However you decide to argue the point, you must consider _all_ the observations
of a reflection (replicates and symmetry related) together when you infer Itrue
or F etc, otherwise you will bias the result even more. Thus you cannot
(easily) do it during integration
Phil
Sent from my iPad
Scale constant in Aimless or Scala should do it. I should probably make that
automatic.
I should probably also add a CIF reader to Pointless. Is there a good (easy)
C++ one out there?
Phil
Sent from my iPad
On 12 Feb 2013, at 08:08, Jens Kaiser kai...@caltech.edu wrote:
Ethan,
The last
Ah I'm not sure about that. It may be possible to tell ctruncate not to do
this. Actually if you started with Fs you don't want to truncate the data.
Maybe use old truncate with the notruncate option
Phil
Sent from my iPad
On 12 Feb 2013, at 18:48, Ethan Merritt merr...@u.washington.edu wrote
Aimless can output scaled but unmerged data
OUTPUT UNMERGED
Or from ccp4i
Phil
Sent from my iPad
On 12 Aug 2014, at 19:32, Kay Diederichs kay.diederi...@uni-konstanz.de
wrote:
Hi Mike,
this requires scaled but unmerged data, and there are few programs that
support unmerged MTZ files
AIMLESS.MTZ with the output file from Aimless (called
“aimless_???.mtz in the iMosflm QuickScale option).
I don’t know how the Scalepack format deals with reflections that strong -
that’s one for Phil Evans to address, maybe with help from ZO or Wladek.
The immediate way round the problem might
Yes. With the caveat that ISYM refers to the symmetry operators in the order
they are stored in the MTZ file
Phil
Sent from my iPhone
> On 22 Jun 2017, at 17:04, wtempel <wtem...@gmail.com> wrote:
>
> Hello all,
>
> Are the following statements regarding AIMLESS unmerge
Aimless
Phil
Sent from my iPhone
> On 23 Jun 2017, at 18:46, wtempel <wtem...@gmail.com> wrote:
>
> Hello Phil,
> the order of reflections, or the order of operators? How would I reproduce
> "Orig." H K L, as VIEWHKL appears to do?
> Thank you.
> Wolfram
followed by (h' k' l') measured. I think the M/ISYM was
> introduced to save file space but it is kind of redundant now! and a bit
> flawed, as it depends on assigned symop numbering , Is it time to chang??
> E
>
>
>
>> On 23 June 2017 at 22:18, Phil <p...@mrc-lmb.ca
It’s probably better to combine the MTZ files with Pointless rather than
sortmtz as that will also check the point group
Phil
Sent from my iPhone
> On 20 Oct 2017, at 18:57, Gottfried Palm <p...@uni-greifswald.de> wrote:
>
> Dear all,
> technically, the ccp4bb (espec
MTZ was always 32 bit floats for the main data, with ASCII headers at the end
Sent from my iPhone
> On 13 Nov 2018, at 21:29, Ethan A Merritt wrote:
>
>> On Tuesday, November 13, 2018 1:06:01 PM PST Zhijie Li wrote:
>> Hi Ethan,
>> Thanks for the information. My guess is that in MTZ only
Nomenclature: pure SIR or MIR without anomalous has almost never been used,
since the beginning of macromolecular crystallography (why would you?). So
those of us who are lazy have often used SIR/MIR when we meant SIRAS/MIRAS: we
should be more precise.
Phil
Sent from my iPhone
> On 23
Indeed, centric reflections should have no anomalous signal after merging
Phil
Sent from my iPhone
> On 31 Mar 2020, at 05:48, Kevin Jude wrote:
>
>
> I've had two more helpful responses to this off-list. My crystal is P43212,
> so there are large swaths of centric ref
than Scala in
some cases
Other things to try.
If you have several crystals, one (or more) may just be bad. You can try
scaling them separately, or using the scale constant option just to diagnose
which crystals would be better omitted
Phil
On 10 May 2013, at 16:04, amit sharma amit_sps2
of
anomalous differences (ANOMALOUS MATCH) but all the tests I've done using this
option gave worse results than just merging everything. For this reason I
haven't implemented the option in Aimless.
