Hi,
The intensity-based likelihood refinement target was in our paper in 1996
(http://www-structmed.cimr.cam.ac.uk/Personal/randy/pubs/li0224r.pdf). It's
perfectly happy with negative net intensities. Basically, the question you're
asking with a negative net intensity is what is the
RoadE-mail:
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk
On 20 Jun 2013, at 22:18, Douglas Theobald dtheob...@brandeis.edu wrote:
On Jun 20, 2013, at 4:36 PM, Randy Read rj
this feature extremely useful?
Best wishes,
Randy Read
On 2 Jul 2013, at 18:41, Petr Leiman petr.lei...@epfl.ch wrote:
I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not
output columns with HL coefficients. I cannot find a combination of
buttons in CCP4i GUI to enable
(corresponding to the LLG after placing
the second component.
I hope that helps! There's also an explanation on our Phaser Wiki:
http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Annotation,
which gets into some even more obscure aspects of this annotation line.
Randy Read
, and I am sorry for not making it clear at the begining.
Thank you so much!
Sincerely,
Chen
On Wed, Jul 31, 2013 at 6:35 AM, Randy Read rj...@cam.ac.uk wrote:
Dear Chen,
For each component that is placed, Phaser reports the Z-scores for the
rotation function (RFZ) and translation
Hi Alice,
I've got an LG DM2352D-PZ passive stereo monitor, which seems to be comparable
to the Zalman and works under the Zalman setting in coot and ccp4mg on my Mac.
I've been happy with it, at least since I worked out some video settings (very
different from the defaults) that made it
Hi Frank,
How long of an incubation period between structure, insight and application are
you willing to accept? Here are a few possibilities, leaning towards longer
incubation times.
1. Structure of DNA - necessary for understanding of replication, translation,
sequencing, etc: contributed
much luck -- probably I've been doing something wrong!
The next time I have a problem like this, I'll have to try Situs colores, which
I hadn't heard about until this discussion.
Best wishes,
Randy Read
On 19 Sep 2013, at 16:03, Pete Meyer pame...@mcw.edu wrote:
Another vote for Situs colores
) and then use either pointless or
xtriage to see if those Fcalcs obey higher symmetry. Another good approach is
to use the zanuda program in the CCP4 suite, which is designed to answer
questions about pseudosymmetry and other related problems.
Good luck!
Randy Read
-
Randy J. Read
Hi Eleanor,
Yes, the initial LLG scores in Phaser are highly dependent on the assigned
sequence identity, which is translated into an initial estimate of the
effective RMSD of the model. However, the latest versions of Phaser refine the
RMSD estimate at the end of the job and, assuming that
sometime in
the new year once they're confident that it is stable.
The motivation is exactly as you say: to save time for both the depositors and
the annotators, and to improve the quality of the deposited structures!
Best wishes,
Randy Read
On 31 Oct 2013, at 15:25, Debasish Chattopadhyay debas
in one search, Phaser should have accounted
for the tNCS implied by the Patterson peak.
Best wishes,
Randy Read
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building
Chain Here,
and then it just moves the original copy of that chain to the new symmetry
position. Once you've adjusted all the chains to what you want, you just save
the model. No more need for emacs or grep or even vi!
Regards,
Randy Read
On 21 Nov 2013, at 18:24, Phil Jeffrey pjeff
for in the same job by clicking the Add
another search button.
I hope that answers the question you were asking!
Best wishes,
Randy Read
On 2 Dec 2013, at 04:11, Prem Prakash prem...@gmail.com wrote:
Dear All,
The density obtained after molecular replacement using phaser at 2.5 Angstrom
Hi Fred,
Send me the logfiles (off-line), because this shouldn't be happening and I'd
like to have a look. That said, we've been seeing some similar problems in
certain circumstances, i.e. B-factor refinement refines to significant negative
B-factor values, and data at high resolution have
/index.php/Molecular_Replacement#Annotation.
Best wishes,
Randy Read
On 5 Dec 2013, at 08:36, vellieux frederic.velli...@ibs.fr wrote:
Hiyya all,
I have a question about the latest Phaser output, concerning TFZ = and TFZ ==
.
I do not know how to interpret outputs of the type
TFZ = 5.2
like:
PURGE ROT ENABLE ON
PURGE ROT PERCENT 50.0
I've just tested and this works for me. Let me know if you're still having
trouble with this.
Best wishes,
Randy Read
On 5 Dec 2013, at 10:11, LISA science...@gmail.com wrote:
hi all,
I try to solve the crystal structures of a mult
files where they were still mentioned,
but the documentation has just now been updated.
