: [ccp4bb] XDS question
Thank you to all!
@Frederic
I have a problem with the following sentence:
if I collect all spots I get good map, but it is impossible to solve
the structure by molecular replacement - if you have a good map (I
assume electron density map) then the structure is solved... for me
Marco,
indeed, as Fred says, the space group I422 may not be the correct one
for the large cell.
Use the model from the small cell for molecular replacement in the large
cell. You may try I4(1)22, I4(1), I4 first, then lower symmetries: look
into the International Tables what subgroups of
cell may look like.
Your situation might be different, but I would definitively try it.
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Marco Lolicato
Sent: Monday, June 13, 2011 5:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] XDS
, 2011 5:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] XDS question
Thank you to all!
@Frederic
I have a problem with the following sentence:
if I collect all spots I get good map, but it is impossible to solve
the structure by molecular replacement - if you have a good map (I
assume
look like.
Your situation might be different, but I would definitively try it.
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Marco Lolicato
Sent: Monday, June 13, 2011 5:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] XDS
Thank you to all!
@Frederic
I have a problem with the following sentence:
if I collect all spots I get good map, but it is impossible to solve the
structure by molecular replacement - if you have a good map (I assume
electron density map) then the structure is solved... for me a good map
the space group is I422 do you have any other suggestion?
Yes, how certain are you of the space group? For myself, I'm never
entirely certain of the space group until I have solved the structure...
I always keep in mind the other possibilities for space group
assignment, if need be. And
Dear Marco,
in terms of using XDS, STRONG_PIXEL=99 is _highly_ non-standard (I
personally try to stick with the defaults ... although at synchrotrons I
do use STRONG_PIXEL=6 instead of the default of 3). I realize this is
just a way to pick the strong reflection for indexing (since
Dear all,
I have a particular problem...
so, I have a beautiful crystal with nice diffraction pattern at 2.7A. The
diffraction images are composed by very strong spots and weak spots.
With XDS, if I collect all spots I get good map, but it is impossible to solve
the structure by molecular
Hi,
I have a problem with the following sentence:
if I collect all spots I get good map, but it is impossible to solve
the structure by molecular replacement - if you have a good map (I
assume electron density map) then the structure is solved... for me a
good map is a map I can interpret.
On Sat, 11 Jun 2011, Vellieux Frederic wrote:
If the diffraction pattern originates from 2 crystals (in different
orientations, a case I've had with one large crystal plus a satellite
crystal attached to it in the same loop), it is in principle possible to
snip
crystal. I don't think such a
Hi
I'd just process it in iMosflm, and run the Quickscale task after integration.
With almost no effort you should get a rapid visual indicator (in the graphs
produced by Scala) of the discontinuities between the wedges.
If the discontinuities are too big, then you might encounter some items
On 03/31/11 18:08, Patrick Loll wrote:
We've just collected a number of inverse beam data sets. It turns out the
crystals showed little radiation damage, so we have a lot of data: 2 x 360 deg
for each crystal, broken up into 30 deg wedges. The collection order went like
this: 0-30 deg,
We've just collected a number of inverse beam data sets. It turns out the
crystals showed little radiation damage, so we have a lot of data: 2 x 360 deg
for each crystal, broken up into 30 deg wedges. The collection order went like
this: 0-30 deg, 180-210, 30-60, 210-240, etc.
Now, assuming no
Pat,
at least give it a try with the one sweep approach.
We have collected plenty of 360deg data sets on a Rigaku system which requires
two omega sweeps at phi 0 and 180 deg. These data sets are for in-house
phasing. We haven't seen big issues with running XDS over these images as one
Dear ccp4bb,
I am quite a fan of XDS and have just upgraded to the latest version.
Normally, to assess the quality of my data, I look at the tables in
CORRECT.LP and especially the table SUBSET OF INTENSITY DATA WITH
SIGNAL/NOISE = 0.0 AS FUNCTION OF RESOLUTION.
However in my latest run
Dear Simon,
I don't know how to change the output written to the log-file (maybe with the
TEST-card), but I wonder why you don't want to look at all of your data but only
those with I/sigI 0? XDS reports all reflections with I/sigI -3 for a good
reason.
Cheers, Tim
On Tue, Feb 08, 2011 at
Hi Tim,
could you write a bit more about this cutoff. I've been using the 0 cutoff for
the longest time as it seemed to be much more stringent to report.
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria
Hello Juergen,
since sigma is always positive, a negative I/sigI means that the measured
intensity is negative, hence I would refer you to the truncate reference
On the treatment of negative intensity observations by S. French and K.
Wilson, Acta Cryst (1978) A34, 517-525.
Why exactly -3 is
Hi,
I've pasted below the reasons from Dan Gewirth and the HKL2000 manual
authors for having a -3 sigma cutoff... I'll add briefly that if you
assume the weak data has a Gaussian distribution around zero a -3
sigma cutoff allows you to record ~99.8% of the data.
-bob
SIGMA CUTOFF
Cutoff for
Hi,
oh, I'm also surprised people seem to use something else than '-3' as the
cutoff, i.e. are throwing away data. This, obviously, brings into new light all
the discussions (which I definitely don't wish to restart) on the 'cutoff
values' in R(sym) and I/sI which you use to determine the
Hi Simon,
I've put my answer into the XDSwiki article FAQ
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/FAQ#why_do_the_latest_XDS.2FXSCALE_versions_only_give_a_single_table.2C_with_I.2Fsigma.3E.3D-3_cutoff.3F
because I was asked this privately a couple of times, after this was
On Tue, Feb 8, 2011 at 7:17 AM, Simon Kolstoe s.kols...@ucl.ac.uk wrote:
XDS [...] signal/noise = -3.0.
i'd be interested to know if there is an equivalent in scala...
perhaps 'REJECT 6 ALL -8'
-Bryan
No cutoffs in Scala
Phil
On 8 Feb 2011, at 20:13, Kay Diederichs wrote:
Hi Simon,
I've put my answer into the XDSwiki article FAQ
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