Hi all
We have a job posting closing on Sunday to develop next generation web
based molecular graphics software. For details see the following:
https://jobs.york.ac.uk/vacancy/research-associate-in-software-development-for-structural-biology-475985.html
Regards,
--
Professor Kevin Cowtan
Hi all
We have a position available at York to develop web based tools for
molecular graphics and model building. For details, see this page
<https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885_web_page_id=475985>
.
--
Professor Kevin Cowtan
Email: kev
Kevin Cowtan
Email: kevin.cow...@york.ac.uk
Pronouns: Please use they/them when referring to me in professional
contexts
ORCiD: -0002-0189-1437 <https://orcid.org/-0002-0189-1437>
Disclaimer: http://w <http://www.york.ac.uk/docs/disclaimer/email.htm>
ww.york.ac.uk/doc
ee play mode.
If anyone wants to host any other games (maybe a Minecraft Java server,
Animal Crossing or European-style board games), please feel free to do so
and publicise them here or on the conference forums once they open.
--
Professor Kevin Cowtan
Email: kevin.cow...@york.ac.uk
Prono
Hi all
The problem turned out to be that the user had a space in their username.
Creating a new account solved it.
Regards,
On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan wrote:
> Hi!
>
> I have a student trying to run i2, and a task to import merged data from
> cif which works fine f
011/04/00/ba5158/index.html;>
PDF
$$
--
Professor Kevin Cowtan
Email: kevin.cow...@york.ac.uk
Pronouns: Please use he/him or they/them when referring to me in
professional contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York
send them to me!)Project Description
A PhD position is available to work in the group of Dr Kevin Cowtan on
computational methods for automatic building of protein structures. Both
X-ray crystallography and electron microscopy can give us a picture of the
electron density clouds in a protein
nces are that mine is in the default location, and that machine has
> not had an earlier version of ccp4 installed.
>
> Can you check "set" to see what is set in the environment.
>
> Charles
>
> On 13 Feb 2019, at 11:29, Kevin Cowtan wrote:
>
> Hi! Can anyone ru
pdb
12/02/2019 15:42 u
12/02/2019 15:42 v
12/02/2019 15:42 w
31/08/2018 15:5224 windows_reserved_words.txt
12/02/2019 15:42 x
12/02/2019 15:42 y
12/02/2019 15:42 z
--
Professor Kevin Cowtan
Y
Applications are invited for a postdoctoral research position for up to 18
months to work with Dr Kevin Cowtan on a BBSRC-funded project on novel
methods for refining macromolecular models to explain crystallographic
observations. You will be based within the York Structural Biology
Laboratory
Hi!
I don't know if anyone else is having problems with ccp4i fonts looking
very ugly under Linux, in particular recent versions of Ubuntu? I couldn't
find anything about it online.
Well, if you are, I have the solution.
1. Install at least the xfonts-75dpi or xfonts-100dpi packages
2. Create a
I'm not sure, but I think you'll have to do a 'run and edit command file'
and add the following keyword:
GRID SPACING 2.4 2.4 2.4
Give it a try.
On 14 October 2014 17:31, Steven Chou stevezc...@gmail.com wrote:
Dear All,
I'm trying to generate a mask from a pdb coordinate file using the
in
the control panel.
Kevin
p.s. If you for some reason really have to access the old one, it is still
available here: http://www.ysbl.york.ac.uk/~cowtan/sfapplet-old/sfintro.html
On 29 September 2014 10:15, Kevin Cowtan kevin.cow...@york.ac.uk wrote:
I don't *think* they did that in the old
Hi folks!
Nearly two decades ago I wrote the interactive structure factor tutorial,
to help people understand diffraction beyond the simple explanation of
Bragg's law. As such it has been one of the longest lived interactive
teaching tools on the web.
However time and technology have caught up
Further to Jurgen's comment, in the GUI comit is under 'Map and Mask
Utilities', although if you want to run it in slow mode with refinement
you'll have to use the script.
