Dear CCP4ers,
many thanks to all of you who replied to my request!
I wish you a Merry Christmas and a Happy New Year!
Dirk.
Forwarded Message
Subject:[ccp4bb] Calculation of generalised R-factor?
Date: Tue, 20 Dec 2016 14:47:00 +0100
From: Dirk Kostrewa
Reply-To
On Tuesday, 20 December 2016 10:28:44 PM Pavel Afonine wrote:
> Hi Dirk,
>
>
> I want to check the validity of the refinement of anisotropic B-factors vs.
> > TLS + isototropic B-factors using the Hamilton R-value ratio test as
> > described in Ethan Merritt's paper "To B or not to B", Acta Cryst
Dear All,
I want to built a 3d model of DNA to be used to show the path of genome
transfer in a tailed phage electron density map, during infection.
It will be helpful if The model can be generated as an mrc file or of a
similar file format.
Any suggestions?
Thanks
Andy
Sent from my
Hi Dirk,
I want to check the validity of the refinement of anisotropic B-factors vs.
> TLS + isototropic B-factors using the Hamilton R-value ratio test as
> described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol
> 68, pp 468. This test uses the generalised R-factors (assuming
Hi Scott,
That would be great if you have some references handy?
Thanks very much,
Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide
On Wed, Dec 21, 2016 at 1:48 AM, Scott Horowitz
Hi Pavel,
That worked a treat! Thanks again for your help,
Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide
On Tue, Dec 20, 2016 at 3:18 PM, Pavel Afonine wrote:
> Hi Andrew,
>
>
Thanks Nicolas and Paul! I am using active 3D with Quadro 5000 graphics
card and Nvidia 3D kit in Fedora system (Fedora 23). Everytime I update the
kernel (dnf update), I lost the 3D in both the updated new kernel and the
old kernel, I have to reinstall the driver again, but can not make every
rei
Dear Paul,
I am currently not working under Ubuntu OS, so I can't try your fix.
But if my memory is still good, it was exactly the problem (the dynamic
menus). And I am sure that some ccp4bb reader will be happy to find and
try this solution.
Thank you.
Nicolas
Nicolas Foos
PhD
Structural
On 20/12/16 16:21, Nicolas FOOS wrote:
Dear Lei,
I already try :
Ubuntu Mate (no problem), Xubuntu (no problem), Ubuntu (standard) (I
had problem with coot due to unity desktop).
A shot in the dark, but maybe your problem is with dynamic menus?
If so, try this:
$ export UBUNTU_MENUPROXY=0
Dear Lei,
I already try :
Ubuntu Mate (no problem), Xubuntu (no problem), Ubuntu (standard) (I had
problem with coot due to unity desktop).
Also alternatively : Mageia5 (no problem), Manjaro (python3 as default
in environment create some difficulty for several Macromolecular X-ray
soft).
Hi Andrew,
Based on the atoms and distances you are mentioning, these don't sound like
steric clashes, but like a chalcogen bond between the S and O atoms, and
CH...O hydrogen bonds between the O and CH3. These are common and
well-accepted interactions, but unfortunately aren't usually treated as
Hi Dirk,
You need the "Overall weighted R2 factor". The reference for the paper I
meant is
http://onlinelibrary.wiley.com/doi/10.1107/S056773947293/abstract
Cheers,
Robbie
> -Original Message-
> From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de]
> Sent: Tuesday, December 20, 201
Dear Robbie,
thanks for your reply. According to the REFMAC5 manual, the weighted
R-factor is just:
weighted R factor = sum w ||F_o -|F_c ||/sum w |F_o |
So, unfortunately, it is not the generalised R-factor.
Do you have a reference for that follow-up paper?
PDB_REDO does too much for my pu
The value for the Hamilton test is written by Refmac as the weighted R-factor.
There was a follow-up paper that showed that you shouldn’t use the normal
R-factor for the Hamilton test.
PDB_REDO does the Hamilton test automatically, but you can also feed two Refmac
logfiles to the bselect prog
I'd be interested as well.
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk
Kostrewa
Sent: Tuesday, December 20, 2016 8:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Calculation of generalised R-factor?
Dear CCP4ers,
I want to check
Hi all,
I'm running Coot 0.8.7 (as distributed with the CCP4 package) on OSX
10.11.6.
As soon as I click to enter CA-baton mode, coot crashes (terminal output
pasted below).
All I have done prior to this is load a pdb and an mtz, build skeletons and
pick a start point.
Has anyone seen this befo
Dear CCP4ers,
I want to check the validity of the refinement of anisotropic B-factors
vs. TLS + isototropic B-factors using the Hamilton R-value ratio test as
described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D,
Vol 68, pp 468. This test uses the generalised R-factors (assumin
The Institute of Cancer Research, London, is one of the world’s most
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Dear All,
A post-doctoral position is available immediately in the laboratory of Dr
Joe Cockburn, at the Astbury Centre, University of Leeds, UK to perform
structure-function studies on ciliary proteins.
The position is funded by The Wellcome Trust and is available immediately
for a period of
Dear Andy,
You've mentioned that MR doesn't work in any of the space groups you've tried,
but there are different scenarios that you might be able to recognise from
where the MR fails.
1. You might have the wrong protein, e.g. crystallised from a contaminant. In
that case, I would expect to s
Hi Pedro,
quick answer: no.
Longer answer:
see article "13 typical occupancy refinement scenarios and available
options in phenix.refine" here:
http://phenix-online.org/newsletter/
Pavel
On Tue, Dec 20, 2016 at 12:29 AM, Pedro Matias wrote:
> Hi Pavel,
>
> If the occupancies are 1 does phenix
Hi Andrew,
One of the atoms should be in altconf A and the other in B. Otherwise
the problem remains.
Pedro
Às 01:48 de 20/12/2016, Andrew Marshall escreveu:
> Hi all,
>
> Thank you for your suggestions. I tried the pdb file edit (making the
> offending atoms of both the ligand and the protein
Hi Pavel,
If the occupancies are 1 does phenix still refine them? Anyway, they can
be explicitly fixed if necessary.
Pedro
Às 03:00 de 20/12/2016, Pavel Afonine escreveu:
> Hi Perdo,
>
> technically this should work too with the caveat that non-blanc altid
> will trigger occupancy refinement fo
Dear Andrew,
If you're sub 2 Angstrom - give Archimboldo a shot. We recently solved the
crystal structure of a unknown protein this way. You perhaps have the advantage
of knowing what be in there.
Antony.
--- Antony W Oliver ---
--- sent from my mobile account ---
On 20 Dec 2016, at 08:18, A
Thanks Tim,
Yes, I may give that a go next time (the wild-type was actually solved by
S-SAD, very nice ordered bridge)
Orperhaps time to seed / derivitize / mutate and get different packing.
Still, not before xmas!
Andy
-Original Message-
From: Tim Gruene [mailto:tim.gru...@psi.ch]
I am in the mailing list of subscribers for ccp4bb with current yahoo mail
account. I am going to discontinue this mail account. kindly change my email
account to my gmail account, ranvirsin...@gmail.com
Ranvir SinghDept cum NCHGSRPanjab UniversityChandigarhINDIA.
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