don't 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
rnals.iucr.org/d/issues/2011/04/00/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
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
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
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 1
"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/
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.
Feedback
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 refused
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 t
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.
- I'v
...
Regards
-- Ian
On Mon, Nov 22, 2010 at 10:01 AM, Eleanor Dodson wrote:
It is a program Kevin Cowtan wrote - here is the info you get when you try
to run it..
E
[c.
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, c
It looks like something has been corrupted in your CCP4 installation.
Possibly there is a post-install script which should have been run but
wasn't?
If you do:
ls $CCP4/share/python/
then you should see something like this:
CCP4pipeline22.py* CCP4pipeline.pyc
CCP4pipeline.py*subproce
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 correl
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
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 i
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 ge
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.
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 blt-2.4-21.z.el5.i386.r
to finally
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 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
Scientific
of bltwish for ccp4, or am I
obliged to dump it in /usr/bin ?
-Kevin A.
On Fri, Nov 13, 2009 at 10:18 AM, Kevin Cowtan 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'
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
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 will
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 c
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 ma
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 fa
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).
Mi
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 cou
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, an
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 ce
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 ba
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 pu
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 da
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
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 c
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, beca
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 m
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 t
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 f
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 A&A' and C&C', and another to cover chains B&B'.
On 06/23/10 18:51
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 fragment
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.
Kevin
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 present/prote
s you 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
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 th
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 m
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.
K
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
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).
W
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 recipr
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? Whi
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
colum
First question: do you need to run makereference at all? If you are
using a recent version, then reference data is supplied in
$CLIBD/reference_structures
In fact, if you are using the latest version of pirate, you don't need
to specify a reference structure at all.
So the only reason you mi
Tricky...
My guess would be that it comes from the commonplace use of symbols in
one common definition of a Gaussian:
y = a exp( - b x^2 )
(although that doesn't explain the capitalisation).
Rajesh Kumar Singh wrote:
May be too trivial, I was just wondering
what "B" stands for in the term "B
J. Appl. Cryst.
I have used it for things which I think need publishing, but are of more
abstract subjects and less direct interest to the biological
crystallography.
However, politics and finances may dictate otherwise. Acta D has for
some reason a rather poor impact rating, and J. Appl. Cr
Thanks for the insight into how the system works. I see now why the
procedings go out in January. I am not encouraged by the logic of the
system. h-factors will probably help though.
Acta D should improve a bit in 2006, since one paper alone from the 2004
procedings was cited 326 times in 2006
Two things:
1. You can do overlap removal in NCSMASK using the OVERLAP keyword.
2. You shouldn't be using 6 masks anyway - you only need one mask.
Dmmulti generates the rest internally.
Jianghai Zhu wrote:
Dear all,
I have two low resolution (3.8 A) MAD data sets from two different
space
d by the author.
MolProbity by contrast includes new data from a large number of high
resolution structures solved since the introduction of ProCheck and
refined using more modern algorithms. In any disagreement between
MolProbity and ProCheck, I would consider the MolProbity output to be
authoritativ
Well,
cp solve.com test.inp
would be your starting point. You should now be able to run it.
Next you might want to use your favourite editor (say gedit on Linux,
which is a bit like notepad on Windows) to make some changes to it, if
it doesn't do exactly what you want. To do that, you will hav
You are absolutely right! The difficulty in getting from MTZ to any
other format or back is unacceptable. Expecting working
crystallographers to write Fortran format statements is ridiculous. I've
been trying to address this by adding support for other formats to
clipper, but my pace has been g
On a more general note, having looked at mtz2various it looks a lot
better than last time I used it, and the problem of keeping I's is a
separate issue.
But we still get fairly regular format conversion questions on both this
and the coot list. From memory, the most common questions concern
c
OK, from the replies I've got a fully automatic CNS->MTZ conversion
utility which is part of CCP4, requires minimal or no user input and
converts the whole file, including gathering Bijvoet differences would
be a good thing.
Send me files and I will try and do it.
What I want is as many CNS f
Does anyone have a genuine CNS file (i.e. not exported from CCP4) which
has HL ABCD coeffs in it?
I need the complete file, and also the spacegroup and cell.
Thanks,
Kevin
OK, here's my first attempt at an automatic file converter. It's not
complete, but I think it should do the majority of files. What it does:
1. Reads a non-anomalous CNS file, either with or without labels in the
main data block. There must be a complete set of 'DECL' lines at the
beginning of
Here's an updated version of cns2mtz. The new version automatically
merges anomalous data, generates a full set of CCP4-style free sets from
the CNS test column, completes the data (unless you tell it not to), and
can take the cell and spacegroup information from a pdb file as well
as from the
cad job to fix. I'll code it properly when I have time.
