I always start MR by running chainsaw - you need a pit file or fast or
blast output with the sequence alignment of the template and your new
protein.
chainsaw will edit the template to a) renumber residues taking account of
any insertions and deletions b) prune and rename residues to the given
search model.
2) There is only one molecule - does it pack reasonably or are there great
holes in the map with suspicious density for a 2nd molecule?
I would refine the molecule you have and rebuild if possible, then use that
model to search again
Eleanor Dodson
On 19 April 2012 03:24, Ed
Thank you very much!
Eleanor
On 19 April 2012 19:43, Bret Wallace bretw...@gmail.com wrote:
I noticed this missing when I first installed v. 6.2 as well.
They noted this in the problems page. You just need to replace the
phaser_MR.tcl file with the updated version in the updates page. I
Simplest is to submit your current structure to PDBe - they have software
which moves all waters to lie close to protein. However the waters IDs
don't help you know if A OH 123 matches B OH 123 for example.
The very old utility water tidy tries to give meaningful names to your
waters, but those
Two points.
1) the fit to ideal geometry as flagged in coot validation does not
guarantee a correct model - the best model should be the one that fits the
experimental data best, without having unlikely geometry. You could easily
get a model with perfect geometry which was incorrectly placed in
What I would do - not net ideal!
1) the ASP looks in the wrong place - shift it into green density and one
OE is probably a water..
2) MET notoriously hard to model - I suspect there often are multiple
conformations.. And of course at some wave lengths the S contribution
should be down weighted
I think you will find the dictionaries for coot and refmac are different..
REFMAC default dictionary will $CLIBD/monomers/n/NAD.cif
Good knows where coot finds its dictionaries - Paul?
1) check the REFMAC restraints in that dictionary are sensible - spec, are
the planes and chiral centres as
Well - I have found lots of molecules but usually not in a single run.
The first thing to think about is: is this likely to be a dimer? trimer?
tetramer?
Things to consider - a) any non-cryst translation? b) tthe self rotation
might give a clue - c) is the model a multimer, c)what do the
Is there a fix for this? It has been a perennial request for some time..
eleanor
On 9 May 2012 10:53, sonali dhindwal sonali11dhind...@yahoo.co.in wrote:
Dear All,
I want to take the backup of all my data which i have refined using CCP4.
Can you please guide if I copy all the ccp4 data
Baverage gives you a plot of B value against residue number and chain ID -
that would allow you to visually see which parts of each structure are best
ordered.
If you have run TLS refinement and NOT used TSLANL to add the anise and
individual contributions to B then the plot will give you the
Those error messages are warnings - not fatal errors - there must be
something else reported in the log file to cause that.
But as Garib says DNA standard names vary according to program and year -
see if your atom names are those in the $CLIBD/monomers/g/GUA.cif
That is where REFMAC will find
It is a long time since I did this, but don't you need just one master mask
- then that is converted using your rotation matrix to mask the related
part of the structure ?
Eleanor Dodson
On 15 May 2012 15:56, Yu Feng yufengc...@gmail.com wrote:
Dear De-Feng Li,
Thank you for your reply
On Wed, May 16, 2012 at 8:26 AM, Eleanor Dodson eleanor.dod...@york.ac.uk
wrote:
It is a long time since I did this, but don't you need just one master
mask - then that is converted using your rotation matrix to mask the
related part of the structure ?
Eleanor Dodson
On 15 May 2012 15:56, Yu
I am not familiar with CNS restraints, but whatever the program restraints
are - if you do a omit map, or just set the occupancies of the metal and
its surroundings to 0.00 and do a few cycles of refinement, I believe any
model bias will disappear and what you see will be pretty accurate
On 17 May 2012 21:27, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
I am not familiar with CNS restraints, but whatever the program restraints
are - if you do a omit map, or just set the occupancies of the metal and
its surroundings to 0.00 and do a few cycles of refinement, I believe any
lovely density - i would like to know what % of series have multiple
conformations - it would need a survey I guess of PDB depositions, not just
coordinates, but checking maps..
Eleanor
On 21 May 2012 22:21, Uma Ratu rosiso2...@gmail.com wrote:
Thank you All for you inputs.
Uma
On Mon,
You need to say what the cell dimensions are for these 2 options..
Eleanor
On 29 May 2012 15:59, Andrey Lebedev andrey.lebe...@stfc.ac.uk wrote:
Hi Mike.