On 26 August 2014 19:47, dusky dew duskyde...@gmail.com wrote:
Can you people please tell me how to calculate a composite
Can you send me the rest of the logfile?
I think I've seen an error like this where the number of atoms built
dropped to zero, in which case there is something seriously wrong with the
input phases. But I expect there are other ways to trigger a refmac fail -
I can't tell for sure without more
Hi!
Just a list of atoms with type or element set to SE should do it. (Note
that your heavy atom program may not have allocated the atom type).
Having said that, the heavy atom info biases the sequencing to try and get
MET/MSE in the right place, but if the sequence doesn't want to fit it
won't
VACANCY - (SENIOR) POSTDOCTORAL RESEARCHER IN GENE EXPRESSION FOR
STRUCTURAL GLYCOBIOLOGY, University of York, UK
We wish to appoint a postdoctoral researcher to work on the expression of
mammalian genes, for 3-D structural and chemical mechanistic studies, in
the area of eukaryotic glycobiology
VACANCY - SENIOR RESEARCHER IN GENE EXPRESSION FOR STRUCTURAL GLYCOBIOLOGY,
University of York, UK
Applications are invited for a Senior Researcher to play a major role in
establishing mammalian gene expression for 3-D structural and chemical
mechanistic studies in the area of eukaryotic
New version of Nautilus (my nucleic acid building program).
Main changes:
- Now available for both OSX(x86) and Linux.
- It no longer corrupts the residue names of any existing non-nucleic
acid model you feed in.
- Most cases where the output model clashes with itself have been fixed.
-
On 10/05/2011 03:42 PM, Peter Canning wrote:
When I run Parrot to do density improvement and NCS averaging, Parrot
works beautifully (final FOM is 0.87) but NCS averaging causes the
average NCS correlation coefficient to drop (from 0.94 to 0.64) and the
average mask volume to increase from 0.31
On 09/29/2011 03:55 PM, Dima Klenchin wrote:
I have a feeling that the lack of Windows software continues to be
mostly due to the irrational animosity toward it rather than the
platform-specific issues. After all, there seemed to be many developers
who were happy to code for MacOS 7-9 but
Here's an alpha release of my nucleic acid model building program for
the early adopters among you to try out. There's no GUI, there's only a
Linux binary for now, the features are rather limited, and it's only
been tested on synthetic data. On the other hand, it seems to work for me.
Crystal structure of a monomeric retroviral protease solved by protein
folding game players
The paper (Nature SB):
http://www.cs.washington.edu/homes/zoran/NSMBfoldit-2011.pdf
The game:
http://fold.it/portal/
Can you send the command script, and mapdump output for any input maps?
Also, if you are entering a PDB file, the cell, spacegroup, and an idea
of range of X, Y, and Z values?
On 09/06/2011 09:56 AM, Ingo P. Korndoerfer wrote:
hello,
it seems i am recently getting the above error quite a lot
OK, here's the solution (also to BB in case anyone else has this problem).
The PDB file appears to come from CNS.
The coordinate file contains the following atoms:
ATOM 2244 CG LEU A 452.000.000.000 1.00 0.00 A
ATOM 2245 CD1 LEU A 452.000.000.000
Straw poll:
Are you interested in software to autobuild polysaccarides?
Kevin
p.s. I expect I'll have to spend at least a year working on the problem
before before I spell polysaccharide consistently.
If you are trying to make a mask in spacegroup P21, that;s not the way
to do it.
Make the mask in NCSMASK without a symmetry keyword. Then run mapmask to
change the spacegroup to P 21 and use EXPAND OVERLAP to generate the
symmetry copies of the mask.
Hailiang Zhang wrote:
Hi,
I want to
First three numbers are the Euler angles. The next 3 are the
(approximate) centre of mass of the source molecule. The last 3 are the
corresponding point in the target molecule.
(This is a little more complex than the form used in 'dm', but
unfortunately the simpler form was missing important
The skeletonisation option in dm rarely produces any benefit. I wouldn't
use it.
