Hi everyone,
Thanks for all your input. I will consider processing and depositing
the data out to 2.35 A, but refining only against data up to 2.55 A.
Just to give a little more information, and make sure what I'm doing
is reasonable, I am attaching below the table of statistics vs.
resolution f
Hi all,
I am trying to refine a structure in CCP4 and the final R factor is about 1%
lower than the initial but for the first “task/cycle” within the same
refinement job in CCP4, R factor starts off higher than the input data R factor.
I have a structure with multiple sugars attached, I did the
Dear Eleanor and Jie,
I replied to Eleanor off-list to say that I can credit Isabel Uson with
being the first to report this bug. The bug has been corrected for the
recent phenix release. The phenix and ccp4 releases of phaser will be
synchronised with the next ccp4 update, which is imminent.
Dear Airlie and Randy
Thank you! I have seen this error for quite some time and get it around by
using ccp4-6.3 for Phaser. Will try to be the first to report next time :-)
All the best
Jie
- Original Message -
From: "Airlie McCoy"
To: "jie liu"
Cc:
Sent: Tuesday, May 20, 2014 1
Hi,
I guess Airlie only replied to Eleanor off-line. This is a problem that Isabel
Uson had already reported to us. It’s fixed in the current version of Phaser,
which is in the pipeline to be released through the CCP4 update mechanism.
Best wishes,
Randy Read
On 20 May 2014, at 16:53, jie l
Dear Eleanor
I've been getting this error for a while. Switching back to ccp4-6.3 would
solve the problem. I guess it's a bug of version 6.4.
Best
Jie
- Original Message -
From: Eleanor Dodson
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, May 20, 2014 5:26 AM
Subject: [ccp4bb] o
Oh no, I’ve been meaning to update that page for a while! It’s much easier to
cut out density now than it was when I wrote that. In CCP4, Kevin Cowtan has
the program cmapcut, and in Phenix Tom Terwilliger has the program
phenix.cut_out_density. For most purposes, I think you’ll find those pr
Dear all,
Firstly - many thanks to Kay Diederichs and Graeme Winter.
The “memory” error was in fact due to certain diffraction images having very
few (weak), if any spots - essentially they were ‘blank’.
By excluding these images, and with a combination of Xia2, plus XDS + Aimless,
I was finall
MAPMAN contains several related options, e.g. CEll, SPacegroup, TRanslate and
GTranslate, PAste (see the manual for caveats -
http://xray.bmc.uu.se/usf/mapman_man.html ). Saving as an ASCII file and
editing may also work, if you know what you are doing.
--Gerard
On Tue, 20 May 2014, Edwar
But, if you convert to structure factors and recalculate the map in a different
cell,
the features will be "stretched" to fill the cell, which I take it is the
original problem.
I found Kleywegt's RAVE package very convenient for doing this,
but i believe the functionality is now available in
c
Hi ccp4bb
Two postdoctoral positions in X-ray crystallography/drug discovery are
currently available at University College London/Magnus Life Science. Please
see link for further details.
http://www.magnuslifescience.co.uk/careers/
Best
I should be sending thids to the phaser team I guess, but maybe there is an
easy fix..
This is the end of the log file..
Sg I222 or I212121
Scoring 500 randomly sampled orientations and translations
Spreading calculation onto 2 threads.
Generating Statistics for TF SET #1 of 2
0%
2014. 5. 20. 오후 4:25에 "JinSoo.Bae" 님이 작성:
> Dear all,
>
> Is there any one who have 2 references as below?
>
> Processing of X-ray diffraction data collected in oscillation mode.
> Methods Enzymol. 276: 307-326
>
> PROCHECK - a program to check the stereochemical quality of protein
> structures.
Hi Thomas,
strictly speaking, there is no need to re-process the data (because it wouldn't
change the data anyway). It may even be that the data beyond 2.55A contain some
signal (CC1/2 should tell you about that), which future refinement programs can
use - so you could deposit at the RCSB all d
Dear Tony,
I renamed your LP_01.tmp to INTEGRATE.LP and ran XDSGUI - this shows nicely
that after frame 150 things "fall over".
So pls try the recommendations in the "Difficult datasets" article of XDSwiki.
Normally you should not need to run two processing jobs; just prevent
refinement from "
Dear Almudena,
if you follow the recommendations given in the "Difficult datasets" article on
XDSwiki, your problem would have a good chance to be solved.
best wishes,
Kay
On Mon, 19 May 2014 18:18:46 +0200, Almudena Ponce Salvatierra
wrote:
>Dear all,
>
>I am looking for some suggestions h
Dear Tony,
OK, clearly Tim's suggestion is spot on, to remove the offending images
from processing (this is easily done by splitting your input xinfo or the
automatically generated one, I will copy an example below)
I suspect that the "memory error" results from
IMAGE IER SCALE NBKG NOVL N
Dear Matt,
I am afraid you are in a difficult position. With poor 4Å data, you need a
convincing MR solution to be sure that the solution is correct.
The large number of molecules in the a.s.u. is probably causing the poor
diffraction.
Things I would do are:
If you have more crystals, try them
Dear Thomas,
I would object to Zbyszek's recommendation. If I calculated correctly
(2.55/2.35)^3, roughly 20% of your reflections were integrated as noise.
Due to how profile fitting and scaling work this may affect your overall
data quality. Also your parameters may be partially refined against
n
Dear all,
Is there any one who have 2 references as below?
Processing of X-ray diffraction data collected in oscillation mode. Methods
Enzymol. 276: 307-326
PROCHECK - a program to check the stereochemical quality of protein
structures. J. App. Cryst. 26: 283-291
please kindly send to me.
tha
Dear Niu,
Provided you have a complete asymmetric unit (unit cell in P1), you could also
convert this map to structure factors and manipulate those, e.g. with sftools.
To calculate structure factors you could use sfall and also clipper has
utilities to convert a map to structure factors.
Best,
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