You couldnt have the wrong TLS spans could you - if you have added extra
residues have you included them in the TLS group?
Eleanor
Sun Tang wrote:
Hi James,
I did check teh B-factors and they are similar to the flanking regions (about 40). The difference density appeared at the later stage of
You know you can convert the CNS FreeRflags to the mtz file?
Use Reflection utilities / convert to mtz and say you are inputted CNS /
Xplor data
Eleanor
But I believe there is an inevitable difference between CNS and Refmac
FreeRs - CNS scaled the work and free data seperately which for lower
As always, Dale hits the nail on the head.
Your R factor is a function of your scaling algorithm as well as your
model, and as you point out the apparent R factor increases when you
include the low resolution data. This doesnt mean your model is worse -
it is still the same model!
All refinemen
What sort of file? Coordinates or reflections or map?
Look at the GUI - reflection utilities or coordinate utilities and see
if it offers what you want?
Eleanor
francesco zonta wrote:
Goodmorning. I need to convert a file form ccp4 to spider or situs format.
The only programs I found to do t
It has just worked for me?
convert to mtz
file type mmCIF
then I had to put in my own cell and spacegroup.
And I will have to calculate phases before I can use coot with it..
Eleanor
Eleanor
It looks like this..
#
_audit.revision_id1_0
_audit.creation_date 2005-03-22
_audit.update_re
I agree that the difference in Rwork to Rfree is quite acceptable at
your resolution. You cannot/ should not use Rfactors as a criteria for
structure correctness.
As Ian points out - choosing a different Rfree set of reflections can
change Rfree a good deal.
certain NCS operators can relate refl
I think you have just found a symmetry equivalent of your original
structure solution.
In P6122 there are 12 possible symmetry operators to choose from - only
one of which will be the identity (equivalent to alpha=beta=gamma=0)
One certainly will have alpha or gamma = 180, and beta 0, equivalen
It is hard to say exactly - do you mean the mutant "dimer" is not exact
ie - one chain different to native, and one the same?
Eleanor
yang li wrote:
Dear All,
I have a protein which has the function unit as a dimer. I got two
structures of it. One is the native structure, one is the muta
About to leave for 6 weeks - but try expanding map to P1 and using that
- SFALL only supports a limited set of spacegroups..
Eleanor
Dirk Kostrewa wrote:
Dear CCP4ers,
I've created an artificial map in C2 with MAPMAN and made sure that
the axis order and sampling is consistent with SFALL, wh
It is recorded by SCALA - if you use that data processing procedure.
You can still do a run of scala after SCALEPACK or XDS or whatever
providing you output integrated, unmerged intensities.
You are right though - we need a data analysias tool..
Eleanor
James Pauff wrote:
Hello all,
Silly
It is not really possible to detect twinning by the simple moment and
cumulative distribution tests for data from a crystal with pseudo
translation. As Bart says, twinning decreases the value of the moments,
whilst pseudo-translation increases them, so the two effects tend to
cancel out.
The
Not real advice, but be careful if Phaser and DM use the same column
labels by default - best to assign them to something distinctive. I have
had cases where programs got confused between input and output.
And to be safe I would run REFMAC with the output model then use the FO
PHIC FOM after
Q1) Rms xyz and rmsd mean exactly the same . And as for what you should
report - that depends on the problem. As long as you state clearly what
has been fitted ( all atoms, CAs, loops excluded etc etc )
Q2) The algorithms for SSM and LSQKAB are different - SSM fits secondary
structure elements
ves a rmsd (or a rms xyz I don't mind) non null for
glycine side chains ?
thanks a lot
nathalie
Eleanor Dodson a écrit :
Q1) Rms xyz and rmsd mean exactly the same . And as for what you
should report - that depends on the problem. As long as you state
clearly what has been fitted ( all
icing this!