I would be more careful about incorrect space group. Yes, sometimes
auto-indexing gives strange results.
However, in your case two sets
Well - I am not familiar with the PHENIX dictionary but you are right; if
you restrain metal bond distances the structure will reflect the restraints
but if you don't restrain the distances then the respective gradients for a
light atom and a heavy one can produce some very odd and unrealistic
Why would anyone ignore the anomalous data they had collected? It will always
help the phasing, and decide the hand for you..
Eleanor
On 6 Jun 2012, at 03:55, Stefan Gajewski wrote:
Hey!
I was just wondering, do you know of any recent (~10y) publication that
presented a structure
Well - I guess you need to check the input mtz file.
do mtzdmo this.mtz and check that the columns you have selected are present and
have non-zero values. You need a FOM there.
Eleanor
On 14 Jun 2012, at 12:58, Appu kumar wrote:
Hello Dear all
I am trying running
If you use the superpose mo;lecules task, using LSQKAB , and fit
molecule A over molecule B say, asking for all atoms to be fitted, you
will get a list of large deviations for main and side , which should
include all those residues with side chains in different rotamers.
Eleanor
On 20 June
Beware do ing this - you may just find the coordinates are on a different
origin or a different symmetry equivalent.
Eleanor
On 20 June 2012 09:20, Mark J van Raaij mjvanra...@cnb.csic.es wrote:
LSQKAB (superpose in CCP4i GUI) also outputs in its log-file the
translation parameters and
You can View input command file, when working from the GUI.
Could you cut and paste this into your message - obviously some inmportant
parameter is not set, but I cant tell which without seeing that file.
Eleanor
On 20 June 2012 05:25, Appu kumar appu.kum...@gmail.com wrote:
Thank you for
Try emailing ebi - they have some sophisticated search tools to do things
like this..
Eleanor
On 19 June 2012 17:26, stanley5101 stanley5...@yahoo.co.uk wrote:
Hi,
Is there such a database that will allow me to search for particular
structural motifs involved in protein interactions. For
, then the input data IS sorted, and converted to the standard
asymmetric unit.
Eleanor Dodson
On 18 June 2012 14:28, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
Well - I guess you need to check the input mtz file.
do mtzdmo this.mtz and check that the columns you have selected are
present
I wonder if this could have happened here?
Some one in the lab has yet again been trapped by a feature?? of REFMAC.
Say your MR solution is found to be in P21212 after you searched various
orthorhombic SFs,
but the input MTZ file has the space group still listed as P222 (i.e. the point
I suspect you didn't request the FreeR assignment on the TRUNCATE interface?
This calls amongst other programs, CAD and CAD makes sure that the reflection
list is unique and that it is in a standard asymmetric unit. Most people do it
by default so don't hit these problems...
I suggest you just
I use the GUI with most of the defaults , and just ask for SCALES constant
And anomalous on of course but that is by default in SCALA ..
Eleanor
On 3 Jul 2012, at 16:43, Phil Jeffrey wrote:
I'm not exactly a Scala veteran so am looking for advice as to what would be
the best way to run
On 11 Jul 2012, at 03:36, dengzq1987
don't understand the question really. What DELPHI do you mean?
Many programs output DELPHI (refmac, SigmaA etc ) and they are usually used as
input to a difference map using FFT
Eleanor
Hi all,
recently，I want to use DelPhi to calculate the
Well - the problem may well be here - in the REFMAC dictionary (see
$CLIBD/monomers.s.SO4.cif ) the chiral volume calculation uses at the order
of the O numbering around the S atom .
So if your O numbering is not right handed you will have the chiral volume
calculated as positive, not negative.
All this is best done from the GUI - pointless will sort out batch numbers,
check indexing etc..
But you still have to identify any rogue batches, and decide on when to
jettison the data st..
The Sigma level is related to the number of observations of each reflection, so
this will decrease as
It isn't that your space group is wrong, but are you sure that your mtz file
has that space group in its header?
MR will test all possible alternatives - in this case P3121 or P3221 - but
won't change the symmetry information in the input mtz.
You need to do that with a utility like
mtzutils
Don't forget you will need to adjust the contour level to see something with
occupancy 0.3 - easily done with coot
eleanor
On 27 Jul 2012, at 11:25, Steiner, Roberto wrote:
Or refine the occupancies with Refmac...
Roberto
From my iPhone
On 27 Jul 2012, at 11:04, Tim Gruene
The old fashioned water tidy will try to assign matching (non-standard) names
to matching H2Os which is useful for analysis of structural waters, but cannot
be deposited.