Eleanor Dodson wrote:
How do you solve the anomalous data Q - this might be useful for SHELX
too - the reflections do not have to follow each other, or I believe
even by hkl and -h -k -l; they can be a symmetry equivalent..
E
This is a replacement for cns2mtz, which fixes all the reported bugs in
that program, is rather more convenient, and handles other ascii file
types as well, including at least SHELX hkl files and XtalView PHS files.
Changes include:
- Spacegroup headers are now generated correctly. (I hope).
The file you need to run should end .class or .jar. If you don't have
such a file, you'll need to compile it first. You probably need a java
sdk rather than jre, although gcj might do the trick.
Then:
javac Switch.java
should make the .class file. (You may need to include the path to your
jav
Miguel Ortiz Lombardia wrote:
I was thinking in the "less scary" widgets-based interface for
not-so-used options. If possible, I think that all options should be
available to the interface.
My programs at least have a load of options which I put in for the
purposes of testing out ideas, which
Clemens Vonrhein wrote:
One thing I found very confusing though, is that the com-files created
by the CCP4i will often have (nearly) all possible keywords set, even
if I haven't changed any of the defaults in the gui. Often, a CCP4
program has defaults itself and only requires keywords if one wan
Setup your path to find the phenix version (i.e. phenix goes first in
your path).
Then in CCP4i, go to System Administration/configure interface
and at the bottom of the External Programs folder add the CCP4 paths for
the conflicting applications explicitly, i.e. add 'phaser' in the lefts
hand
Hi!
Your problem is probably this: you don't have 3 domains. You have 3 NCS
copies, but only 1 domain.
In CCP4I, instead up using the 'Add domain' button to add new operators,
you should be using the 'Add operator' button.
Kevin
Jay Thompson wrote:
Hi.
I'm having a problem with running
More likely the issue is that some of us do not find stereo to be
necessary of beneficial for crystallographic model building.
In which case, given the power of modern PCs and graphics cards, a basic
off-the-shelf PC costing $1000/£500 is completely adaquate for typical
structure solution and
I'm afraid there is no ambiguity. You can't use the CCP4 version 6.*
libraries in GPL software.
The approach adopted by Coot, which is GPL'd, is to use the CCP4 5.0.2
libraries, which are LGPL, along with some patches currently maintained
by Ralph Grosse-Kunstleve to address the more serious d
cense imposes additional restrictions on
redistribution - in particular (but not limited to) an indemnity clause.
Ethan A Merritt wrote:
On Tuesday 03 July 2007 06:55, Kevin Cowtan wrote:
I'm afraid there is no ambiguity. You can't use the CCP4 version 6.*
libraries in GPL software.
This
Details here:
http://www.york.ac.uk/univ/mis/cfm/vacancies/vac_detail.cfm?vacno=BR07299&mode=standard
Software Engineer in Protein Crystallography Graphical Model Building in
"Coot"
Structural Biology Laboratory, Department of Chemistry
Vacancy reference: BR07299
You will work
Hi!
A crystallography wiki was discussed at the last CCP4 developers
meeting, and I've been looking into it.
Setting up a wiki is not hard, but keeping it up-to-date and secure is.
(We've had problems with this at York, where we've been running one for
a few years). Therefore I suggest it is
Yes, that is our intention. CCP4 would probably be at the third level of
a hierarchy including:
Macromolecular crystallographic techniques
Structure solution, analysis and visualisation software
The CCP4 suite
So there would be room for other software packages at the same level as
CCP4,
You could try buccaneer to build an initial model, followed by ARP/wARP
to complete the model. I've see some good results on maps in the
2.5-3.5A range with buccaneer, but model completion is still not so good
(although it gets better with each new release).
http://www.ysbl.york.ac.uk/~cowtan/
Does it matter what the PDB use? They will export PDB and mmCIF for us
to use, so what they use internally doesn't matter. (IIUC the EBI uses SQL).
From my perspective as a developer I am not bothered in the slightest
whether we use PDB or mmCIF, because I read everything through MMDB
which ha
A couple of buccaneer releases have gone by since I last made an
announcement:
release 0.7.2:
- new 'correlation mode' gives better results after MR or when
completing an initial model.
- sequenced fragments are now renumbered to match the position in the
final sequence.
release 0.7.3:
I support CCP4 adopting the hybrid36 and 2 char chain id extensions too.
