for COOT
On 16/11/2017 13:28, Edward A. Berry wrote:
(set-go-to-atom-molecule 0)
(set-go-to-atom-chain-residue-atom-name "B" 42 " CA ")
Would those be also on the command line, or where?
You can use them on the command line like this:
coot --pdb input.pdb -c '(set-go-to-atom-
Is there a way to open the "geometry" window (the box you open by
"measures":"distances and angles") in the initialization script, and perhaps set its
position on screen as well?
Is there a way (interactively now) to center the screen at specified x,y,z
coordinates (as opposed to centering on
Hi Yao-Wang,
If I understand the problem correctly, then if you have built two adjacent
molecules, you can superimpose molecule 1 on molecule 2 to get the operator.
Then apply this operator to molecule 2 to make 3, to moolecule 3 to make 4, and
so on around the helix for as far as you want to
(P6(1) or P6(5), not P6!)
On 06/11/2018 10:16 AM, Edward A. Berry wrote:
Hi Yao-Wang,
If I understand the problem correctly, then if you have built two adjacent
molecules, you can superimpose molecule 1 on molecule 2 to get the operator.
Then apply this operator to molecule 2 to make 3
, Tsinghua University
Room 255, New Biology Building, Beijing, China, 100084
*From:* Edward A. Berry <mailto:ber...@upstate.edu>
*Date:* 2018-06-11 22:16
*To:* COOT <mailto:COOT@JISCMAIL.AC.UK>
*Subject:* Re: rotation and translation when building model in cryo-em map
On 07/16/2018 05:15 PM, Xiao Lei wrote:
Hi All,
Is there a way to measure the distance between an atom and another atom in
symmetry mate models? I tried to measure the distance usually by clicking two
atoms, coot only gave very long distance between the two atoms in ASU, even
though the
FFT
program as I originally stated.
Thanks for the correction!
Cheers
-- Ian
On 19 April 2018 at 17:44, Edward A. Berry <ber...@upstate.edu
<mailto:ber...@upstate.edu>> wrote:
On 04/19/2018 08:57 AM, Ian Tickle wrote:
Hi, first maps are produced by Refmac, not Coot, and
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 deviation
from the mean. The equation for the RMSD can be found in any basic text on
statistics, e.g.
On 01/08/2019 11:27 PM, Yong Tang wrote:
Happy New Year to all,
I'm solving many structures of the same protein and would like to find a quick
way to inspect like 10 selected residues of the 250aa protein in coot, for
every structure against the matched electron density maps.
What is the
Dropdown menu "Calculate", "other modeling tools, choose "undo" molecule.
On 02/04/2019 12:16 PM, Ahmad Khalifa wrote:
I have three structures open in Coot. I have only one displayed that I was
working on. Oddly enough, when I press undo, I get a warning about how Coot
can't undo
What is the format for match-list in:
lsq-match imol-ref imol-moving match-list
(or where is it described).
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I would appreciate instruction for getting a downloaded coot binary to run.
I got coot-0.9.7-binary-Linux-x86_64-centos-7-python-gtk2.tar.gz
There is no README file in the top directory.
I edited bin/coot to set
#PYTHON=/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/include/python2.7
OK, thanks.
I guess it is time to upgrade to CCP4 v8.
Ed
From: Paul Emsley
Sent: Tuesday, August 8, 2023 1:14 PM
To: Edward A. Berry ; COOT@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: Problem installing coot binary
On 08/08/2023 06:49, Edward A. Berry wrote:
I
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