Hailiang Zhang wrote:
Hi all;
It is described by http://www.ccp4.ac.uk/html/dm_skeletonisation.html;
that the skeletonisation has two adjustable parameters (join point
cutoff, and end point cutoff), but the DM
cphasematch will do it in reciprocal space and give you a variety of
statistics, including F- and E-map correlation.
Go to reflection data utilities/phase comparison.
Maher Alayyoubi wrote:
Hi Everybody, I am a new user on the ccp4 bulletin, I have a question on
how to calculate the map
Bryan Lepore wrote:
does cmakereference v0.2 in ccp4 6.1.13 require 'project', 'dataset'
or 'crystal' to be in the .mtz? because i thought by default, these
were eponymous
I'm pretty sure it doesn't.
e.g my .mtz - that has labels F and sigF - :
* Dataset ID, project/crystal/dataset names,
On Mon, Nov 22, 2010 at 10:01 AM, Eleanor Dodson c...@ysbl.york.ac.uk wrote:
It is a program Kevin Cowtan wrote - here is the info you get when you try
to run it..
E
[c...@roo mariaH]$ csymmatch
BFONT COLOR='#FF'!--SUMMARY_BEGIN--
html !-- CCP4 HTML LOGFILE --
hr
pre
You could try:
convert2mtz -hklin my.cv -mtzout my.mtz -cell
30.0,40.0,50.0,90.0,90.0,90.0 -spacegroup 'P 21 21 21'
Marni Williams wrote:
Hey
I have a problem with converting a CNS created file in .cv format to
.mtz for use in CCP4. I suspect it is because the Fortran model and the
Try both and look at the maps. Both are easy to run.
(Which works best seems to vary a lot from case to case.)
Yamei Yu wrote:
Hi all,
To decrease model bias from molecular replacement we can either use
Parrot or prime-and-switch-phasing. What's the difference between these
two programs?
Hailiang Zhang wrote:
If I have the model phase PHIC, exp Fo, and sigmaa-weighted FWT, is that
more reasonable to use Fo/PHIC or FWT/PHIC as the input of CCP4-DM?
You want Fo, sigFo, PHIC and the FOM from sigmaa or refmac.
You might want to try parrot as well. If you feed it your MR model it
zhan...@umbc.edu wrote:
Hi Kevin:
Thanks! Could you explain why the DM (NCS concerned) input should be
Fo/PHIC/WCMB instead of FWT/PHIC? I thought DM is just a real-space phase
improvement method, and the latter (FWT/PHIC) suffers less from model
bias...
No, DM does phase combination in
George M. Sheldrick wrote:
Perhaps I should mention that with the SHELX method of specifying
the space group symmetry using the symmetry operators, alternative
settings, specified in IT or not, cause no problems. But then we
would not have had this thread (or the H3/R3 and P21221 threads).
Florian Schmitzberger wrote:
Dear All,
I am encountering a problem when using Parrot (for combined density
modification and non crystallographic symmetry (NCS) averaging) in ccp4
6.1.13, run via ccp4i.
Parrot does not detect the (2-fold) NCS present among my heavy atom
substructure with 20
Well, CCP4 programs using the core libraries should ignore the
spacegroup symbol and use the operators instead, which bypasses the
whole problem. I would advise anyone using the CCP4 libraries in their
own programs to do the same.
That works for mtz and map, but not for pdb files of course.
Michael Thompson wrote:
Hello All,
I am currently solving a structure at 2A resolution with phases obtained from molecular replacement. Using the MR solution, I began refinement with Refmac using NCS restraints. I am currently building the parts of the model that were left out of the MR search
Maybe your PYTHONPATH isn't set?
echo $PYTHONPATH
should give
/sw/share/xtal/ccp4-6.1.13/share/python/
(This should happen automatically from the setup scripts however)
Alexander Batyuk wrote:
Dear all,
I'm having trouble running buccaneer 1.5 from within ccp4i on mac os x 10.6.4
with
Gerard DVD Kleywegt wrote:
For a five-minute illustrated introduction to PDBprints (including
instructions on how to include them in your own webpages) point your
browser to:
http://pdbe.org/pdbprints
Good idea.