Best wishes,
Randy Read
On 9 Dec 2013, at 09:20, Rojan Shrestha ro...@riken.jp wrote:
Hello,
Can somebody tell me how the Phaser degenerate function can be used with
MR_BTF?
My script is as follows
separated by the
same translation). If there's higher order tNCS, then this works less well in
the current version. We give some examples in the paper describing the
algorithm: http://journals.iucr.org/d/issues/2013/02/00/dz5268/dz5268.pdf.
Best wishes,
Randy Read
On 29 Jan 2014, at 13:30
option to find sites or run HySS
separately and provide the substructure PDB file to the pipeline.
Thanks for reporting the problem!
Best wishes,
Randy Read
On 29 Jan 2014, at 17:33, Roger Rowlett rrowl...@colgate.edu wrote:
Is there a scripting error in
ccp4-6.4.0/share/ccp4i/scripts
Hi,
Another example is the Shiga-like toxin B-subunit pentamer (i.e. the
cell-surface binding component of this A-B toxin), which binds 3 Gb3
trisaccharides per monomer:
http://pdbe.org/1bos
http://www.ncbi.nlm.nih.gov/pubmed/9485303
Best wishes,
Randy Read
On 4 Mar 2014, at 10:41, Derek
by ccp4i and the
commands expected by the installed executable, for any CCP4 program, this would
be a good place to look.
Best wishes,
Randy Read
On 21 Apr 2014, at 00:19, Edward A. Berry ber...@upstate.edu wrote:
I seem to have a version incompatibility between phaser 2.5.6
and the current ccp4
if something doesn’t work as expected.
Best wishes,
Randy Read
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road
of the model, and possibly
the quality of the model for the target protein.
Best wishes,
Randy Read
On 16 May 2014, at 16:03, Niu Tou niutou2...@gmail.com wrote:
Dear All,
Recently we collected some data of a MBP fusion protein, at around 4A
resolution. The protein itself is about half of the MBP
programs
easier to use.
Best wishes,
Randy Read
On 20 May 2014, at 14:52, Edward A. Berry ber...@upstate.edu wrote:
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
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
and translated. If you look at that file,
you’ll see that it doesn’t contain the ENSEMBLE definitions, so those still
have to be provided in the script that refers to the .sol file.
Best wishes,
Randy Read
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute
experimental phasing.
Best wishes,
Randy Read
On 12 Jun 2014, at 20:14, Appu kumar appu.kum...@gmail.com wrote:
Hello All,
I have tried MR in Phaser, MRage, Molrep , Mrbump but i am
not getting the true solution which it supposed to be. Although the resoution
of data
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 rrowl
in a similar way.
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631636/)
Some indication of completeness probably would be a good thing to include in
the validation reports.
Best wishes,
Randy Read
On 10 Jul 2014, at 20:26, Katherine Sippel katherine.sip...@gmail.com wrote:
Hi all,
I've
Hi Paul,
What you might be remembering is the following paragraph from our Validation
Task Force report:
The Cambridge Crystallographic Data Centre (CCDC) has recently entered into
collaboration with the wwPDB partners. As part of the agreement, wwPDB will
have access to Mogul, which will be
map. If so, then you
should try Molrep from the current CCP4 or a newer version of Phaser (recent
Phenix release, or upcoming CCP4 release).
Regards,
Randy Read
On 19 Apr 2012, at 07:20, LISA wrote:
Hi all,
I am trying to solve one structure by molecular replacement with phaser in
CCP4
, Michael Rossmann wrote a program years ago that will extract
coordinates from a stereo pair, and I'm sure one could do much better with
multiple images.
Regards,
Randy Read
On 19 Apr 2012, at 15:09, Antony Oliver wrote:
This subject raised (and keeps raising) its head above the parapet not all
where the identical side chains are left
intact, and other residues are trimmed at most to the gamma atom.
We're always interested in feedback, so if there are still cases where Phaser
rejects good solutions we'd like to hear about them!
Regards,
Randy Read
On 1 May 2012, at 00:18, Ho Leung Ng
of the
estimated RMSD at the end of the automated search, so the negative LLG should
become positive or, at worst, zero.
Best wishes,
Randy Read
On 19 Jun 2012, at 09:43, LISA wrote:
Hi all,
does anyone solve their structure by molecular replacement with phaser with
LLG 0?
Thanks
lisa
molecules that look
better in density than others.