Phil
On 14 May 2013, at 12:07, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote:
It's not about
the space group by
inspection afterwards
Phil Jeffrey
Princeton
the TRUNCATE YES option in Truncate ?
Does the output MTZ from Scalepack2mtz show the number of reflections
you expect ?
Phil Jeffrey
Princeton
On 7/5/13 3:24 PM, Ursula Schulze-Gahmen wrote:
Sorry for the non-CCP4 question.
I am confused about the sigma cutoff used by HKL2000 for scaling. I
scaled
Scalepack files and ShelX files: these are not normally suitable for
scaling, but may be used for statistical analysis in Aimless with SCALES
CONSTANT or ONLYMERGE options
Combat may be useful for conversion of other file formats not read by
Pointless, but caveat emptor
Phil
In response I felt I had to post the low-tech version (not mine)PhilOn 16 Jul 2013, at 11:57, Edward Lowe edward.l...@bioch.ox.ac.uk wrote:At Elspeth's request, here's a link to a picture of the rack we use fordrying out shipping
)
Using mmCIF as an archive format makes sense, but I doubt it's going to
make building structures any easier except for particularly large
structures where some extended-PDB format might work just as well or better.
Phil Jeffrey
Princeton
On 8/5/13 9:53 AM, Pavel Afonine wrote:
Editing
I hope that some [X]Emacs expert can rewrite Charlie Bond's wonderful pdb-mode
to work with mmCIF files (or at least the coordinate bits)
… for exactly the reasons Phil Jeffrey points out
Phil
On 8 Aug 2013, at 00:54, Jeffrey, Philip D. pjeff...@princeton.edu wrote:
Nat Echols wrote
.
Phil
://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.8.7.osx10.8static
which may help
Phil
On 12 Aug 2013, at 11:01, Sheena McGowan (Med) sheena.mcgo...@monash.edu
wrote:
Hi
Thanks for that. The latest build of OSX pointless gave us the same error
(dyld: Symbol not found: __ZNSt11range_errorD1Ev
multiplicity = 1.0?
On 14 Aug 2013, at 15:59, Yafang Chen yafangche...@gmail.com wrote:
Dear All,
I recently processed a dataset, in which I/sigmaI of the last shell is 2.3,
while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0?
The completeness is 100 (100). Thank
The question you should ask yourself is why would omitting data improve my
model?
Phil
On 27 Aug 2013, at 02:49, Emily Golden 10417...@student.uwa.edu.au wrote:
Hi All,
I have collected diffraction images to 1 Angstrom resolution to the edge of
the detector and 0.9A to the corner.I
the name CC_IMEAN. It's now called
CC1/2 in Aimless (and Scala) following Kai's excellent suggestion.
Phil
On 28 Aug 2013, at 08:21, Bernhard Rupp hofkristall...@gmail.com wrote:
Based on the simulations I've done the data should be cut at CC1/2 = 0.
Seriously. Problem is figuring out where
Aimless does indeed calculate the point at which CC1/2 falls below 0.5 but I
would not necessarily suggest that as the best cutoff point. Personally I
would also look at I/sigI, anisotropy and completeness, but as I said at that
point I don't think it makes a huge difference
Phil
On 28 Aug
As long as the .sca file is scaled but unmerged, then one way is
pointless -copy scain denzo.sca hklout denzo.mtz
aimless hklin denzo.mtz EOF
scales constant
onlymerge
EOF
Phil
On 18 Sep 2013, at 11:21, Francesco Angelucci francesco.angelu...@uniroma1.it
wrote:
Dear All,
I am wondering
ones
should I expect? And is there a distinction between merged and unmerged data?
confused (easily)
Phil
On 17 Sep 2013, at 15:30, Peter Keller pkel...@globalphasing.com wrote:
Dear all,
At Global Phasing, we have seen that there are still issues with the way that
different applications
quotes if they occur at
both ends of the token will probably fall over somewhere
Phil
On 18 Sep 2013, at 15:41, Peter Keller pkel...@globalphasing.com wrote:
Hi Phil,
I agree that the issue that you raise (about the need to define the data
items and categories propery) is an important one
range) and speed.