I think coot has a tool to move waters to be near the protein but maybe that
isn't all you want. Why not start deposition
What do you mean - running REFMAC directly on the output file?
Are you sure you have the same space group given in the mtz file and the PDB
file? If the MR has placed your structure in P32 say, nd the input mtz has SG
P31, you need to change the mtz header to include the now-known SG. There
/Rfree result.
Thanks a lot for your help.
Best wishes,
Qixu Cai
2012/7/31, Eleanor Dodson eleanor.dod...@york.ac.uk:
More details - what do you mean by pesudo-translational symmetry ?
Are there two molecules related by a translation vector? or its it
something more complicated
Brilliant illustration - even in 3D!
eleanor
On 3 Aug 2012, at 14:01, Laurie Betts wrote:
I couldn't resist this shot. It might not make the cut.but
IMG_20120803_085837.jpg
I am surprised if the numbers are wrong, maybe your chosen superposition isn't
the same as that used for superpose - there are 2 methods available - are you
using the secondary structure matching, or the assigned residue match?
Eleanor dodson
On 5 Aug 2012, at 15:17, Zhou, Tongqing (NIH/VRC
Before any further attempts you must check that the crystals have the same unit
cell volume. I usually do this using matthewscoeff from the GUI
( By the way why isn't the volume automatically written into the mtz header
asap!!!)
If the cell volumes differ by as much as 5% no reindexing or any
Begin forwarded message:
From: Eleanor Dodson eleanor.dod...@york.ac.uk
Subject: Re: [ccp4bb] CC1/2, XDS and resolution cut off
Date: 8 August 2012 10:10:55 GMT+01:00
To: Marcus Fislage marcus.fisl...@vib-vub.be
Cc: CCP4BB@JISCMAIL.AC.UK
Like Ian, I tend to use as much data
These are the atom names you should have in your monomer. No mention of H_N4
there..
NH4 HN4HH 0.000 0.0000.0000.000
NH4 N NNT1.000 -0.5810.302 -0.782
NH4 HN3HH 0.000 -1.2321.041
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. All of the parameters containing protein MW, nucleic acid
MW, extent of X, Y, Z and center of
I haven't seen that message, but I think you could provide Arp/Warp with the
model, plus the original data, and it would probably work.
Eleanor
On 25 Aug 2012, at 16:38, Ben wrote:
I recently processed a dataset in HKL2000, imported the scaled data to mtz
format in CCP4, and obtained a
I wish I could give a sensible explanation, but this feature is very common
with heavy atoms.
Possible problems. The default wavelength for all atomic scattering functions
is Cu Ka - you can see the formula used and details in the file
$CLIBD/atomsf.lib.
The atomic scattering values are much
Like Tim says SORTMTZ expects a different format used for unmerged reflection
lists.
And I think this space in the filename causes the SCALEIT problem - linux
operating systems often treat spaces as filename terminators..
But the … marks around a file name are meant to override the space
Why don't you calculate the FFT over the whole asymmetric unit? That is the FFT
default I think
Eleanor
But I think the COOT option works too, but it will also require that your input
map covers the asymmetric unit.
Eleanor
On 19 Sep 2012, at 23:25, Niu Tou wrote:
Dear colleagues,
Is
You could use COOT to do the map rotation - then the parameters seem to work
The conventions should be the same. I thought but I can't really speak for COOT.
If you look at the CCP4 documentation for MAPROT, and use the Superpose
molecules GUI task to fit A to B using lsqkab - that gives you a
This is interesting. In principle m and D should provide an optimum map, and
at high resolution they do a reasonable job.
The answer about occupancy is a good point.
You don't say what resolution your data is at, but maybe it is rather low?
I suspect that below ~ 3A the estimates of both m and
, and I would hesitate to alter those
unless yu have special knowledge.
Eleanor Dodson
On 15 Oct 2012, at 12:36, Danilo Belviso wrote:
Hi! Does anybody know which is the range is used by REFMAC to vary bond
distances, angles, and torsions of a ligand molecule during a refinement
process
Or put all files into pointless..
It will read XDS and do the indexing checks
Eleanor
On 19 Oct 2012, at 12:45, vellieux wrote:
Well, the first thing I note is that P6(3) is a polar space group.
Hence what I would do myself is the following:
take your crystal 'number 1' (as a reference);
You can use superpose LSQKAB to fit various residues by number..