If no-one else steps up to do it, I'll try and patch mmdb to support it
when I get time.
Kevin
George M. Sheldrick wrote:
I like your hybrid_ 36 scheme and will implement it and the two character
chain IDs PDB file colum
Wow! Those are two pretty amazing structures.
For those of you who haven't had a look, the ordered molecules are in
layers with *huge* gaps in between, much greater than in 2hr0.
And yet both of these structures were solved with experimental phasing
(SIRAS) unlike 2hr0, and the data is to hig
Yup. cphasematch
It gives unweighted and weighted mean phase errors and F and E
correlations. It'll also try the opposite hand if appropriate.
It's in the GUI under Clipper utilities.
For an example script, run it in the GUI and then view the command file.
Kevin
Winter, G (Graeme) wrote:
H
Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst.
D50, 760-763.
as well as any specific reference in the program write-up.
Copyright 2007 Kevin Cowtan and University of York. All rights reserved.
Please reference:
Cowtan K. (2006) Acta Cryst. D62,
I've released new versions of buccaneer (model building) and sequins
(validation) today, with some fixes and new features:
buccaneer 0.7.5 new features:
Substantially improved sequencing algorithm. This uses a full
sequence-alignment type calculation to get the best fit of the expected
sequen
User error I'm afraid.
You are using the 'add domain' button in the GUI, you should be using
the 'add operator' button instead.
Kevin
Bernhard Rupp wrote:
Thanks to Pete and Juergen - seems that the
GUI sticks the offending
domain 1 -
domain 2 -
line in the script. Both the linux and
This is great! But before we all get carried away, a quick reality check
is in order. This isn't an area I've thought about, but my limited
understanding raises the following issues
Given that an MTZ file contains a cell, an indexing of the data, and
possibly phases involving a choice of o
Eleanor Dodson wrote:
Offering a selection of space groups compatible with a point group will
not require reindexing.
Some point groups of course permit reindexing, but one hope you have
chosen a consistent set as you combine data sets into an MTZ file -
pointless and the GUI both offer ways to
OK, that's a good question. Unfortunately the answer is hard, otherwise
I would have done it already.
The a[] and b[] coeffs are the Gaussian coefficients used for
calculating an atomic shape function in reciprocal space, i.e. for use
in a structure factor calculation.
The aw[] and bw[] coef
If you did a binary install, did you remember to run the post-install
script: install.sh?
Does the $CEXAM/unix/runnable/run-all test work?
Meyer, Peter wrote:
Hi Li,
setpaths.sh (and variants for other shells) are generated during the cctbx build process (with ccp4-6.0.2, this might happen o
Hi!
Remove the colin-wrk-free keyword completely, and things should behave
as you expect.
Kevin
Bryan W. Lepore wrote:
running pirate 0.4.9 w/ gui 1.4.4.2 ; the documentation suggests that
R-free can be left unassigned - yet, pirate fails, claiming :
colin-wrk-free /*/*/[Unassigned]
CCP4
Not at the moment, but I'm open to suggestions!
Bryan W. Lepore wrote:
do any of fffear/pirate/buccaneer use SIGFP in a significant/meaningful
way?
-bryan
To add to Kay's announcement...
There is also going to be another, "official", ccp4 wiki, distinct from
Kay's wiki, and fulfilling a different purpose. We're in the early
stages of developing it at the moment. The precise roles will probably
evolve over time, but currently we see them as follows:
Having just sampled a few Linux apps, the most common behaviour for the
close decoration seems to be to close without warning if there is no
unsaved work, or to close with warning otherwise.
At first glance, the CCP4i main window never has an unsaved state, so I
was going to disagree with you.
Refmac (and dm and pirate and probably some other programs like phaser
too) will only restore missing reflections if there are entries (albeit
bblank ones) for those reflections in the MTZ file.
So it's not a matter of running uniquify before refmac, its a matter of
running uniquify before you
I agree with Paul and George that it is vital that PDB files from TLS
refinement contain ANISOUs which reflect the results of that refinement,
and would like to reinforce Paul's point below.
There are many possible parameter-frugal approximations to full
ADP-refinement: TLS is just one of them
Turn off the 'set map extent' option. Then it'll cover the whole of the
molecule.
Nathan Henderson wrote:
Hello all,
I am trying to do some map averaging from my crystal with 4 molecules/asu.
The mask I am trying to create contains the D monomer. However, the output
mask seems to be defined in
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