A quick comparison (using Pointless)
Read 5.3e6 reflections from a formatted XDS INTEGRATE.HKL file, 608MB, 15 secs
Read equivalent binary MTZ file, 262MB, 2.6 secs
Phil
On 18 Sep 2013, at 15:58, yayahjb yaya...@gmail.com wrote:
Dear Colleagues,
There are two major issues
) may have multiple
indices hkl attached to it, and this doesn't fit neatly into a rectangular
array without padding.
Phil
On 19 Sep 2013, at 12:11, Eugene Krissinel eugene.krissi...@stfc.ac.uk wrote:
Completely agree. Perhaps there could be a distinction between working and
deposition formats
Please explain how you think that cutting back the resolution will improve your
model
Phil
On 10 Oct 2013, at 21:57, Yafang Chen yafangche...@gmail.com wrote:
Hi All,
I have a structure at 2.45A which has been well refined. However, since the
R-merge at the last shell is above 1 (although
of the P21 asymmetric unit if it was really
P212121 and you could overlap the maps corresponding to the different
monomers using those programs.
Phil Jeffrey
Princeton
:
ftp://ftp.rcsb.org/pub/pdb/data/structures/obsolete/XML/js/1jsq.xml.gz
Phil Jeffrey
Princeton
On 10/17/13 10:26 AM, Nat Echols wrote:
On Thu, Oct 17, 2013 at 6:51 AM, Lucas lucasbleic...@gmail.com
mailto:lucasbleic...@gmail.com wrote:
I wonder if there's a list of problematic structures
That won't work. Aimless expects intensities not Fs. I would think you could do
it with sftools
Phil
On 25 Oct 2013, at 09:54, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Rojan,
I would try aimless with the option 'onlymerge'.
Best
I had this problem last week but it seems to have been solved by reinstalling
the ccp4 6.4.0 package today, slightly updated I believe
There was message from Eugene Krissinel which may be relevant to this
Phil
On 28 Oct 2013, at 16:00, Dmitry Rodionov d.rodio...@gmail.com wrote:
Good day
It should be printed at the end of the log file
P.R.Evans and G.N.Murshudov, 'How good are my data and what is the
resolution?' Acta Cryst. D69, 1204-1214 (2013).
Phil
On 8 Nov 2013, at 11:35, Zheng Zhou zhengzho...@gmail.com wrote:
Dear all
I am also looking for aimless reference
Always deprecated, hopefully never common!
On 14 Nov 2013, at 11:27, Mark J van Raaij mjvanra...@cnb.csic.es wrote:
It used to be common to only include reflections for which I x sigma(I) in
refinement, with x often being 3.
However, nowadays this is not considered good practise, as
hope you don't have something like that, but it's possible.
Phil Jeffrey
Princeton
On 11/14/13 5:22 PM, Niu Tou wrote:
Dear All,
I have a strange MR case which do not know how to interpret, I wonder if
any one had similar experiences.
The output model does not fit into the map at all, as shown
AFAICS the .doc files look as if they were auto-generated from the .html files
in 6.3.0. Certainly the only documentation I have written for Pointless and
Aimless is in html
Phil
On 15 Nov 2013, at 14:33, Edward A. Berry ber...@upstate.edu wrote:
(assuming of course the .doc files aren't
I've generally found that adding lines to the standard table works, and they
are not removed by editors
On 19 Nov 2013, at 09:32, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Graeme,
On 11/19/2013 09:02 AM, Graeme Winter wrote:
[...]
that the fourth molecule is not what you think it is, or may be
statistically disordered
Phil Jeffrey
Princeton
On 11/21/13 12:35 PM, Meisam wrote:
Dear CCP4ers
I have a data set that diffracts 1.96 Å. It scales in P21 Space group with 7%
linear Rfactor.
The Mattew coefficient gives 10% probability for 3
I use emacs and/or
grep for this.