Best wishes,
Randy Read
On 31 Jul 2012, at 13:11, Qixu Cai wrote:
It's a P212121 dataset. I have used phaser to find four solution in ASU.
This is the phaser log file:
PEUDO
, and
this works for me.
Good luck!
Randy Read
=
On 15 Aug 2012, at 10:07, Eleanor Dodson wrote:
The ensemble should be a set of coordinates
Eleanor
On 15 Aug 2012, at 04:42, 李华 wrote:
Dear ccp4er,
I try to use Phaser MR to solve a structure. A mtz file from oasis was
used as a ensemble
prematurely, but now
waits until the choice is unambiguous), so there shouldn't be a real incentive
to submitting separate jobs for the possible space groups.
Thanks for reporting it, and sorry for the trouble!
Randy Read
On 20 Aug 2012, at 16:06, Jan Abendroth wrote:
Hi all,
we have been
. One way to do this
manually is to check whether the Fcalcs from the MR solution have higher
symmetry, but I think the Zanuda server is doing that kind of thing
automatically.
Best wishes,
Randy Read
Begin forwarded message:
From: Randy Read rj...@cam.ac.uk
Date: 7 September 2012 09:10:19
latest version of Phaser is a bit more clever. One side effect is
that Se-Met residues were left out of the models, but now Phaser recognises the
codes of some modified amino acids and carries them along.
Best wishes,
Randy Read
On 2 Oct 2012, at 15:32, Koji Yonekura wrote:
Hi all,
I am
replacement search? Or are they temporarily put aside and them
simply added to the PDB in frame with the molecular replacement solution (but
are not part of the weighted structure factors output in the final mtz)?
F
On Oct 2, 2012, at 7:55 AM, Randy Read rj...@cam.ac.uk wrote
As much fun as it is to bash Nature, Science and Cell, the evidence that they
publish poorer quality structures doesn't actually hold up well. Gerard
Kleywegt (cited below) and I tried to use that supposition as the basis of a
positive control for our case-controlled validation paper in Acta
Dear Karolina,
We had one nice example where the protein could easily be concentrated to about
50mg/mL without crystallising, at which point we realised that it would be a
good project for collaborating with our NMR colleagues, i.e. the RING domain of
the Kaposi's sarcoma-associated
Actually, the symmetry relating these solutions is a 2-fold around the y-axis,
which is not a crystallographic operator in P41. So either this is a twinned
crystal, and the two solutions relate to the two twin components, or the true
symmetry is higher.
What is special about the solutions
is twinned, then it's probably P41
with the twinning increasing the apparent symmetry of the data. But it's
important to look at all the evidence, not just the Rfree after refinement,
especially as the application of a twin target always lowers Rfree.
Best wishes,
Randy Read
-
Randy J
this, there's always a potential issue with twinning. I'd be
interested in seeing the logfile (off-list) for the Phaser run, which should
give an indication of whether the intensity moments suggest twinning, once the
statistical effect of tNCS has been accounted for.
Best wishes,
Randy Read
Hi,
The only tool I'm aware of is Tom Terwiliger's phenix.find_ncs_from_density,
the operators from which can be passed onto his phenix.ncs_average program.
Most programs expect you to have heavy atom sites or protein models from which
the NCS can be deduced.
Regards,
Randy
-
Randy J.
papers are retracted. As
Zhijie noticed, the paper describing 2HR0 still hasn't been retracted, along
with a number of other relevant papers.
Best wishes
Randy Read
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223
on using electron density as a
model! Before Kevin's nice cmapcut program (and Tom Terwilliger's equally nice
phenix.cut_out_density procedure) it was a laborious process that required a
very long explanation.
Best wishes,
Randy Read
On 17 Jan 2013, at 03:20, Wei Feng wrote:
Dear all,
When
Hi,
The definition of new fold at the PDB depends on how it is categorised in
SCOP version 1.75, which was released in June 2009. Once the SCOP database is
updated again, we'll see how many new folds were really represented by PDB
entries deposited in the last few years.
Randy
-
Randy
group. It's worth a
try, especially if the MR attempts in P6222 gave a reasonable peak for the
rotation search.
Best wishes,
Randy Read
On 22 Jan 2013, at 06:25, LISA wrote:
Hi all,
Does anyone know how to check a data is twin and how to detwin?
My data is 3.3 A with space group P6222
, and their standard deviations.
Best wishes,
Randy Read
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road
to select them. To get
the reflections with greater than average intensity, you could use something
like this:
sftools
read NCSanalysis.mtz
select column NcsEps 1
write bigeps.mtz
stop
yes
I hope that helps!