But the icons for published/unpublished, protein
should be able to pick colours which
work for everyone, not just for me.
Flip Hoedemaeker wrote:
Yep, its green-blue vs grey... Bad choice I guess? Perhaps you can
provide a set of examples that work for you?
Flip
On 7/15/2010 13:20, Kevin Cowtan wrote:
Gerard DVD Kleywegt wrote:
For a five
You could feed *both* maps through mapmask with AXIS X Y Z to convert
them to the same axis order.
You may also have a problem with the maps having different XYZLIM
ranges. In that case, using XYZLIM MATCH on the second run of mapmask to
match the second map to the first should fix it.
Buccaneer 1.5 is available from here:
http://www.ysbl.york.ac.uk/~cowtan/buccaneer/buccaneer.html
The new version doesn't have any new model building features, but
incorporates significant new features to automate tidying up of the
resulting model, as follows:
- Model tidying: Chain
Or download the latest refmac 6.6, and it will do NCS fully
automatically, and handle conformational flexibility too.
David Schuller wrote:
I think you should be able to specify two different NCSR lines, one to
cover chains AA' and CC', and another to cover chains BB'.
On 06/23/10 18:51,
Err - no. Not apart from diff'ing the html documentation page.
From memory:
- Rudimentary support for model building after MR, although I've
removed some of the useless features in 1.3
- GUI support for supplying your own additional buccaneer or refmac
keywords. Can be used to access the
LINKR is not part of the PDB format:
http://www.wwpdb.org/documentation/format23/sect6.html
It's also not supported by MMDB, for that reason. I think Eugene put in
some stuff to store remarks, but I don't know if unrecognized keywords
are also stored (Eugene?). So there's a problem here, and
I looked at it and concluded that our FFTs are on the whole too short
for it to be worthwhile, and a lot of calculations aren't FFT bound
anyway. An awful lot of our stuff is simply not very slow.
Also, GPU computing at the moment is crippled for many problems by the
bandwidth bottleneck and
I'm not quite clear what your aim is here, but if you want to reproduce
Wan'g method exactly, DM can't do it as it has a whole lot of more
recent stuff built in (gamma correction, masking algorithms etc).
If you really want to implement Wang's method (and I'm not sure quite
why you would,
My understanding from Gerard K is that the next version of the PDB
format will also use unjustified atom names.
Unfortunately, following mmdb, I also backed the wrong horse and assumed
space-padded atom names were here to stay. A certain amount of
re-engineering is going to be required.
My
I played with this (coded from scratch, both simple algorithm and a few
tweaks) for a couple of weeks for solving heavy atom substructures. With
perfect FAs it works well and quickly. With real delta-F's it didn't
work at all. Can't remember if I tried perfect delta-F's.
Probably SUPERFLIP is
Crank is a good tool for doing this automatically. Follow the
instructions here:
http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_experimental_phasing_with_Crank
Qing Lu wrote:
Hi All,
I am new to protein crystallography. I would like to know the steps
involved in solving a MAD
Yes, this can be done, but you need buccaneer 1.4, which I haven't
released yet. We've seen significant benefits to preserving the heavy
atoms through to the refinement, although the code has been written so
that it can preserve DNA or any other know structure features as well.
I'll try and
SSM is also available in Coot and CCP4MG of course...
Eleanor Dodson wrote:
would ssm serve your purpose?
eleanor
ebi or ccp4i
Miri Hirshberg wrote:
Sun., Jan. 17th 2010
EBI
Greetings,
I am looking for a 3D structure superposition program which takes
two structures and superpose them
This may also be a job for 'convert2mtz', which I think will pick up the
complex columns automatically. Only available from the command line though.