Phil Jeffrey
Princeton
11/21/13 1:11 PM, Appu kumar wrote:
Dear All,
I think i have not explained my problem precisely. This
may be weird one but let me elaborate more. I have have a protein
moleculeA, having N-term, and C-term end
,
Phil Bourne
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anton
Meinhart
Sent: Monday, December 09, 2013 8:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Experience with Biomek 2000 liquid-handling system
Dear all,
does anyone have experience
Scala.
I will investigate, but in the meantime you could just copy an old version of
Scala into the updated ccp4 directory (i.e. into $CBIN == CCP4/bin/)
Phil
On 10 Dec 2013, at 04:05, Jens Kaiser kai...@caltech.edu wrote:
Dear developers,
We have been doing the local scaling with scala
the expedient thing and drop an Au in
there with e.g. 0.5 occupancy (or a range of occupancies) and see what
the refinement does.
Phil Jeffrey
Princeton
On 12/10/13 7:44 AM, PriyankMaindola wrote:
dear members
i am trying to solve this crystal structure but
I am puzzled with an
undefined blob
Indeed that is a bug. I've never tried that combination before. I'll fix it
Phil
On 16 Jan 2014, at 20:32, wtempel wtem...@gmail.com wrote:
Hello,
using merged scalepack intensities and a reference MTZ file as inputs, I
would like to prepare an MTZ of scalepack intensities reindexed so
I/sigmaI
On 12 Feb 2014, at 11:43, Cai Qixu caiq...@gmail.com wrote:
Dear all,
Does the I/sigmaI in “Table 1” mean for I/sigmaI or I/sigmaI ?
Thanks for your answer.
Best wishes,
Qixu Cai
the Kd in the injector. That's not exactly
the same situation, but 80x vs 170x suggests the the considerations are
much the same.
Phil Jeffrey
Princeton
On 2/14/14 12:52 PM, Keller, Jacob wrote:
What a nice idea this ITC dilution is--a great example of a wet lab technique
learned en passant
If you assigns them to different datasets in Pointless, then Aimless will give
you the cross-dataset correlations. By default it will scale them to together
first, but you can skip that if you want
It might not scale well to a large number of files (OK up to about 10 I guess)
Phil
On 14 Mar
The polar angles ϕ, ω define the direction of an axis about which a rotation by
angle κ occurs, i.e. a single rotation around a defined axis. This is different
from Eulerian angles which define 3 successive rotations around principal axes
On 27 Mar 2014, at 06:11, Qixu Cai caiq...@gmail.com
Just tested with a clean binary install on a Mac (running 10.8), and it works
for me
Phil
On 8 Apr 2014, at 15:19, Björn Kauppi bjorn.kau...@karobio.se wrote:
Hi
I run latest CCP4 as of today, 6.4.0 update 12 and CCP4i 2.2.1
When trying to run pointless/aimless from the interface
usually the best thing to do to
start with
Phil
On 26 Apr 2014, at 14:38, Faisal Tarique faisaltari...@gmail.com wrote:
Dear Eleanor and Tim.
i have reprocessed the data through imosflm and run the aimless through the
unmerged output mtz..i am attaching the output log file of the
aimless
with the relevant PDB
file(s).
Phil Jeffrey
Princeton
On 5/14/14 1:37 PM, Gloria Borgstahl wrote:
I vote for Z's idea
On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu
mailto:z...@bmb.uga.edu wrote:
Hello All,
Instead of placing the additional burden of policing on the good
I2 and C2 are different settings of the same group. The official IUCr
convention is to use the one which gives the beta angle closer to 90 degrees.
As far as I know all programs should now be able to use the I2 setting, but if
it worries you, you can reindex to C2
Phil
On 21 May 2014, at 17
Surely Refmac or any other program should honour the symmetry operators in the
MTZ file - that's why they are there!
Phil
On 23 May 2014, at 12:34, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
Someone here has seen his Rfactors leap from 18% to 42% and was naturally
distressed!
We
don't know how to make an mtz file with P 2
21 21 /sgn 18, but I will look into it
Phil
On 23 May 2014, at 12:34, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
Someone here has seen his Rfactors leap from 18% to 42% and was naturally
distressed!