Randy Read
-
Randy J. Read
Department of Haematology, University
. For cases with very small cells and limited resolution, I've
sometimes wondered if we could put some of the cross-validation data back into
the working set, after the model has become sufficiently good, but I've never
really tested this idea.
Regards,
Randy Read
On 26 Mar 2013, at 11:54, Ed
if there are any hints of
other explanations in the output.
Best wishes,
Randy Read
On 27 Mar 2013, at 08:32, Rojan Shrestha ro...@riken.jp wrote:
Hello,
I am trying phasing using homology models with Phaser. We obtained very high
TFZ scores with many clashes. The number of clashes are around
There are two positions available for people to join the team developing
Phaser, funded by the NIH grant that supports the development of the Phenix
package. (Of course, the same version of Phaser goes into CCP4 as well!)
If you're interested, please look at
-validated
sigmaA estimation. Later on, when the model is better, you could
afford to absorb some of those reflections into the working set.
Now, what are the chances that such a procedure would pass through the
refereeing system without raising any eyebrows?
Randy Read
On 17 Jun 2008
mean-square displacement of 1A^2 has a B-
factor of about 26A^2 (8*Pi^2/3).
Regards,
Randy Read
On 11 Dec 2008, at 09:39, Eleanor Dodson wrote:
A small molecule crystallography text would give you the
formulation for an ideal case.
A rough guide is that a B factor of 80 is equivalent
Strange ... I just updated to OS 10.5.6, and fully expected to have to
reinstall X11 yet again, but I still have 2.3.1 on my machine after
the update. Odd that it should be inconsistent from one machine to
another.
Randy Read
On 17 Dec 2008, at 22:54, William G. Scott wrote:
Please, we
for stimulating the discussion about this point!
Regards,
Randy Read
On 8 Jan 2009, at 11:43, Ian Tickle wrote:
All - I didn't get a single response to my posting last week
(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0812L=CCP4BBT=0O=D
X=512817322E87355F7FY=i.tickle%40astex
possible to explain why you're not getting one?
Thanks.
Randy Read
On 9 Feb 2009, at 23:52, Allyn Schoeffler wrote:
Hello all,
We've recently installed the newest version of PHASER, and when I do a
brute rotation function, I don't get an .rlist file output even
though the
job completes
) is more sensitive and
convincingly finds more sites than an anomalous difference Fourier
(which is not iterative).
There's a tutorial on our web page with real (albeit lysozyme) data
illustrating how this works.
Regards,
Randy Read
On 31 Mar 2009, at 18:17, Ethan Merritt wrote:
On Tuesday
the transition
state barrier going in one direction but not the other.
Regards,
Randy Read
On 18 May 2010, at 08:31, Vinson LIANG wrote:
Dear all,
Sorry for this silly biochemistory question. Thing is that I have a
reversible epimerase and I want to mutate it into an inreversible one.
However, I
programs to determine SigmaA values from
cross-validation data), it would probably behave better, but I suspect
something more basic is going wrong.
Regards,
Randy Read
On 4 Jun 2010, at 11:09, Ian Tickle wrote:
On Fri, Jun 4, 2010 at 2:28 AM, zhan...@umbc.edu wrote:
I was using ccp4-6.0.2. I
Forgot to also post this response to the BB.
Randy
Begin forwarded message:
From: Randy Read rj...@cam.ac.uk
Date: 25 June 2010 12:59:12 GMT+01:00
To: Yong Y Wang wang_yon...@lilly.com
Subject: Re: [ccp4bb] error in running Phaser NMA mode
Dear Yong,
Sorry about that! I suspect
Hi Eleanor,
I hate to disagree with you, even partially, but it depends on whether or not
you're doing phase combination with external phases. In the usual case with
just model information, SIGMAA doesn't take the absolute value of 2mFo-DFc so
it can be positive or negative and goes with the
assumption
about the protein having a certain partial specific volume.
Nonetheless, Phaser (and probably other programs) also reports the solvent
content in the cell content analysis step, so you're free to choose the one you
prefer.
Regards,
Randy Read
On 18 Sep 2010, at 19:52, Tim Gruene
that, I would suspect some sort of pseudosymmetry problem, or some
other pathology with the data.
Best wishes,
Randy Read
On 29 Nov 2010, at 13:16, xiuwen zhang wrote:
Dear colleages,
Currently I met problem in a MR case and hope somebody could advise me.