Eleanor
Nathalie Colloc'h wrote:
Hello all,
I have still a question about LSQKAB
Why LSQKAB gives a rmsd (or a rms xyz I don't mind) non null for
glycine side chains ?
thanks a lot
nathalie
Eleanor Dodson a écrit :
Q1) Rms xyz and rmsd mean exactly the same . And as
If you just run SSM with the two files I think you will get the
alignment you want? It seems to be able to sort out subunits from a
whole model.
Eleanor
Paul Emsley wrote:
> conancao wrote:
>
>> Dear all:
>>
>> I have problem to supperimpose 2 homologous proteins(only one subunit
>> is homolog
You must be asking for a MAP to be calculated - see near the top of the
GUI. click off this radio button and the warning should go away.
Eleanor
Chavas Leo wrote:
Dear Sajid --
Thanks for your suggestions to run revise. Suggestions
from Mike Latchem helped me to overcome the problem.
I have
Such things almost always are due to some error - check first cell in
reflection file and the PDB header.
Next is the data very anisotropic? is there one or more rogue reflections?
Eleanor
Khan Amir Rafiq wrote:
Hi,
I have solved a structure by MR, unambiguously, and
partially refined a 2.8A
1) It is a bit hard to find out how MOLREP defines its orthogonal axes -
many programs use X0 || a, Yo || b* and in P21 hence Zortho is || to c*
If that is what Molrep does then your 2 fold is in the a c* plane, 21
degrees or 111 degrees from c*.
The 2 peaks you see are symmetry equivalents.
If
Frankly when faced with these problems of generating symmetry
equivalents i revert to almn, where a) I can guarantee the
orthogonalisation is as I expect, and b) it generates an exhaustive set
of symmetry equivalent peaks.
But that is old technology..
If you have two dimers in the asymmetric
As far as I know SFALL reads PDB files - I dont think there is an option
to input fractional coordinates..
I suspect it thinks everything is displaced one space to the left or
right ..
Can you run pdbset xyzin now.pdb xyzout now+.pdb
end
and see if there is any difference?
When I run the map
Mirek Tarnawski wrote:
Dear all,
I am trying to solve a protein structure with molecular replacement method,
but I'm new to crystallography and I have some problems with it.
Quality of data seem to be good, there is also several search models
available, but I am not able to obtain good solution
Thwe MSD target service has gone, and that was the way I created oca
files comparing sequences?
Is there another web site which will give back the same format?
Eleanor
This is only a suggestion but sometimes it helps.
First idea - try as hard as you can to extend the native data - at 3.6A
resolution all model building is extremely hard!
To work with what you have I would do this - others may have different
ideas.
Combine both data sets into one mtz file, an
Kathleen Frey wrote:
Hello.
I am trying to refine a structure that has 2 ligand conformations as seen in
the electron density. I tried to put both conformations in Coot and format
the PDB similar to a residue alternate conformation and changing the
occupancies to 0.50 for each conformation. This
Vellieux Frederic wrote:
Dear all,
I am looking for some software (computer program) that would take a
full PDB file (including waters) and that would output a list of the
water networks (including the names of the atoms) at the surface of a
protein.
Thank you in advance,
Fred.
watertidy d
parkash wrote:
Hi,
I have one structural refinement problem.
I am working on a protein crystals which diffracted to 2.8 Å. But when
I refine through REFMAC5, with 0.1 wt(geometry to x-ray terms), I get
high B-factors around 70. But if I do TLS refinement, the R-factors
lower down and B-fa
I guess you mean you have one ha per monomer?
To use CCP4 tools - you can use mapmask to mask out a sphere of density
around your heavy atom.
Give the atom a "radius" of 10A of something big to get a decent lump,
and make sure it looks sensible..
(Use your best phases here of course)
Then use
Sampath Natarajan wrote:
Dear All,
I am refining a structure with 2.5A resolution by refmac5. I
could find the solution by MR using molrep. After fitting the model, I
refined the structure again with 0.3 weighting term, but the output PDB file
shows many splits in the residues. So I us
Roni Gordon wrote:
I have used the CCP4 program "re-index" to add a screw axis before (e.g.