We have tracked down the problem
That looks good to me Mean(I/sigma) = 2.0, CC1/2 0.74
See endless discussions on this BB about the uselessness of Rmerge as a
resolution criterion
Phil
On 2 Jun 2014, at 09:27, sreetama das somon_...@yahoo.co.in wrote:
Dear All,
What are reasonable values of Rmerge
(and a few
other conditions, e.g. total fraction). Output from COMBAT may be wrong in this
respect
Phil
On 10 Jun 2014, at 17:23, wtempel wtem...@gmail.com wrote:
Hello all,
suppose I extracted
H K L Intensity sigma[Intensity]
from a file of unmerged intensities, such XDS_ASCII.HKL or scalepack
What version of Aimless are you running? I thought I had fixed that bug
Phil
On 13 Jun 2014, at 11:59, Andreas Förster docandr...@gmail.com wrote:
Dear all,
I'm trying to scale/merge mtz files in ccp4
(Pointless/Aimless/ctruncate/Rfree pipeline) and keep getting an
UNHANDLED EXCEPTION
and probably
consider using NCS to reduce the random deviation between monomers that
actually are identical by symmetry. You may have assigned the
crystallographic 21 down the wrong unit cell axis in that P21 test case.
Phil Jeffrey
Princeton
On 7/11/14 7:33 PM, Chris Fage wrote:
Nat and Misha
map coefficients - so I don't see the benefit of Fc.
The map coefficients, on the other hand, are a checkpoint of the maps
being looked at by the author at the time of deposition and don't
require programs beyond a typical visualization program (i.e. Coot) to view.
Phil Jeffrey
Princeton
On 4/5
Do run the data through Pointless before Scala to check the point group.
Try scales constant just to check that things aren't completely hopeless
Phil
On 6 Apr 2012, at 20:29, Yuri Pompeu wrote:
Hi everyone,
Sorry for the newbie type problems, but I am just starting to use ccp4 for
data
I wouldn't recommend this option
Phil
On 6 Apr 2012, at 21:41, Matthew Chu wrote:
Hi all,
Can someone kindly explain what is that match pairs related by inversion of
indices option doing for handling anomalous data? If I have collected the
inverse beam data, does it mean I have to use
tells us how many
data were used, not their quality nor the quality of the model.
Phil
I've done that in papers
The more fundamental problem is in the end what we want to know are things like
is residue 43 close to residue 146?, which side chains interact with the
ligand? etc etc and resolution is only a very rough guide to the correctness
of such conclusions
Phil
On 9 Apr
or unmerged data (MTZ or Scalepack format, or both)
Phil
On 16 Apr 2012, at 15:42, Jacob Keller wrote:
Where can one find a discussion of the differences between Aimless and Scala?
JPK
On Mon, Apr 16, 2012 at 8:28 AM, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote:
Dear all
We are pleased
Wolfram,
Did you solve these structures independently by molecular replacement ?
It sounds like your two solutions might be related by alternative
origins (0,1/2 along a,c). If you translate the second example along
the a axis by -a/2 does it refine with similar R-factors ?
Phil Jeffrey
Yes
Sent from my iPhone
On 6 May 2012, at 11:21, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
In the crystallography paper table 1, there is Values in parentheses are for
the highest resolution shell. Is this highest resolution shell same as the
OuterShell for the analysis result
Scalepack differs depending on what space group you tell it, since
systematic absences along h00, 0k0 and 00l in P2x2x2x are not written
out. The number of reflections affected is quite small, of course.
Phil Jeffrey
Princeton
On 5/7/12 4:48 PM, Jacob Keller wrote:
Is it true that HKL
SCALA doesn't do anything with the mosaicity, it just reports what was passed
from the integration program.