The crystals belong to sg
Hi,
There are a number of possibilities that come to mind:
1. Use the ROTATE AROUND option of the brute-force rotation function in
Phaser to generate a set of rotation angles similar to your real-space
solution, then use each of these for a full translation search.
2. Use my old program
Hi Eleanor,
A bit more context about what Phaser was doing at the time might help... As a
first guess, it looks like there was an odd character in a text file (PDB
file?). Do you have a PDB file with funny line terminators or something like
that?
Regards,
Randy
On 17 Jan 2011, at 11:50,
comes down to questions
of how much information you have, which you can think about in terms of how
distinctive the shape is at your resolution or even how many reflections you
have.
Best wishes,
Randy Read
On 20 Jan 2011, at 13:35, Simon Kolstoe wrote:
Dear CCP4bb,
I've just started on a new
or a pure 2-fold
(as Eleanor discussed) is more likely to be the problem.
Regards,
Randy Read
On 9 Feb 2011, at 22:08, Jon Schuermann wrote:
Just to add to Phil and Eleanor's response...
I would NOT use Phaser for MR with PTS present. It doesn't handle it
correctly yet, since the likelihood
you look at a map. The fact that you can
define the target in terms of E-values means that, if your model and data are
both good, the likelihood target can be thought of as sharpening the data
anyway.
Best wishes,
Randy Read
On 28 Feb 2011, at 09:02, Dirk Kostrewa wrote:
Dear CCP4ers,
I
Judging from some examples in the literature, if there's no density for the
ligand, you publish in Nature!
On 31 Mar 2011, at 14:32, Huanwang Yang wrote:
If a part of sequence has no density, this part will be cut from coordinates.
If the side chain of a residue is lack of density, the
derivatives.
Regards,
Randy Read
On 13 Jul 2011, at 02:08, Jiamu Du wrote:
Dear All,
I am now working on a low resolution phase determination (around 3.3 A with
Se anomalous signal around 3.8 A).
I can find the Se site and get the phase, but the density map is not so good.
Some part
Hi,
Although it's pretty much true that if TFZ8, the solution is correct, there
are hard cases where a correct solution has a significantly lower TFZ score.
Also, we've been finding that TFZ scores are generally lower for monoclinic
space groups like P21, at least in the search for the first
entry (3o8k) is still present, but perhaps it will become
obsolete later.
Regards,
Randy Read
On 10 Aug 2011, at 22:01, David Schuller wrote:
Time to fuel up the gossip engines for the approaching weekend:
http://www.sciencedirect.com/science/article/pii/S096921260800186X
RETRACTED
Hi Eleanor,
Depends on what makes them rogues. If, say, they have very large amplitudes
then you could do something like:
sftools
read rogue.mtz
select col 1 1
write norogue.mtz
end
Or if it's easier to select just the rogue reflections by some combination of
select commands, you can do
Hi Amir,
When this error was reported before, it turned out that the sequence file used
to define the composition had the one-letter code Z (presumably for Se-Met),
which Phaser-2.1.4 doesn't recognise. I'm not sure what the newer versions in
CCP4 and Phenix would do with this, but at the
Hi,
Could you send me some representative logfiles (probably off-list)? This might
give a hint. It must be something unusual, because we have a fairly wide range
of test cases and none of them have any problems.
Thanks and best wishes,
Randy Read
On 1 Sep 2011, at 14:58, alexander.schif
in the ccp4i GUI). In this situation you
don't want to look for S or Cl atoms as such, because the real part of their
scattering is already accounted for well in the protein model.
Best wishes,
Randy Read
On 1 Sep 2011, at 23:29, Jacob Keller wrote:
Update:
I tried more anomalous maps
from a mono application (and I confess that I
don't really know yet what that means). Once the problem he ran into has been
defined a bit better, we can look into whether it's something we can fix on our
end.
Regards,
Randy Read
On 6 Sep 2011, at 08:25, Petr Leiman wrote:
Dear Randy
If the model is really bad and sigmaA is estimated properly, then sigmaA will
be close to zero so that D (sigmaA times a scale factor) will be close to zero.
So in the limit of a completely useless model, the two methods of map
calculation converge.
Regards,
Randy Read
On 11 Oct 2011, at 19
is that, with a long helix, there will be many nearly-correct
solutions offset by partial turns. So the sequence register could be wrong.
Good luck!
Randy Read
On 17 Oct 2011, at 18:09, Napoleão Valadares wrote:
Hi there!
I got crystals from some synthetic peptides I bought, they are 30
.
