This is tricky I find ..
You can use the NCS ghost to fit the bits of A you like over B, then
work out what bits of B you want to shift into A.
There are tools to rename that bit of B to A and if necessary renumber
it as well..
Then output the renamed file and you will probably have to edit
Paul Emsley wrote:
James Whittle wrote:
Hi-
I'm trying for the first time to work with a structure in spacegroup
H32. Coot reads the CRYST card, but when I build a helix, or look at
a H32 PDB entry, the symmetry mates appear squished. I know there is
some discussion about handling this
Am I alone in thinkingthat the default should be to display symmetry
related molecules - not to have it turned off?
Eleanor
At present the only way to calculate an E map via the input option to
read an MTZ file is to redefine the COLUMN type of E to that of F
Could this be fixed please?
Eleanor
1) The check on GLN and ASN and HIS? for likely hydrogen bonding is very
useful. Do you think it would be worth extending this to THR?
2) The Ramachandran plot includes residues with zero occupancy - it
woyuld help if they were flaggeed somehow differently..
Eleanor
It would be a cock-up map. Unless there is exptl phasing
PHDELWT = PHIC when mFo-DFc is positive, and mFo-DFc is negative it
equals PHIC + 180
Eleanor
Simon Kolstoe wrote:
Dear cootbb,
When building into density I use a map generated from the FWT
amplitudes column and PHWT phases
ccp4 programs now use syminfo.lib ( and have used it for a number of
years) Are you working with a very old mtz file? Or a very old
installation of ccp4?
Why not use distang or ncont or pisa to get your intermolecular contacts
They all use useful symbols like 3/2-X,Y,1/2-Z
Eleanor
Frank von
Why not read the diff map in twice? You can have diff contour levels for
each copy of the map..
Paul Emsley wrote:
Maia Cherney wrote:
If I use a *map_coeffs.mtz file from the phenix.refine, how can I
turn off the negative density?
??? Confusing question. By unclicking the is difference
The manual suggests the sequence view will be coloured according to
secondary structure, but that doesnt seem to be true for me
Eleanor
It is version
Coot 0.6-pre-1 Durham (revision 2334)
pebbleped...@gmail.com wrote:
Hi all
I am trying to find out if coot can export a map file that in text format.
I have created a difference map from two cns maps and want to export
it also in cns format (can be read in text eidtor). But till now, I
can only save it in xx.map format that in
Hmm - do I like updates?
Here is the message from a Fedora 10 based machine..
It was working yesterday evening..
Eleanor
[c...@roo hypFdemo]$ coot-latest
COOT_PREFIX is /y/programs/xtal/coot/coot-Linux-i386-fedora-8-gtk2-python
I agree with wtempel
Once a residue is split it means there is evidence for 2 conformations.
If one atom in one conformation has occupancy reset to 0.00, that
certainly does not imply that the other NZ A say should have occupancy 1.00
It wont the refinement in REFMAC anyway
Eleanor
Paul
This seems to be lost ??
/y/programs/xtal/coot/coot-Linux-i386-fedora-10-gtk2-python/share/coot/python
reads pdb and says:
...
INFO:: NCS chain comparison 306/307
INFO:: NCS chain comparison 304/307
INFO:: NCS chain comparison 306/307
INFO:: NCS chain comparison 305/307
INFO:: NCS chain
It is hard to diagnose this without the mtz file.
A bit of theory - a DANO map musdt have the input phases advanced by 90
degrees from the input phase. To indicate that should be done a Dano
column is flagges type D. You need to check that this is so in the input
mtz. I presume COOT then
On 11/05/2010 07:10 PM, Troy Johnson wrote:
I am looking at environment distances between a GTP molecule and my protein and
wanted to know if there is a way to see all of the contacts the GTP (or any
residue) makes in a list form? I am wanting to compare the changes in contacts
between Wt and
On 11/18/2010 05:45 PM, Phil Evans wrote:
On 16 Nov 2010, at 13:22, Paul Emsley wrote:
Dear Phil,
Sorry for the delay, I am only just back from somewhat extensive travels.
