I agree that looking at the packing is a good idea, but I also agree that
having the wrong space group is a likely possible explanation. That’s the most
common scenario when there are many clashing solutions with high TFZ scores.
Randy Read
On 17 Jun 2014, at 15:52, Roger Rowlett wrote:
> In
/2014 10:52 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] packing
test PHASER
Increase the number of allowed clashes in Phaser, re-run it then look at
the packing of the solution found and identify the source of the clashes.
Possibilities for the clash issue include:
Wrong
Increase the number of allowed clashes in Phaser, re-run it then look at
the packing of the solution found and identify the source of the
clashes. Possibilities for the clash issue include:
1. Wrong space group
2. Flexible loops or termini in search model not present or
differently arranged
Dear ccp4 users,
I get the following message from Phaser when I do a molecular replacement
with two ensembles. One of the ensembles is placed but the second one is
not placed, and then it says this:
Solutions with Z-scores greater than 13.0 (the threshold indicating a
definite
solution) were rej
Dear all,
thanks to everybody who offered their experience and hints.
The most convenient way of preparing a packing diagramme, at least for
me, was via PyMol as suggested by Michael Klein (see below).
One can do something similar with the CCP4 graphics package, but for
some reason the pro
I'd use MAMA to make an extremely simplified mask (either
based on a couple of nicely-positioned spheres, or excessively
smoothed) and they display it with its symmetry mates.
Original message
>Date: Wed, 26 Aug 2009 11:48:57 +0200
>From: Anita Lewit-Bentley
>Su
The cns script neighbours.inp might be useful for this purpose.
From: AntonioLeung
Reply-To: AntonioLeung
Date: Wed, 26 Aug 2009 21:46:26 +0800
To:
Subject: Re: [ccp4bb] packing diagrammes
Hi,
Pymol may do this work, use"Action-->generate-->symmetry mates"
---
Hi,
Pymol may do this work, use"Action-->generate-->symmetry mates"
-- Original --
From: "Anita Lewit-Bentley";
Date: Wed, Aug 26, 2009 05:48 PM
To: "CCP4BB";
Subject: [ccp4bb] packing diagrammes
Dear all,
does anyone know of a programme that would allow the graphical
representation of the packing of protein molecules in a crystal?
Ideally one would like to represent the protein as an elipsoid (or
similar relatively simple shape) corresponding to its volume, over a
few unit cells
92121
phone: (858) 228-1622
fax: (858) 457-5362
[EMAIL PROTECTED]
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Shane Atwell
Sent: Friday, June 20, 2008 1:21 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Packing broke for 2nd molecule in phaser?
I
That was "SEARCH ENSEmble mol2 NUM1" at the end. Bad editing.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Shane Atwell
Sent: Friday, June 20, 2008 1:21 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Packing broke for 2nd molecule in ph
I'm attempting a difficult molecular replacement using phaser and low
resolution data (3.5A). There's almost certainly only one molecule in
the asymmetric unit. Since the entire structure of a homologous
multidomain protein doesn't work, I've broken it down in domains and
have been attempting to fi
Dear all,
Thank you for your replies so far. I feel I should have been more precise in my
original question. There is a dimer in the asymmetric unit and we end up with
two different dimers after molecular replacement (the monomer-monomer interface
is completely different). Each solution refines wi
Tassos Papageorgiou wrote:
Dear all,
I am looking for examples of different packing arrangements in crystals of the
same protein with similar unit cell parameters and space group (eg the protein
adopts different packing although the crystals remain the same both in unit
cell dimensions and space
Dear all,
I am looking for examples of different packing arrangements in crystals of the
same protein with similar unit cell parameters and space group (eg the protein
adopts different packing although the crystals remain the same both in unit
cell dimensions and space group). Can this happen, for
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