Eleanor
On 24 Oct 2012, at 23:59, WENHE ZHONG wrote:
Dear members,
I have one difficult task on hand and would like to ask for your advice.
I want to superpose two enzyme structures just based on several residues
(e.g. 5
You don't say whether you have any indication of non cryst translation or
likely dimer NC axes? The self rotation can help sometimes to select likely
pairings - for instance if one (or both) domain(s) is forming a dimer.
Eleanor
On 26 Oct 2012, at 13:43, Bosch, Juergen wrote:
We had
I don't quite understand this - you can use an editor to add any coordinates
you like in the correct atom format to a pdb. (Don't think you can deposit
them though!)
Then a program like coot can be tricked into thinking the monomer CUB say is
to be displayed in any style it supports.
I think we need more information.
Are the cells and space groups similar
What are the transformations which fit your coordinates to the model structure?
Have you submitted your coordinates to the PISA server at the EBI - that will
suggest possible tetramers?
Eleanor
On 28 Oct 2012, at 07:31,
On 28 Oct 2012, at 14:07, Appu kumar wrote:
transformation matrix.pptx
the structure in coot, the resulting transformation matrix
is attached with this mail. As both Arka Chakraborty and Eleanor Dodson
suggested me to do PISA, I did but i am not getting the correct tetramer
arrangement which i am getting on aligning the our strcture on model
structure first
Read the manual? !!
There is a menu under
Other modelling tools with a task - Add waters. That will scan the map and
add waters conservatively.
Or you can use the validation tool. Find difference map peaks, and decide
for yourseld whether they are waters. If you like the peak click Add atom
at
On the whole it is good practice to refine the 7 molecules you have - correct
sequence etc etc, all with NCS restraints a 3A, then if you like use one of
your improved molecules as the search model. But don't you have some NC
symmetry such as dimers or tetramers - if so take one of the complete
Please send an extract - you probably have a format error..
Or do you have 1500 chais?)
Eleanor
On 30 Oct 2012, at 22:43, jp d wrote:
hi,
i have a large pdb file and i keep getting this error with refmac
ERROR: number of chains 1500
i suspect something needs to be done to my pdb
any
There are several questions here.
1) What is the point Group - P4 or P422.
I find the pointless statistics which check all symmetry operators singly
useful. If the 2 fold kh-l gives about the same CC as the 4 fold operators k-hl
-h -k l -k h l then you probably do have point group P422. ( But
I don't know what exactly the phenix.autosol output is.
If you are satisfied with the solution and have a mtz file containing F sigF
HLA etc, then use Hendrickson Lattmann coefficients.
If there is only Phase/Fom then use that.
I am not sure how you would fare with SAD data directly..
But
Just give CAD the resolution cut off of the new data set..
Eleanor
From the CAD documentation..
RESOLUTION [ RESOLUTION OVERALL dmin dmax ] | [RESOLUTION FILE_NUMBER i
dmin dmax ]
Use either:
RESOLUTION OVERALL dmin dmax
for overall resolution limits, or:
RESOLUTION FILE_NUMBER i dmin dmax
to
Any spurious blob on a symmetry axis is multiplied up of course.
And when you finish building side chains it may reduce in size.
But waters etc can sit on special positions - you just enter them with occ =
0.5 and refine as usual..
Eleanor
On 5 Nov 2012, at 09:49, Crystal Xu wrote:
Dear
I wouldn't expect there is an exact ratio between occupancy and B factor?
atomic density is ~ occ*formfactor * exp(-b s**2)
Eleanor
On 20 Nov 2012, at 09:49, Jim Brannigan wrote:
As an adjunct to B-factor vs occupancy thread, i might expect the b-factor to
halve if the occupancy is set to
Some of us resisted using an orthogonal format for coordinates, arguing that
the output from a crystal structure should refer to crystal axes.
And since symmetry was a crystal property it was important that we could see
it easily. The PDB format won out, but I still use coordconv a lot
to
pisa at the ebi will do this very nicely.
Upload your pdb files.
PISA is part of the CCP4 distribution too, but the EBI output is prettier
Eleanor
On 4 Jan 2013, at 22:11, Brad Bennett wrote:
Hi all-
I have 2 PDB files of the same protein (in slightly different states) and I
want to output
I am afraid now I just use PISA at the EBI to answer this sort of question . It
tells you the answer with lots of other useful information as well, and then
you can use your intelligence to see why that operator is the correct one!