On 01/11/10 12:26, Phil Evans wrote:
If I colour by chain (my preferred option), metal ions disappear
Thanks for the
coordconv xyzin ha.pdb xyzout ha.frc
input pdb
output frac
end
Eleanor
On 04/22/2011 11:14 AM, Paul Emsley wrote:
On 20/04/11 15:48, Francis E Reyes wrote:
Hi all
I'm currently in the process of completing a heavy atom model so I
need to be able to compare fractional coordinates of
The B factor distribution is what you see when the phosphate backbone
has already been refined, but the nucleotide just mutated in..
Eleanor
On 08/15/2011 08:17 PM, Huw Jenkins wrote:
I can reproduce this. Coot 0.6.2 3562, CCP4 6.2.0, installed using fink on OS X
10.6.8
There are 2 data in
Has someone helped you with this?
Re coot and PT - I thought you could just add an atom and call it PT?
Here is the pdb format for a metal compared to a OE1
ATOM312 OE1 GLN B 99 -28.427 -30.882 26.585 1.00 20.00
BO
HETATM 1594 PT PT H 1 0.000 0.000 7.669 0.33
I have added an atom at pointer - asked to have it called ZN (selected
Other option for atom type and put in ZN) and the output file assigns
no atom type or residue type..
I dont think this should happen?
Eleanor
Yes - asterisks are now not used..
Eleanor
On 13 September 2014 14:54, Shane Caldwell shane.caldwel...@gmail.com
wrote:
Hi Helena,
I'm not sure if this is the same issue, but I've run into a problem where
there is a mismatch between atom names and restraints files where some
programs use
Or possibly mapmask.. It does all sorts of sums
Cheers Eleanor
On 21 October 2014 06:42, Kay Diederichs kay.diederi...@uni-konstanz.de
wrote:
I think sftools may be a program to do this?
Kay
Am 21.10.14 um 01:15 schrieb COOT automatic digest system:
Betreff:
map ratios
Von:
Scott
At 2014-11-04 17:50:40, Eleanor Dodson eleanor.dod...@york.ac.uk
wrote:
Check under Measures - are you showing environmental distances, or did you
ask for a distance to be displayed - there is an option there - clear all
distances.
Eleanor
On 4 November 2014 04:55, ly papama...@126
Sorry to be such a luddite, but what is wrong with a text editor!
Eleanor
On 20 January 2015 at 18:09, Sheriff, Steven steven.sher...@bms.com wrote:
Paul:
I just checked one file and indeed reorder chains no longer strips the
insertion residue record. Hurray!
Steven
-Original
Yes - I would like the option to output a list of peaks in PDB format, so I
could consider them.
It would help in various tasks, e.g. from an a nom diff fourier say..
Eleanor
On 24 January 2015 at 17:11, Kenneth A. Satyshur satys...@wisc.edu wrote:
Is it possible to output a list of peak pick
No idea why this is happening to you, but before analysing symmetry stuff
it sometimes helps ro use PISA to generate the best assembly for your 2
molecules in the asymmetric unit. All the symmetry search things only use a
limited number of unit cell translations
Eleanor
On 18 May 2015 at 05:45,
At least it would be good to set new residues to the overall B value.
Eleanor
On 17 May 2015 at 17:57, Bernhard Lohkamp bernhard.lohk...@ki.se wrote:
This is fixed in r5695 (B-factors of side chain atoms having default B
that is).
Setting (refining?!) B-factors more intelligently is on the
-- Forwarded message --
From: onetwo twoon...@rediffmail.com
Date: 9 April 2015 at 19:48
Subject: [ccp4bb] visualizing .mrc maps in coot and model building
To: ccp...@jiscmail.ac.uk
Dear All,
This is regarding the protein structure model building using the density
files or the
I use your method - trial error..
It would be nice if at least there was a list somewhere of unassigned codes!
On 5 June 2015 at 09:16, Lau Sze Yi (SIgN) lau_sze...@immunol.a-star.edu.sg
wrote:
Hi,
What is the proper way of generating 3-letter code for a new ligand? As of
now, I insert my
It is easy to extract a box from a map then display that? several jiffies
to do it..