On 25 May 2012, at 17:12, Ed Pozharski wrote:
I should do more digging, but I hope maybe there is a simple explanation
and someone has seen this before. On some datasets (collected at
program itself inverted the hand due to a bug (this has been know, but not for
a long time)
Phil
On 29 May 2012, at 12:55, Mark J van Raaij wrote:
In different datasets of P321 crystals, when you index them separately, the
hand may be different and you may need to invert it for some
On 29 May 2012, at 15:02, Ian Tickle wrote:
Phil,
On 29 May 2012 14:08, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
NO do NOT invert the hand. If you do you will end up with left-handed
helices etc
Surely not if you take care to also change the signs of the anomalous
differences?
I
a.u. of the
_different_ setting!
Apologies, you are right, for 321 the reindexing operator is (-h,-k,l). But
Pointless will do it correctly (I believe!)
Phil
On 29 May 2012, at 14:29, George Sheldrick wrote:
Which programs require that the data be the 'standard' a.u.? None of mine
require
Phil
On 29 May 2012, at 16:29, Qixu Cai wrote:
Dear all,
thank you for your help.
I think I must describe my case in detail. I collected a native dataset and
two heavy atom derivant datasets （in fact, i don not know whether these two
kind of heavy atom have soked into the crystal, i just
Merritt
We should also encourage people not to confuse the quality of
the data with the quality of the model.
Phil
On 1 Jun 2012, at 18:59, aaleshin wrote:
Please excuse my ignorance, but I cannot understand why Rmerge is unreliable
for estimation of the resolution?
I mean, from
No they were not useless! I used them
(probably better now with cryo data though)
Phil
On 6 Jun 2012, at 16:02, Dyda wrote:
I suspect that pure MIR (without anomalous) was always a fiction. I doubt
that anyone has ever used it. Heavy atoms always give
an anomalous signal
Phil
I
to
be real signal. SCALA allows you the (unrecommended) option to separate I+ and
I- in scaling, but I haven't programmed this in AIMLESS since I have never seen
a case where it would be a good idea.
As far as I know, in CCP4 you only lose I+ and I- if you explicitly remove them.
Phil
On 13 Jun
Personally I'd be happy to share my old datasets if I could find them
Phil
On 3 Jul 2012, at 03:39, Bosch, Juergen wrote:
Dear CCP4 community,
what's the general opinion regarding sharing old published data sets ?
Would you be offended if I asked you for your raw images from say a 5-10 year
to avoid applying things twice.
Thanks
Phil Jeffrey
Princeton
reported by
Scalepack in the log file is I/sigma(I) and not I/sigma(I) for the
shell. The PDB format in REMARK 200 wants the latter.
One of these days one hopes RCSB might include Rmeas in REMARK 200.
Phil Jeffrey
Princeton
On 7/31/12 8:54 AM, Faisal Tarique wrote:
Dear all
i have two basic
programs work perfectly well)
However, Pointless may still be useful to check that you have indexed them
consistently
Phil
On 1 Aug 2012, at 14:36, Harry Powell wrote:
Hi
I'd process (i.e. index, refine, integrate) each data set individually, check
that (at least) they all have the same crystal
prevent
their merging. The program Pointless would sort that out for you.
Phil
On 2 Aug 2012, at 00:45, Edwin Pozharski wrote:
The unit cells is slightly different from each other. For example, one has
a/b/c @ 79/126/83. The other has a/b/c @ 84/127/90. Although they are
collected from
This must be a problem on Windows as it doesn't show up on OSX or Linux, and
this code hasn't changed for a long time, I think
David I guess you will feed this back to me: I don't have any way of testing on
Windows
Anyway, Aimless should be better :-)
Phil
On 4 Aug 2012, at 14:26, David
wouldn't recommend it
Phil
On 16 Aug 2012, at 16:12, Ryan Bauer wrote:
I am working with CCP4 6.1.13 and want to re-process my raw image files to
obtain the multiplicity-weighed Rmeas/Rrim from SCALA. The .x files were
previously processed using HKL3000 at the Advanced Photon Source at Argonne
the angle of rotation is kappa = 160.045deg in this case
On 24 Aug 2012, at 04:33, Appu kumar wrote:
Sir one more help plz i have the following matrix which one shall i use to
calculate the angle.