Kevin
Eleanor Dodson wrote:
I am no expert on CNS files, but do the entries for F_BULK and F_MODEL
correspond to an amplitude and a phase - it
Pavel Afonine wrote:
Dear Ed,
Tightly restrained refinement will be equivalent to
torsion angle parametrization, since bonds and angles are essentially
fixed (but dihedrals are not).
Simply not true. Think why -:) Hint: in restrained refinement the weight
applies to all terms - bonds,
Joe Cockburn wrote:
Dear BB,
We are trying to solve the structure of a complex between two proteins. We
have two crystal forms of the complex, and a partial MR solution in each.
We now want to average the density between these two forms to improve the
maps, using DMMULTI. However, there are a
In ccp4i select Coordinate utilities/Superpose
And then on the first menu select Superpose using secondary structure
matching.
It will automatically superpose based on fold rather than atom
alignment. (This is the same software as used at the EBI for what used
to be called MSDfold).
Miri
I didn't think I had anything to say on this, but following an
interesting discussion on a non-science based forum, I'd like to expand
on a point that both Dale and Felix made in different ways.
In the retraction of these 12 structures (and the 6 structures last
year), we are not seeing the
Kay Diederichs wrote:
Kevin Cowtan schrieb:
Emsley P, Lohkamp B, Scott W, Cowtan K (2010)
Features and Development of Coot Acta Cryst D66 (in press)
Sorry, I wouldn't like to cite a paper whose contents I don't know.
Excellent!
I think the corresponding author may be able to provide
Two things for Coot users...
Firstly, I have just uplaoded the remaining Linux binaries for Coot 0.6,
i.e. Fedora 8, Fedora 10 and Ubuntu 6.06 (with python and gtk2 gui).
You can find them on the Coot website here:
http://www.biop.ox.ac.uk/coot/software/binaries/releases/
Secondly, please
Simon Kolstoe wrote:
1. Can the map averaging function in coot cope with averaging
across twenty monomers
Yup. Just tries it with 1c9s (22-fold ncs)
The 'all' button is handy for turning off the 19 maps you aren't
interested in, then turning on the one you are.
The averaged density
For a global CC:
Reflaction Data utilities/Phase comparison
For residue by residue:
Map and Mask utilities/Map correlation
Note that the global CC will not be the average of the residue by
residue, since it also correlates over solvent, etc.
Kevin
Vellieux Frederic wrote:
Dear all,
I am
, or am I
obliged to dump it in /usr/bin ?
-Kevin A.
On Fri, Nov 13, 2009 at 10:18 AM, Kevin Cowtan cow...@ysbl.york.ac.uk wrote:
The Linux i386 version works on Fedora and Ubuntu. Not tried RHEL.
ftp://ftp.ccp4.ac.uk/ccp4/6.1.2/extras/Tcl-Tk++-linux-i386.tar.gz
Kevin Anderson wrote:
I'm
Did you try here?
ftp://ftp.ccp4.ac.uk/ccp4/6.1.2/extras/
Kevin Anderson wrote:
I am currently trying to run CCP4 6.1.2 under RHEL5 (actually
Scientific Linux 5.3) and have run into the apparently-familiar
problem of not having bltwish.
Specifically, while I can download
be working now; I just had to compile it on a 32-bit machine.)
-Kevin A.
On Fri, Nov 13, 2009 at 10:00 AM, Kevin Cowtan cow...@ysbl.york.ac.uk wrote:
Did you try here?
ftp://ftp.ccp4.ac.uk/ccp4/6.1.2/extras/
Kevin Anderson wrote:
I am currently trying to run CCP4 6.1.2 under RHEL5 (actually
lei feng wrote:
comparing with the old version ( I used CCP4 6.0.2 on my windows xp
computer and finished my Ph.D projects.), I found the new version of
coot is kind of slow in moving to the next residue of the structure by
hitting the space. Can we adjust this to make it faster? or that is
Sloop can generate both a best conformation and ensembles.
http://www.ysbl.york.ac.uk/~cowtan/sloop/sloop.html
Coot has both its own loop building code, and an interface to loopy from
ARP/wARP. If people like sloop we'll add that to Coot too in due course.