Eleanor
On 28 August 2018 at 16:20, Andrea Thorn wrote:
> Hi,
> I would like to mark a box in an .mrc file (ccp4 format map); I know the
> xyz coordinates of the corners.
> Can I do something similar to "show
Paul - what about a useful log file? Not recording centred on A 237 but
including potentially useful info like SSM matrices (in orthogonal and
fractional system) - difference map peaks with the map they come from, etc
etc..
Eleanor
On Fri, 12 Apr 2019 at 17:13, Ahmad Khalifa wrote:
> I want to
Which version are we running hrre in York?
Eleanor
On Thu, 14 Mar 2019 at 18:34, James Moody wrote:
> Paul,
>
> We deleted the coot path from our $PATH variable and all of the problems
> we were seeing disappeared (Previously we had seen the rotamers and
> dihedral angles functions not
Does coot care? Coot Auto read mtz just looks for FWT and DELFWT etc...
Will test it ...
E
On Sat, 24 Aug 2019 at 09:03, John Berrisford wrote:
> Hi Eleanor
>
> It this case that won't work as the CIF files we produce don't have F and
> sigF columns.
>
> John
>
> On 24
You can read your cif file and convert it to an mtz - easy with the GUI -
import merged data task - then read it into coot as always..
eleanor
On Fri, 23 Aug 2019 at 21:17, John Berrisford wrote:
> Dear Mark
>
>
>
> In the mean time please see the instructions at
>
>
by default - how to get rid of them???
e
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
I am afraid I always renumber - I hate insertion codes because they seem to
generate so many obscure problems..
Eleanor
On Fri, 8 Nov 2019 at 19:51, Seth Harris wrote:
> Hi all,
>
> I'm sure this has been asked, but after some searching I can't find hints.
> Apologies if redundant, but can
-- Forwarded message -
From: Charles Ballard - UKRI STFC
Date: Mon, 14 Oct 2019 at 09:29
Subject: [i2dev] FW: Multiple dictionaries in COOT
To: ysbl-ccp4i2dev-gr...@york.ac.uk
-Original Message-
From: CCP4 On Behalf Of Stránský Jan
Sent: 14 October 2019 09:03
To:
under display molecule
bonds - default colour by atom type, but there is a menu with option -
colour by chain..
e
On Fri, 27 Dec 2019 at 15:35, Edwin Pozharski wrote:
> I believe "bonds colour by chain" option in display manager does color
> chains differently.
>
> On Wed, Dec 25, 2019, 12:06
I am running CCP4I2 on my rather ancient MacBook Pro and worry that I will
use up all the disk space.
When I delete a job nothing appears in Trash? Do the files evaporate
somehow??
Cheers Eleanor
To unsubscribe from the
Very pretty though!
E
On Sun, 20 Sep 2020 at 15:25, Paul Emsley wrote:
> That looks odd. I wonder if the problem lies with Coot or the program
> that generated the map. How does this map look in PyMOL or Chimera (for
> example)?
>
>
> Paul.
>
>
Re Refmac - I doubt it would unless you gave a specific LINK 26 C - 40 N
type L-peptide..
Not sure of the syntax..
Eleanor
On Sat, 25 Jul 2020 at 10:59, Paul Emsley wrote:
> On 24/07/2020 14:42, Yong Tang wrote:
> > Dear all, I have a loop truncation that could be explained as
> >
ha ha
On Tue, 8 Dec 2020 at 14:54, Coot Boot wrote:
>
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
>
Very festive! Your work paul? Happy Xmas everyonr
On Tue, 22 Dec 2020 at 15:49, Coot Boot wrote:
>
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
>
I think it is a sphere refine problem. Just use the old real space refine..
sphere refine hates clashes , so before you try to fix something you need
to delete any feature which will create one..\
I argue with Paul about the philosophy but he has the expertise!