We do pretty exhaustive tests, but they don't include compiling on one
architecture and testing on another, so if everyone had suffered in silence we
would never have been aware of this problem! So we (and, I'm sure, other
developers) really do appreciate bug reports.
Best wishes,
Randy Read
Hi Eleanor,
I think you should find it in the Additional Parameters section, second line,
labelled Packing criterion. The default (chosen largely because you had been
asking for something like this!) is to allow a number of clashes equal to 5% of
the number of residues.
Let me know if it
simultaneous separate
jobs!
Regards,
Randy Read
On 9 Nov 2011, at 07:21, Ed Pozharski wrote:
See page 3 of this
http://www-structmed.cimr.cam.ac.uk/phaser/ccp4-sw2011.pdf
On Wed, 2011-11-09 at 09:22 +0900, Francois Berenger wrote:
Hello,
How faster is the OpenMP version of Phaser
crash any more,
but unfortunately, it didn't solve the structure either.
The bug is fixed now for future versions of Phaser.
Best wishes,
Randy Read
On 29 Nov 2011, at 10:11, Sita Ram Meena wrote:
Hi CCP4 community.
While running the Phaser in the CCP4 GUI, It was terminated and giving
I just realised that my reply on this issue only went to Arko, and not to the
BB. I think that the problem was because of an internally out-of-synch CCP4
installation that was made available for Windows for some time. Here's my
reply, which makes a similar point to David's.
=
As Tim
at 8:40 PM, Randy Read rj...@cam.ac.uk wrote:
I just realised that my reply on this issue only went to Arko, and not to the
BB. I think that the problem was because of an internally out-of-synch CCP4
installation that was made available for Windows for some time. Here's my
reply, which makes
Just one thing to add to that very detailed response from Ian.
We've tended to use a slightly different approach to determining a sensible
resolution cutoff, where we judge whether there's useful information in the
highest resolution data by whether it agrees with calculated structure factors
relevant papers from Brunger's group)
Best wishes,
Randy Read
On 30 Jan 2012, at 07:09, arka chakraborty wrote:
Hi all,
In the context of the above going discussion can anybody post links for a few
relevant articles?
Thanks in advance,
ARKO
On Mon, Jan 30, 2012 at 3:05 AM, Randy
has not become
standard best practice in the 14 years since it was published?
phx
On 30/01/2012 09:40, Randy Read wrote:
Hi,
Here are a couple of links on the idea of judging resolution by a type of
cross-validation with data not used in refinement:
Ling et al, 1998: http
,
Randy Read
On 2 Feb 2012, at 16:43, Brennan Bonnet wrote:
Hi all,
I have a strange result using Phenix's AutoSol to look for xenon sites in
lysozyme.
For a few months now I have been trying to produce xenon derivatives of
lysozyme using pressures in the range of 50-350psi and time ranges
an improper rotation.
On the other hand, if you combine a crystallographic symmetry operator with
that transformation, you might still find that it's equivalent to a proper
rotation.
Regards,
Randy Read
On 21 Feb 2012, at 13:47, Francis E Reyes wrote:
Hi all
This structure has
parallel to the axis.
Regards,
Randy
decomp.f
Description: Binary data
On 21 Feb 2012, at 14:01, Randy Read wrote:
Hi,
I'm sure there's a way to do this in CCP4, but using some little jiffy
programs I've collected over the years...
That's a 133 degree rotation around an axis defined
Hi,
Just one correction to this. Phaser doesn't substitute values with the same
name in an output MTZ file. To get the anisotropy corrected F and SIGF values,
you have to run phaser in the separate anisotropy correction mode, and even
then it appends the string _ISO to the column names and
to say
that all the refinement programs that handle twinning will do this
appropriately.
Regards,
Randy Read
On 2 Mar 2012, at 08:01, arka chakraborty wrote:
Hi all,
I will like to know, as a follow up of what Prof. Randy Read said, what
should be done to do the refinement against
website (and getting ccp4i to interpret the command phaser as
phenix.phaser).
Best wishes,
Randy Read
On 12 Mar 2012, at 16:06, Anastassis Perrakis wrote:
Hi -
I agree with Garib that its likely a pseudo-translation issue.
I also agree with that the advice he gives is correct
translation and reindex in a smaller cell, throwing away the weak half
of the data, but I think the y-component of your translation is too far from
zero for that to be a reasonable alternative.
Best wishes,
Randy Read
On 13 Mar 2012, at 09:21, vincent Chaptal wrote:
Dear ccp4,
I have a case
1 - 100 of 212 matches
Mail list logo