Eleanor
On 11 Jan 2013, at 01:05, James Stroud wrote:
The
Hard to say without data - but I would generate the 3 symmetry copies of the
molecule you would have in P213,
then do rigid refinement of those coordinates with the P212121 cell
dimensions and symmetry. There are so many possibilities for origin shifts
But you don't say how non-equivalent the
The FFT software tries to limit the volume to the asymmetric unit for the
spacegroup. This has to be a 3-D box, so cubic spacegroups give more peaks
than expected, but not a full list of 1260 ..
However there may not be a complete list - these S are in di-sulphide
bonds, and at limited resoluton
I usually leave them in although their position is so uncertain; they
probably have multiple conformations but that is hard to model at 2.8A .
But that is not a hard and fast rule - lots of people set the occupancy to
0.00 and check whether the later maps give better guideance..
Eleanor
On 21
The general rule is that a Patterson peak should be ~ 20% of the origin
before considering it significant so none of those would really need to be
considered.
Eleanor
On 25 February 2013 12:48, Michele Lunelli efu...@yahoo.it wrote:
Dear all,
I have an orthorhombic crystal (pointless
Old tools still work.
mtzutils allows you to select a zone
eg: only output reflections with h even and k even
look at the documentation to select what you want.
Eleanor
On 26 February 2013 10:03, Randy Read rj...@cam.ac.uk wrote:
Hi,
In your specific case, you can predict that reflections
I guess I have known lots of incorrectedly fitted ligands, and am never
sure quite how to be confident they are correct. Your resolution is good,
so one hopes the density is pretty clear?
Common sources of error.
By far the most common is caused by having an incorrect dictionary. Look
very
Sivaraj Ramesechan was outlining the physics of multiple wavelength anom
scattering in the 1960s as a method for solving insulin.
It was purely theoretical then; no instruments to make the measurements..
Eleanor
On 13 Mar 2013, at 17:19, Peter Moody wrote:
When I started my PhD (in 1980!) at
I would keep the hexagonal lattice, assuming your integration was OK - no
missed spots and then index the data as P1.
If the anom Pattersons should then show the correct symmetry - if the Patterson
shows P6/mmm symmetry you should be safe
in either assigning P6122 or P6522 to the structure SG.
Well - you seem to have absences for virtually all the (0 0 4n+1 4n+3) and
(2n+1 0 0) reflections which is consistent with P42 212 but you can be
misled. Is there any pseudo translation with either X or Z 0.5 - that could
give you similar absences. As Ian says, be wary..
Eleanor
On 15 March 2013
Umm - this is tricky.
First of all you need to reindex the C2221 data into the P21 cell - do you
know the operator?
then expand that data set to spacegroup P21. There is a cad option to do
this..
Then add that FreeR to the re-processed P21 data.
Eleanor
On 24 March 2013 14:37, Appu kumar
First - I dont think you have a 3rd molecule where you have put it - or at
least not one with full occupancy. Those maps are a clear indication that
something is wrong. What is the Matthews coefficient for the numbers in the
asymmetric unit?
Presumably your processing gave you a lattice which
Well - if you know how the residues match then LSQKAB can compare all atoms and
will give you RMSDs for matching pairs.
SSM machos things according to secondary structure, and PISA analyse structure
so you can compare the chemistry of the matched pairs..
But there is no easy option that I know
1) At least four to get the H-bonding..
2) No - depends on the number and arrangement of beta sheets. Protein
structures vary a great deal!
You could find the % of residues in protein structures which form helices
and beta sheets I guess but there is such huge variation that it may not be
very
, especially in ion coordination,
vary with context even if the involved atoms are the same.
** **
Cheers,
Robbie
** **
** **
*From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
*Eleanor
Dodson
*Sent:* Friday, April 26, 2013 13:30
*To:* CCP4BB
Not sure I follow you completely.. You dont say what anom scatterer you
expect, or what the wavelength is.
1) How did you find the anomalous peaks? If from an anomalous difference
Fourier there will inevitably be noise.
In practice when there are S to check this can be very helpful in deciding
There isnt much information here!
Funny that 3 chains are poor - does that mean one and a half heterodimers?
I presume you have checked spacegroup? Zanuda will test to see if any
higher symmetry is present..