P6 -> P61, P2 -> P21), but never to change the point group (e.g. PG4 ->
PG422).
I initially re-indexing the reflections without error, but refmac5 later
complained that there were too many reflections for
Partha Chakrabarti wrote:
Hi,
Is it possible to cut out a spherical map around a heavy atom site
directly without having to make bones or building something? I want to
place that in a larger P1 cell and use that for phased molecular
replacement (Phaser / Molrep).. can someone point me how to do
It sounds like something the CCDC software might do?
Eleanor
DISTANG will do it for pdb input
Kristof Van Hecke wrote:
Dear all,
I apologize for the off-topic question.
I'm looking for some software that is able to read in (small molecule)
structure files (e.g. .pdb, .cif,..)
and subseque
You almost certainly have a wrong format statement - it is tricky
getting them correct for more complex cns inputs.
Eleanor
Miller, Mitchell D. wrote:
You could also try cns2mtz?
http://www.ysbl.york.ac.uk/~cowtan/cns2mtz/cns2mtz.html
Regards,
Mitch
-Original Message-
From: CCP4 bul
Ariel Talavera wrote:
Hi all,
I am working with a 2.5 Å resolution structure with Wilson B factor
37,5 Ų. It is already 100 % built but after the TLS refinement the
average B factor was quiet low (4.6 Ų) and of course also the B
factors for each atom were also very low. For that reason I ra
If the structure factors are available for the original protein you can
use ALMN to check if there is an agreement between
the two data sets.
(Very old technology but a useful trick)
Other things to check - Does the crystallographic 2fold in P43212
generate a tight dimer?
is there a non-crys
When all else fails you can dump the file as an ASCII format using
mtztona4, edit that file to correct the spacegroup and reconvert it to
mtz using na4tomtz.
Eleanor
Petr Kolenko wrote:
Dear colleagues,
I have a ?.mtz file from integration with missing info about the space
group in the SYMINF
I would run the TLS again!
Eleanor
Clemens Grimm wrote:
Dear all,
after re-indexing a dataset I had to re-orient my coordinates accordingly. The
model contains some 24 TLS-tensors.
Now my question is how to apply the rotation matrix also to the TLS-tensors.
What is the mathematical operation
William Scott wrote:
Hi Citizens:
I realize this is one of those warranty-violating questions, but is
there a simple way to down-weight figures of merit, or the equivalent
in terms of Hendrickson-Lattman coefficients?
I'm trying to generalize and automate a procedure for solving RNA
structu
One question - do you have two pairs of molecules, each related by the
PST or is there extra non-crystallographic translation ?
Averaging or NCS restraints dont give much extra information for
molecules in the same orientation.
Certainly any pseudo translation will generate sets of weak and st
I vote for an inclusive BB - it is easy to delete the irrelevent (to
you) messages, and nice to know there is a helpful community out there
who are prepared to help..
Presumably copyright violations do not result from sharing with one
request..
Eleanor
Jayashankar wrote:
Dear All,
Scot
The simplest suggestion is to move molecule B by that symmetry operator!
But bewate - the older REFMAC uses the LINK record differently to the
PDB - it has now renamed the line as
LINKR and you should check the refmac documentation to see how to set it up.
Eleanor
Peter Chan wrote:
Good Day,
Are you sure of your spacegroup?
eleanor
Check for Se by doing an anomalous difference map using the PHIC FOM
output by refmac.
You will have to CAD together the two files - one with the Dano from the
data processing with the REFMAC output before doing the map.
eleanor
Sampath Natarajan wrote
Ariel Talavera wrote:
Hi again,
I am trying to calculate the rscc of the model to the electron density
map. Any help will be appreciated.
Thanks,
Ariel
Go to GUI - map utilities - map correlation task.
