary for - not
> one known to ccp4.
>
> I can create the cif for the monomer (and the pdb) and
Hi,
I'm wondering why adding alternate conformations to ligands (i.e. non
amino acid residues) restricts the occupancy ratio to 50:50. I
understand that ligands don't have rotamers (at least not ones that
coot would know about) so I can't pick rotamers but I'd like to be
able to specify the ne
2009/3/2 Nathaniel Echols :
> Is this even possible? Either Python or Scheme would be okay. I figured
> out how to hide everything (in Python), but I'm trying to reload files via a
> button, and they always have the same name, so the display manager becomes
> confusing quickly.
> thanks,
> Nat
2009/2/25 Frank von Delft :
> I'm totally not with Paul on this one (is scheme object-oriented???), and
> eternally grateful to him and Bernhard for implementing python scripting.
I think that the point was that scheme is not imperative and not
particularly object-oriented (but allows both).
>
2009/2/24 Victor Alves :
> Hi
>
> I have looked at the reference manual and can't seem to find a way to
> fulfill my desire to change colors of the active map or molecule at
> key-press.
>
> All the commands I found use "imol" which means you have to know the exact
> number. If you're launching Ref
tire
> residue)...
>
> On Wed, 2008-07-23 at 16:48 +0100, Judit Debreczeni wrote:
>> Even though it's not showing up in the terminal window, 'Add Alt Conf'
>> does have a schemey equivalent: (altconf), so do many of it's siblings
>> -- see sectio
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