Tommi Kajander wrote:
Dear all
I
People keep asking me if buccaneer can build loops. In response to which
I usually point them to 'loopy' and 'rapper', both of which do an
excellent job.
However, I seem to have written a loop building program by accident, and
since people have been asking I guess I may as well release it.
William G. Scott wrote:
In my case at least, it isn't a question of failing to take an interest,
but rather a complete sense of frustration when trying to communicate
with people who insist on speaking utter jibberish. The point of the
postmodernism generator website is to show just how
Looks like a problem with your file.
Can you try:
od -a scala_protein_3_001_180.mtz | head
If your file is an mtz file, you should get output starting a bit like this:
000 M T Z sp ! o etx nul D A nul nul nul nul nul nul
If that is OK, then try:
strings
William G. Scott wrote:
On Oct 6, 2009, at 1:32 AM, Morten Kjeldgaard wrote:
teleports the students across the hermeneutic circle ;-)
(As a consequence, I recommended the postmodernism generator website to
the students: http://www.elsewhere.org/pomo/ )
It is easy to mock postmodernism,
Waterman, David (DLSLtd,RAL,DIA) wrote:
Bill's example is nice because the compression is transparent,
so no extra work needs to be done by developers. However, this
is one for Macs only.
Actually, ZFS is available on Linux too as a user space filesystem, and
Sun are considering a kernel
There are two known issues with ctruncate: one with the anisotropic
correction and one with the fitting of F^2 as a function of resolution.
The first is easily addressed - try turning off the anisotropy
correction. That may solve the problem.
Ricardo Aparicio wrote:
Dear all,
For the same
Buccaneer is giving good results on a lot of cases now, and can work at
resolutions down to ~3.7A when the phases are very good. However, when
the starting phases are poor, it struggles.
I've recently been analysing some of the hard cases from my test data -
in particular one case at 3.0 and
If you want to display CNS maps in Coot and have them on the right
scale, then you need to do one of two things. Either:
1. Don't use the map file, use the reflection file containing the map
coefficients, or
2. Change the setting in CNS which controls the extent of the output
map. Instead
Hi!
We've had a few program crashes reported to the BB and by email
recently, and working out what is going on can be quite difficult and
time consuming.
It is useful to consider when writing such a report how interested you
are in receiving a helpful answer. If you just want us to know
Sorry, I was not trying to criticise.
I have been trying to deal with a number of queries on and off the board
recently where identifying the problem has involved an excessive number
of extra exchanges to obtain information. I therefore thought it
appropriate to provide some suggestions on
This message means that the starting electron density map is completely
flat, which makes any density modification impossible. There are several
possible reasons for this:
1. No FOM specified on LABIN.
2. FOM specified, but all FOMs are equal to zero.
3. All F's equal to zero.
4. Input map
Replies to kamzh...@riken.jp
Postdoctoral Fellow Position in Computational Structural Biology at the
Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, Japan
We are seeking a highly motivated and experienced computational
structural biologist to join the Zhang Initiative
Not sure if this is relevant, but all clipper programs (and I think all
programs wince 6.0) take the symmetry operators as the source for the
spacegroup rather than the spacegroup symbol.
So I would expect changing the spacegroup number or symbol would not
affect most programs in any way.
Maps generated by CCP4 are CNS-formatted and they are
not accepted with Discovery Studio (DS) and Maestro.
DS and Maestro use only CNX-generated maps.