Eleanor
It is an absolute pain!
do you mean you have residue 1 A 1A 2A 2A 3A 3A etc where they should be
numbered 1 2 3 4 5 6 A?
or should it be 1A 1B 2A 2B 3A 3B etc?
Eleanor
William Scott wrote:
Hi folks:
I am hoping there is a simple answer I have overlooked to the
following question. I have
phasematch is in the GUI
E
Graeme Winter wrote:
Hi David,
There is a clipper utility called "cphasematch" which will do exactly
this. More info here:
http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html
or you can get the updates against ccp4 6.0.2 through the ccp4 downloads pages.
Cheer
It is not accepting your input pdb; can you give more details? eg the
command script..
eleanor
Xie Jiabao wrote:
Hello,
I am trying to run the CCP4 program DISTANG from the command line (in order to do a translational grid search of a molecule over the asymmetric unit). But the program abort
Se the twinning rules in http://www.ccp4.ac.uk/dist/html/twinning.html
P3
pace group number space group point group possible twin operators
143 P3 PG3 -h,-k,l; k,h,-l; -k,-h,-l
144 P31 PG3 -h,-k,l; k,h,-l; -k,-h,-l
145 P32 PG3 -h,-k,l; k,h,-l; -
Lisa Wang wrote:
Hello all,
I have a complex structure with resolution 2.7A The total molecular weight
is 80KD, and about 10% is disordered. I refined this structure to R and
Rfree 25.5% and 29.7% with CNS. I also tried refmac5, but the R and Rfree
have no difference with CNS. I use sfcheck of c
Can you send a bit of your PDB including the CA and CL? Eleanor
Louise Gourlay wrote:
Dear All,
I installed CCP4 on my Mac OS X Leopard system using fink. I have some problems
with Refmac, it doesn't refine calcium or chlorine atoms, or any non-protein
atom in general. In the log file it do
You need to move the CA and CL names one character to the left
ATOM 6190 O HOH W 6426.387 33.040 -0.685 1.00 40.92 O
ATOM 6191 CA CA B 137.417 44.961 41.022 1.00 12.13 CA
more like this..
Eleanor
Louise Gourlay wrote:
ATOM 6189 O HOH W 63
James Pauff wrote:
Hello all,
I have a refined structure at 2.6 angstroms that at about 73% completeness at
this resolution. The I/sigma is about 2.0 at 2.6 angstroms, and the omit
density for my ligands is great contoured at 3.0sigma. My Rcryst is 19 or so
and the Rfree is 24.5 or so.
HOW
ll of your insights here!
Best,
Jim
--- On Wed, 8/20/08, Eleanor Dodson <[EMAIL PROTECTED]> wrote:
From: Eleanor Dodson <[EMAIL PROTECTED]>
Subject: Re: [ccp4bb] Lower completeness, decent R factors, but low B factor...
To: [EMAIL PROTECTED]
Cc: CCP4BB@jiscmail.ac.uk
Date: Wednesday,
rerun truncate with input amplitudes..
eleanor
James Pauff wrote:
If I've lost my SCALA MTZ, and have only the truncated.mtz for my dataset,
which program is the quickest means of obtaining a Wilson plot?
Thank you again,
Jim
--- On Wed, 8/20/08, Eleanor Dodson <[EMAIL PROTECTED
This clears up some terrible confusions in my mind..
could one of you experts contribute a summary to the CCP4 Wiki or the
crystallographic information site:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/
Eleanor
u need
for applications (such as MR and F^2 based refinement)
which demand F^2.
Cheers
-- Ian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Eleanor Dodson
You can use the ancient but useful watertidy script - that assigns water
names coded according to the residue they are linked to. So ones with
the same link code are related..
But I also use distang.
Make a file with the two or more sets of waters - then do a distance
search with the approp
This is a very educational thread but I should remind you that the
assumed distributions are NOT reliable when either a) the data is very
anisotropic, or b) the data is very incomplete or c) there is a
non-crystallographic translation vector in the structure or d) the data
is twinned.