Eleanor
On 29 April 2013 06:02, sonali dhindwal sonali11dhind...@yahoo.co.inwrote:
What is the relationship between the molecules in the spacegroups - it
seems likely that in the bigger cell there is a NC translation of
~(1/2,y,z)? ? (A2 ~ twice a1) That can be checked by the native
Patterson..
If so that gives a class of significantly weaker reflections for h odd, and
that
You knowe there are alternative indexing for H3 - you couldnt have solved
one as h k l and the other as k h -l?
And alternate origins - H3 is a polar spacegroup so if you redid the
molecular replacement you may finish up anywhere along the c axis..
Easiest is to do a superpose of both sets of
I guess you can use this one - it certainly isnt restricted to
crystallographic Qs..
Eleanor
Justin Schmitz wrote:
Morning every body!
Does anybody know a board for NMR releated questions which has a
quality like this?
Thx for your answers
Sometimes this sort of disorder is due to an error , so the first thing
is to check very carefully that the solution makes sense.
Why are you so sure there are 6 copies in the asymmetric unit?
In situations like this I first worry about SG.
Is there a pseudo-translation vector? This can make
I guess I would go back to the data.
Could there be twinning?
Is the a pseudo translation vector which means there are systematically
weak zones of data? ( hklview might show something strange)
Rfree seems rather close to R to me for this resolution - maybe it
should go up a bit?
How many
To understand this one at least needs the P1 unit cell..
Operators 3 4 and 5 are almost the same rotation.. It is unlikely that
they are all 2 folds?
Eleanor
Daniel Adams wrote:
Hi bb,
I am working on P1 dataset, SAD phasing resolution is 3.5 and trying
to build model. However I am facing
Just an aside to this - I have had R factors 55% which then refine..
It is when they dont refine you are in trouble ..
Eleanor
Jiamu Du wrote:
*Dear Prata:*
First, I think you'd better check your subgroups. Maybe you got
opposite hand of the data.
Or change a model. When the Rfactor is
Well - if you reindex k,l,h then your cell will be more or less the same
as theirs.
But that moves the 2 fold axis. If your space group is truly P21212 with
those cell dimensions then it would become P21 2 21
However maybe you just know the point group?
Check the absences
Eleanor
U
overlapmap does this for any set of coordinates and any map.
Eleanor
Charles W. Carter Jr. wrote:
Is there a CCP4 program that will calculate residue-by-residue
correlation coefficients for a molecular replacement solution and an
experimentally phased map?
Thanks,
Charlie
There are many and various reasons for unpleasantly high R values, and
twinning is undoubtedly one of them.
But you can only have twinning with apparently good diffraction if the
cell dimensions allow it.
It is always a possibility in trigonal, tetragonal and cubic cells.
Certain other
Have you tried pisa (www.ebi.ac.uk/msd - choose msdpisa
You can download coordinates and it does various calculations to
estimate binding energies.
Eleanor
Xu TAN wrote:
Hi, all
Does anybody have experience with binding energy calculation of
ligand-protein
interaction? What are the
Well - the idea of NCS refinement is to restrain the 2 NCS related
models to be the same so that is problematic if they should be somewhat
diffeent..
You can get the matrix using SSM superposition ( see the GUi -
superpose molecules)
This will match using Secondary structure and give a list of
.
Dmmulti generates the rest internally.
On Feb 22, 2007, at 4:54 AM, Eleanor Dodson wrote:
You just need one mask for your master molecule, which will be
transferred by the matrices you give to all the other copies.
I make the mask from the crude model, with a generous border round it
- the program
Such a twinning operator can also indicate that you spacegroup has an
extra symmetry operator (h,-h-k,-l)
That is in fact one of the symmetry operators for P3i21 H32 P6i22
Have you solved the structure in the lower symmetry and is that missing
density properly generated by this operator?
mathias wrote:
Dear all,
Can anyone of you guys recommend free software, or any open access
internet server, to calculate VDW interactions of small molecules
binding to protein. The only information I need is an output file
which lists all amino acids of the target protein which make VDW
shivesh kumar wrote:
Dear all,
I have a data set at 2.2A, of the selenomethionene labelled
protein.How should I process the data.Thanx for the help.
Shivesh
I think you should ask your local crystallographer for help. There are
several programs ( MOSFLM in CCP4, DENZO, XDS, D*TREK ) but
John Bruning wrote:
When using Refmac how does one find/calculate R-free error in the
highest resolution bin?
Look at your loggraph for the final R Rfee - that gives the numbers in
resolution shells.
Eleanor
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