Eleanor
On Wed, 2 Jun 2021 at
Why not rename chains and if necessary renumber residues to make a sensible
single chain? Very easy with the edit options and much simpler than
creating an unrealistic link??
I find myself going that often after an build molecule run.
Eleanor
On Thu, 1 Apr 2021 at 00:40, Paul Emsley wrote:
> On
What model is it?
Eleanor
On Sat, 4 Dec 2021 at 08:29, Yuqi Zhang <
64676fd7756a-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi, all!
> I met a problem when I upload the PDB file to wwPDB. There is an error
> about the occupancy was larger than 1. So I checked the model in COOT.
> There are many
First - are they in the same spacegroup but on different origins? If that
is so it is very easy to first shift A to B (match molecule to reference,
then just recalculate structure factors and redo the maps..
But if they are in different cells/spacegroups
But when I tried map tools/ transform map
Could Andrew T please send an example of a data set that fails for testing?
Eleanor
On Wed, 30 Mar 2022 at 22:24, Paul Emsley wrote:
>
> On 29/03/2022 22:26, DeLaitsch, Andrew T. wrote:
>
>
>
> I am working on refining antibody-HIV-Env structures in COOT. The problem
> I have is that both
Hear Hear - hard to remember life pre-COOT
Eleanor
On Tue, 12 Apr 2022 at 16:16, Kenneth Satyshur <
302c79f8ddd1-dmarc-requ...@jiscmail.ac.uk> wrote:
> You deserve a medal, award, or something for the enormous effort in the
> programming. Without your effort I don't know where we would all
d just be a coordinated metal.
> But there is a covalent link from DRG C2 to SG Cys417
>
> Thanks
>
> Wendy
>
> On Fri, 1 Sept 2023 at 13:19, Eleanor Dodson
> wrote:
>
>> *COOT problem first: or is it REFMAC ? *
>> REFMAC outputs coordinates in both pdb and cif
*COOT problem first: or is it REFMAC ? *
REFMAC outputs coordinates in both pdb and cif format. They are identical
*This model has ZN linked to CYSs etc..*
The PDB files provides the link records but the cif file does not.
eleanor@wombat job_187 % grep -i link
Is that coot in the latest ccp4 distribution?
On Fri, 1 Sep 2023 at 17:37, Paul Emsley wrote:
> Dear Eleanor
>
>
> On 01/09/2023 13:19, Eleanor Dodson wrote:
>
> *COOT problem first: or is it REFMAC ? *
> REFMAC outputs coordinates in both pdb and cif format. They are
>
Congratulations to you all!
I look forward to swearing at the changes, and appreciating the new
features.
Eleanor
On Tue, 31 Oct 2023 at 17:10, Paul Emsley wrote:
> 18 months after the release of Coot 1 it's time for Coot 1.1
>
> Coot 1.1 is a major change beyond Coot 1. It has required a lot
acid" *NON-POLYMER * 24 14 .
#
On Thu, 21 Sept 2023 at 21:53, Eleanor Dodson
wrote:
> Check the dictionary has labelled it as peptide
> like ALA
> data_comp_list
> loop_
> _chem_comp.id
> _chem_comp.three_letter_code
> _chem_comp.name
> _chem_comp.g
Check the dictionary has labelled it as peptide
like ALA
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
ALA ALA ALANINE *peptide* 13 6 .
On Thu, 21 Sept 2023 at 18:58,
ure core facility - PTPSP
> EPFL SV PTECH PTPSP
> AI 2146 (Bâtiment AI)
> Station 19
> *CH-1015 Lausanne*
> *Switzerland*
> Email: kelvin@epfl.ch
> Phone: *+41 21 69 34494*
>
>
>
> On 21 Sep 2023, at 22:56, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ
I cat answer th. coot behavior, but if you read in the coordinates twice,
then refine molecule 0 say the old structure will be displayed as well as
the refined version..
Eleanor
On Fri, 17 Jun 2022 at 21:34, Biertuempfel, Christian (NIH/NHLBI) [E] <
7fb73c55f9c4-dmarc-requ...@jiscmail.ac.uk>
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