I for
I dont think you need to worry much about the strong stacking
reflections; TRUNCATE really only modifies the weakest data - and
anything > 3Sigma is barely altered . There is a slightly wrong estimate
of for that resolution shell, but in practice it seems to have
no observable effect..
An
It is likely to be a difference in the scaling.
Can you merge the two data sets, run scaleit or something to analyse the
difference v resolution?
Eleanor
Sabine Schneider wrote:
Hello everyone,
I am puzzled about differences I see when I refine the very same
structure against data processed
ALMN can plot the rotation function as a map - although I challenge
anyone to make much sense of it! More or less the same methodology as
MOLREP.
More useful - it lists all peaks generated by the symmetry operators in
Eulerian, and polar angles and gives the direct cosines of the rotation
ax
A postdoctoral position is available in the BMAD group in the
Bioinformatics Institute Singapore
The projects combine Bioinformatics knowledge, building models and
carrying out MD simulations to work on a range of proteins, establishing
mechanisms of action, predicting testable hypotheses whic
First check - look for anom peaks.
If your S atoms are showing up in the Dano map, them you can check
whether this is a compound with S in it. crystallisation and
cro-protectants contain a wealth of small molecules which often bind
Eleanor
9 sigma peaks are rarely due to multiple site waters
Jenny wrote:
Hi, Dear All,
Does anyone have suggestions about what good programs are available that
could be used to evaluate proteins?Like how good is the packing, hydrogen
bonding pattern, aggregation prediction, solubility, hydrophobic surface
burial etc. Thank you very much.
Jenny
The e
Yes:
There are details in the coot manual
1) Get a dictionary for your ligand from PRODRG or somewhere. - you have
obviously done this..
2) CHECK IT IS CORRECT!!! Right chirality, planar groups, etc..
3) Import dictionary into coot, and a set of coordinates.
4) Import 2mFo-Dfc and mFo-Dfc m
Joe Smith wrote:
Hello,
I have been building a protein model (resolution 2.2A) which has one
small loop of 6 residues having poor density. I cannot see any side
chain in this region but I can see relatively poor main-chain density
which at least clearly indicate the loop conformation. I am trying
I cant follow this very well.
Try SFCHECK as well which will do the same tests and give a differently
formatted output..
or TRUNCATE which gives you plots of these stats v resolution..
/^2 : 2.351 This is higher than the expected value of 2 for untwinned data.
(1.5 for perfectly twinned data
It is tricky, but maps can work.
My procedure was:
Extend map file to P1
Put a dummy "atom" at the position you feel is about in the centre of
the molecule density.
Make a mask around this atom with a radius of nA which you feel is big
enough to cover most of your molecule.
Use this mask to m
should I do? I did not deal with any twinning dataset. Any
comments and suggestions
will be greatly appreciated. Thanks!
Yingjie
On Thu, Oct 16, 2008 at 12:24 AM, Eleanor Dodson <[EMAIL PROTECTED]>wrote:
I should have said - most likely explanation is point group is reall P321
Eleano
Peter
2008/10/16, Eleanor Dodson <[EMAIL PROTECTED]>:
People dont read the CCP4 documentation on twinning! Grrr
PG P3 can have 3 twinning operators; and these are:
k,h,-l ( or symm equiv) - if this is a crystallographic operator the PG
becomes P321
-h,-k,l (or symm equiv) - if
You have an error in your mtz file..
OK- so I am sorry! But the Warning will not disappear..
Eleanor
That answer is as useful as any! I had to kill, kill kill till it
disappeared..
Eleanor
[EMAIL PROTECTED] wrote:
To quote Terry Pratchett:
+++ Divide By Cucumber Error. Please Reinstall Universe And Reboot +++
Couldn't resist :)
Artem
You have an error in your mtz file..
OK- so I am
I dont think that is a twinning law, and that SG and cell dimensions are
unlikely to be twinned.