INFO:: coordinates transformed by orthonal matrix:
| -0.6927, -0.7191,0.0564|
|
constant
exclude sdmin 2.0
sdcorrection fixsdb noadjust norefine both 1.0 0.0
anomalous off
EOF
Corrections, comments or outright repudiation of this script quite
welcome - this was my first attempt.
Phil Jeffrey
Princeton
On 9/4/12 6:14 PM, Michelle Deaton wrote:
I am trying to obtain an Rpim
Hello Jose,
Depending on what data integration program you used, trying XDS may help
you out a little with spot overlap.
Example #3 in my rather out-of-date page:
http://xray0.princeton.edu/~phil/Facility/Guides/MolecularReplacement.html
illustrates how you could find 8 domains, especially
Perhaps it's an artisan organic locavore fruit cake.
Either way, your *crystal* is not vitrified. The solvent in your
crystal might be glassy but your protein better still hold crystalline
order (cf. ice) or you've wasted your time.
Ergo, cryo-cooled is the description to use.
Phil Jeffrey
anyway) will
automatically switch on the Anomalous flag if there appears to be a significant
anomalous signal, unless you explicitly tell it not to (to avoid accidentally
rejecting good anomalous differences as outliers)
Phil
On 5 Dec 2012, at 09:35, Tim Gruene wrote:
-BEGIN PGP SIGNED
not god I don't think I wrote that bit!
Phil
On 5 Dec 2012, at 15:06, Ed Pozharski wrote:
Francois,
I did not realize Phil Evans is god (perhaps a minor one as he did not
yet earn a capital G).
I do concur that insertion code is evil. I had to re-refine an old
antibody structure
It is internally consistent, though not necessarily correct
On 7 Dec 2012, at 16:23, Alan Cheung wrote:
Related to this, I've always wondered what CC1/2 values mean for low
resolution. Not being mathematically inclined, I'm sure this is a naive
question, but i'll ask anyway - what does
The Pointless and the Pointless/Aimless tasks in ccp4i will allow multiple
input MTZ (or XDS) files to be combined and scaled together. The combining is
done in the program Pointless
On 11 Dec 2012, at 03:51, Yuri Pompeu wrote:
Thanks for all the suggestions on and off BB.
I used the GUI
… is 20.12.2012
Happy Christmas everyone!
Phil
You can do much the same with Aimless but I'm not sure about ctruncate. No
access to documentation at present
If the Is came from Fs by squaring them in Pointless then it is important not
to truncate them, just square root them
Phil
Sent from my iPhone
On 12 Feb 2013, at 19:46, Clemens
It's nothing to do with Scala! It's something to do with chaining successive
programs in a task I think. I have seen it happen but I can't remember what the
cause is
Phil
On 8 Mar 2013, at 11:49, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote:
(Is it time to change the macabre title
what happened to all the even l h reflections?
Phil
On 15 Mar 2013, at 15:09, gengxiang zhao gzh...@gmail.com wrote:
Dear CCP4s,
I am looking for more experienced concerns to determine which space group my
crystal is. At present, we take it as P42212 (#94).
HKL is below
the molecular replacement solution
(or, perhaps with it stripped to ALA). While you could use Autobuild,
this is the CCP4 list and so you should use CCP4 programs.
Phil Jeffrey
Princeton
On 3/27/13 12:22 PM, Tom Van den Bergh wrote:
Dear members of ccp4bb,
I need some help with the refinement
that RCSB gives about this field is very weak, which accounts
for the variation.
I'm interested in what ab initio phasing really means, but I've been
too lazy to mine the actual entries for details.
Phil Jeffrey
Princeton
On 4/15/13 9:48 AM, Raji Edayathumangalam wrote:
Hi Folks,
Does anyone know
or Xtriage I
wouldn't suggest that.
A final question is how much disordered structure is missing from your
models ? Could a partly ordered but unmodeled segment be driving up
R-free ?
Cheers
Phil Jeffrey
Princeton
On 4/26/13 5:38 PM, Patrick Loll wrote:
Hi all,
Here is a problem that's been
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