There's your problem. CCP4 application do not generate CNS-formatted
maps, they generate CCP4-formatted maps. The two formats are
This is absolutely correct - in the analysis you present, the
non-anomalous scattering drops with resolution, but the anomalous part
does not. And since counting noise varies with intensity, we should
actually be better off at high resolution, since there is less
non-anomalous scattering to
Marc SCHILTZ wrote:
I agree with everything but would like to add the following: if we
assume an overall atomic displacement parameter, the drop-off in both
the anomalous and non-anomalous scattering is the same. Therefore, the
ratio of anomalous differences over mean intensity (which is what
Coot will read CNS maps. Is the CNS mask format different to the CNS map
format? If so, convert your CNS mask to a CNS map first. (I presume CNS
can do this - I've not used it.)
Xiaowei Pan wrote:
hello Crystallographers
I have generated a solvent mask by CNS ,how can I open the .mask file
Why molecular weight? That's just arbitrary.
There is a simple way of referring to proteins which avoids any
ambiguity - by it's sequence. When referring to a protein, we should use
its sequence as an identifier. No ambiguity.
Now, I understand that some smart people in America are now
Jayashankar wrote:
I am still confused with what is right and wrong in this world of
research where the point of reference changes with time and condition.
Some body made me to accept that science and philosophy are verymuch
different?Are they ?
No,
Charles Ballard wrote:
no idea why buccaneer fails. The best I can do is try to reproduce the
problem and take a look at the core dump to determine why. We have just
received a small update from Kevin, so it would be good to see if this
fixes the problem.
The fix I sent will make no
I hacked up a little program to do composite omit maps a couple of years
back. The purpose of the program was to try out an idea I had - an
ML-omit map based on real space restraints on the rest of the density,
using the same mathematics as is used for statistical density
modification. This
is the
easiest method. sftools checks the Free-R flag and asks if you want to
fix it. I did this:
sftools
read resolve.mtz
Y
write ccp4.mtz
Kevin Cowtan wrote:
Is there any way on the CCP4 GUI to covert the free-R flag from a
resolve mtz file (where 95%=0, 5%=1) to a CCP4 style free-R flag
Try:
[EMAIL PROTECTED]
Mark Collins wrote:
I have been trying to contact Dr. Thomas Schneider
([EMAIL PROTECTED]). But this email address, listed in
the ESCET documentation, just comes back with delivery problems. So does
anyone has current contact info for Dr. Schneider?
If not can anyone
The size of the cell makes no difference. The size of the grid might -
but this is checked for. The program should stop if the grid is too big.
Unless you've got a map which won't fit in 4GB of RAM...
Kevin
Jinghua Tang wrote:
Mapmask behaves normally with small input map. But when I try it
Fire up a recent version of coot and go through every step on the
validation menu - but most im protantly the Ramachandran plot, the
density fit analysis, unmodelled blobs, rotamer probabilities and
finally and most importantly difference maps peaks.
Then run molprobity (via the web site if
John R. Horton wrote:
I've tried several ways to get an Rfree flag into my mtz
file...converting from a CNS to mtz (with existing flags) and scalepack
to mtz and etc etc...with the same result, i.e. that the bin number
that the reflection is in (0-19) is put in mtz file as the Rfree flag
and
Another factor may be that phenix.refine does not make a full use of
experimental phase information in its calculation of the error
parameters - I've been discussing this with Peter, Randy and Ralph. I
don't know that this is the cause, but I see inferior results when
recycling buccaneer with
OK, the first problem is whether you are using maprot in mode 'from' or
'to'. Depending on which you are using, the operators may be the inverse
of what you expect.
The second problem arises from the distinction between crystallographic
and non-crystallographic maps. A crystallographic map
to
calculate something like a 3mFO-2DFc map.
Thanks,
Pete
-Original Message-
From: Kevin Cowtan [mailto:[EMAIL PROTECTED]
Sent: Mon 7/7/2008 10:18 AM
To: Meyer, Peter
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Definition of Fourier coefficients
Probably because in the classic
Hi!
The interesting thing is that it works on other systems. So there is
something odd about your ubuntu system.
Ah - maybe I have it. You are from Switzerland? What is your locale set
to? Could the commas in the symops be being interpreted as decimal points?
Does it make a difference if
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