It could be really P1 I suppose with a twin operator -h,k,-l - ie the
SYM op is actually a twin operator..
But twinning usually shows up in the intensity statistic plots - have
you looked at the TR
we index the dataset triclinic and look at the truncate graphs
again, we can find the same distribution for the acentric reflections
(no straight line). The observed cumulative intensity distribution
fits very well to the theoretic one.
Thanks for the fast answer and the help,
Michael.
Eleano
I thought H 32 was a PDB requirement?
CCP4 programs take a belt-and-braces approach - read the symbol but also
check the cell dimensions and set up symmetry accordingly..
But it is a pain if headers are inconsistent with PDB deposition
requirements - des anyone know more details?
Eleanor
Ber
In the $CHTML/twinning.html it tries to explain:
From the table:
# All *P2i3* and related *2i3* space groups:
(h,k,l) already equivalent to (-h,-k,l) so we only need to check:
real axes: (a,b,c) and (b,a,-c)
reciprocal axes:(a*,b*,c*) and (b*,a*,-c*)
/i.e./ rein
You can read phases into both MOLREP and Amore and search for the
translation against the phased map.. It often gives good results.
Eleanor
Pietro Roversi wrote:
Dear Ed,
in the past we have successfully searched in an
electron density map (computed in the whole cell) with M
Truncate doesnt "truncate" intensities or modify them in any way except
to apply a guesstimate of the absolute likely scale based on the no of
residues in the asymmetric unit. Truncation is only applied to the
amplitudes for negative or very weak intensities. Obv. you cant take the
square roo
I have just come back from a meeting where the following problem reared
its ugly head
MOLREP was used to test a set of SGs and found a good solution in one of
them; P2 21 2 for example.
But the refinement against the original data stuck.. The explanation is
this:
Although the MOLREP wrote
This scaling is a real pain..
However If you look at the plot of v ( a loograph under
Rfactor v resolution plots)
it often gives a clue. I think it is usually due to poor estimation of
the bulk solvent correction, espec if the model is incomplete. (We could
discuss that if there was any inter
Answer is NO to difficulty; H32 is no easier or harder in principal than
any other SG..
However do you have a NCS translation? or twinning?
Is your model likely to be an oligomer?
Eleanor
Shane Atwell wrote:
I'm struggling with a molecular replacement. Its a kinase, for which we
have the str
being used as "arbitrary small
number to prevent overflow", or if it's serving another purpose? I
wasn't sure from reading truncate.f.
Thanks,
Pete
Eleanor Dodson wrote:
Truncate doesnt "truncate" intensities or modify them in any way except
to apply a guesstimate
Not more eloquent..
But there is no need to reprocess to change from P222 to P212121. You
integrate data in a crystal class ( ie trigonal, monoclinic,
orthorhombic, tetragonal, hexagonal, or cubic), scale and merge data
data in a point group.
In your case the point group is the same for the
Vellieux Frederic wrote:
Dear Colleagues,
I am looking for a program (if there is one...) that would allow to
list all interactions at a dimer interface (polar, ie hydrogen bonds
and salt bridges, and non polar).
Thanks in advance for your replies.
Best regards,
Fred.
Have you tried MSDpi
It is hard to say without the program output as well, and information
about the unit cell.
However it seems that you have a three fold axis at 120 degrees to the
C2 2fold axis,
and 3 other NCS 2-folds perpendicular that 3 fold.
It is possible your space group is really H32 - run your data (eith
I guess my hunch would be that there is some sot of order-disorder
problem; either twinning or crystal dislocation.
Some ideas -
reindex the PG222 data set h/2,k,l so that a~=b and test that data for
twinning - you can just run truncate on the output Is and see the
moments and cumulative inten
Olga Boudker wrote:
Dear all,
I am working with a relatively low res. crystal structure with
multiple protomers in the asymmetric unit related by NCS. I am
currently running rounds manual model building in Coot and refinement
using Refmac5. Could anybody suggest a shortcut for the following
I think you should be able to detect twinning from the intensity
statistics regardless of the spacegroup you have processed in...
