John:
I recently (22-Nov) pointed out to Paul Emsley that if one entered potassium
through the popup menu, it places the "K" of potassium in the wrong column of a
PDB file, column 13 rather than column 14. The element is right-justified, so
single letter elements use only column 14, but two let
Paul:
Thank you!!
Steven
-Original Message-
From: Mailing list for users of COOT Crystallographic Software
On Behalf Of Paul Emsley
Sent: Tuesday, June 8, 2021 10:49 AM
To: COOT@JISCMAIL.AC.UK
Subject: Re: Feature suggestion: Check/Delete Waters, toggle hydrogens on/off
[Use CAUTION w
Paul:
I second this request, which I have made to you by private (as opposed to
mailing list) email.
Steven
-Original Message-
From: Mailing list for users of COOT Crystallographic Software
On Behalf Of CRAIG A BINGMAN
Sent: Friday, June 4, 2021 2:45 PM
To: COOT@JISCMAIL.AC.UK
Subject
Santhosh:
Modern molecular replacement programs, e.g. PHASER and MOLREP, look for and
take, at least translational, NCS into account.
Modern refinement programs, e.g. BUSTER, REFMAC, and PHENIX.REFINE, use LSSR
(Local Structure Similarity Restraints) for NCS and improve geometry to
resolutions
that one could just use
UNK is incorrect as that is reserved for unknown amino acids. According to this
document, I should have suggested UNL for an unknown ligand.
Steven
From: Rachel Kramer Green [mailto:kra...@rcsb.rutgers.edu]
Sent: Tuesday, June 16, 2015 10:21 AM
To: Sheriff, Steven
Cc
All:
Why the concern for unassigned three-letter codes? The wwPDB isn’t going to let
you assign a three-letter code, it will choose its own code.
At BMS (a pharmaceutical company), we do many hundreds of structures a year
with ligands and we assign the same, already assigned, three-letter code
Emilia:
It appears to me that based on discussion on the CCP4BB by Thomas Holder and
James Holton that you should do the following:
· Run MAPMASK twice, first on an asymmetric unit to normalize, and a
second time to extend the map over your molecule
· Issue the command “unset
All:
Following up on Carsten's comment. Buster also does not add hydrogen atoms
automatically. It does have a command external to buster, hydrogenate, which
uses the Duke University (read MolProbity) group's reduce underneath along with
CIF restraint files for ligands to allow reduce to properl
Even better than my suggestion ...
-Original Message-
From: Mailing list for users of COOT Crystallographic Software
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Paul Emsley
Sent: Tuesday, February 17, 2015 1:57 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: NCS ligand
On 17/02/15 18:02, Phil Evan
12:51 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: Reordering chains in a pdb file
On 20/01/15 17:32, Sheriff, Steven wrote:
>
> Rex:
>
> COOT->Extensions->Modeling...->Reorder Chains...
>
> But be forewarned that if the PDB file has insertion residue numbering
> this pr
Rex:
COOT->Extensions->Modeling...->Reorder Chains...
But be forewarned that if the PDB file has insertion residue numbering this
process will strip the insertion residue character from the ATOM records, so
the file will end up with multiple residues with the same apparent residue
number.
Ste
Bill:
From earlier COOT mail:
=
-Original Message-
From: Paul Emsley [mailto:pems...@mrc-lmb.cam.ac.uk]
Sent: Tuesday, February 11, 2014 9:43 AM
To: Yong Wang
Cc: COOT@JISCMAIL.AC.UK
Subject: Re: symmetry operator style in new coot
On 10/02/14 21:46, Yong Wang wrote:
> Dear Coot user
All:
I second Mark's points
1. that "electrons/A3" doesn't make any sense in the context of an r.m.s.d.
level, i.e. the "electrons/A3" should be deleted. Moreover, I would note the
inconsistency in nomenclature between that line and the previous one where
"with B factor greater than: A^2
Oliver:
Why not use PyMol for this purpose?
Steven
>-Original Message-
>From: Mailing list for users of COOT Crystallographic Software
>[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Oliver Clarke
>Sent: Wednesday, June 26, 2013 8:29 AM
>To: COOT@JISCMAIL.AC.UK
>Subject: Animated gif of densi
Paul:
It appears to me that you have provided the Python rather than the Scheme
version of this command, at least based on the use of underscores rather than
dashes and the fact that the entire command is not in parentheses as opposed to
just the parameter. Are you switching entirely to Python
All:
Although I also like Dale's idea of paying attention to HETNAM records, I think
we should stay in concordance with PDB rules and use HETNAM records only for
IUPAC names. Fortunately, the PDB also has HETSYN records and that is where we
place the BMS name (number) of a compound when we sto
All:
At BMS, we use the same ligand identifier, e.g. LG1, for all compounds that
bind at overlapping sites. If we have multiple compounds bound in a single
structure, i.e. non-overlapping sites, then we would use LG2, etc. for them.
Using a common naming system makes it easy for upstream and d
Tim:
Calculate->Scripting[->Scheme]
(set-rotation-centre x y z)
Used to work at least before the choice of Python or Scheme, but when I just
tried it, 0.6.2.-pre-1-revision-3237 crashed before it presented a scripting
window.
Steven
>-Original Message-
>From: Mailing list for users of
Paul:
Dirk's is a great idea. I had been wishing that COOT would at least ask if the
residue was a Gly or Pro, but at least with good side chain density the real
space positioning might work better and choose the proper path for the main
chain and side chain.
Steven
>-Original Mess
Phil:
Paul or the people who know what is really going under the hood in COOT can
tell you more. However, my understanding is that COOT uses distances to draw
bonds and the Se atom in the MSE residue must be outside of that radius. I
have occasionally, although not recently, seen this pheno
Simon:
If you want to get rid of all the files, why not get rid of the coot-backup
directories? In which case, it should be simple:
find . -name "coot-backup" -print -exec /bin/rm {} \;
where the "dot" following the find will start from wherever you currently are,
but you could specify
Andy:
To get Dynamic Distance to work, one first has to activate part of the molecule
to be movable, e.g. with Rotate/Translate Zone. Then go to Measures->Distance
& Angles...->Dynamic Distance and click on two atoms, one of which must be in
the movable part of the molecule. Surprisingly, I
Francis:
When I had a similar issue, Paul told me that one had to mutate a residue to be
sure that the stereochemistry is correct. Moreover, as of the last time I
checked with Paul, COOT does look at the chiral volumes for pseudo-chiral
centers such as Leu and Val, so it is no surprise that
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