Have you tried SFCHECK or looked at the truncate plots?
A word of warning - FreeRs and Rfactors for twinned data are somewhat
different to those for untwinned data,
Wim Burmeister wrote:
Dear all,
I have a 3 A structure refined with REFMAC which gives consistently
average atomic B-factors of 40 A2, whereas the B factor from a Wilson
plot is about 60 A2. Is there any explanation for such a discrepancy?
There are no obvious problems:
No twinning, spacegrou
but onerarely uses it at that resolution..
So it is a bit like comparing apples and pears - I doubt if any
sensible conclusions can be drawn.
Eleanor
Wim Burmeister wrote:
Eleanor Dodson a écrit :
Wim Burmeister wrote:
Dear all,
I have a 3 A structure refined with REFMAC which gives consisten
you need to select the Free R in the highest possible Laue group , then
use cad to extend this to all reflections in the chosen point group.
This is best done immediately post-truncate..
eg if you twinning operator is k,h,-l, then if
1,2, 3 is assigned to the free set so should 2, 1, -3 be.
P
I think if you cant see it dont build it, but deposit the data..
There are many (most?) structures with missing loops
Eleanor
Pavel Afonine wrote:
This might help:
Acta Cryst. (1997). D53, 540-543 Local Improvement of
Electron-Density Maps
Pavel.
PS> It will be implemented in PHENIX som
There are useful plots from scala showing various measures v frame
number. I usually look at those and do some hand waving to decide where
the increasing R_xs indicate you are measuring nothing, or measuring
something different from the first frames because of radiation damage
Eleanor
Frank
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 to a mean vibration
about the coordinate of 1A
But for proteins the B factor becomes the collection bin for all sorts
of other errors - unrecognised mul
劉家欣(NTHU) wrote:
> Dear All:
>
> We have a crystl with P4222 sg.
> All statistics look fine.
> However, there is a system absense in l axis.
> Any body have experiences on that?
> Any suggestions would be high appreciated.
>
> jaishin
>
can you give more details, eg all reflections along the pa
tensity Sigma I/Sigma
>
> 0 0 17 -5.3 21.3 -0.2
> 0 0 19 7.2 24.9 0.3
> 0 0 21 -13.4 22.0 -0.6
>
> - Original Message - From: "Eleanor Dodson"
> <[EMAIL PROTECTED]>
> To: ""劉家欣(NTHU)"" <[EMAIL PROTECTED]>
> Cc:
> S
I wish I knew more about OMIT maps, but after testing Kevins procedure
(which omits overlapping sphers with perturbation) and SFCHECK (method
unknown) I got quite biased results. It is years since I have run the
full CNS/Phenix procedure which attempts to remove bias by simulated
annealing.. ma
there is a ccp4 utility coordconv
it can take some ractional formats and a ha file used for phasing heavy
atoms to pdb
eleanor
Anthony Addlagatta wrote:
Katja,
SHELXPRO in SHELX-97 can do this under the option "[G] Generate PDB file from .res
or .pdb".
Anthony
On Mon, 15 Dec 2008 12:07:34
Cheers,
Graeme
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Eleanor Dodson
Sent: 11 December 2008 09:41
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] About system absence in P4222?
劉家欣(NTHU) wrote:
Dear All:
We have a crystl with P4222 sg.
(note that ccp4i
uses the default, i.e. the space-group specific routines).
Cheers
-- Ian
-Original Message-
From: owner-ccp...@jiscmail.ac.uk
[mailto:owner-ccp...@jiscmail.ac.uk] On Beha
Alun R. Coker wrote:
Hi All,
I have been in the habit of transferring my initial free R assignments
to any new data sets or to isomorphous data sets such as substrate
complexes. Although theoretically this is necessary to obtain a valid
free R many of my colleagues maintain that this is comp
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