Hmm - I think this is a bug..
Garib - what do you think?
Eleanor
Jianghai Zhu wrote:
Dear all,
I have some N-acetyl-glucosamine (NAG) in my structure. When I
searched the monomer library in CCP4 6.0.1, I found out that NAG is
actually N-acetyl-glucose, which is much less common, I believe.
You dont say the spacegroup. Different MR solutions can exist relative
to any of the acceptable alternate origins.
Eg If it were P21 say the two solutions could lie anywhere along the b axis.
Try running superpose (coordinate utility ) matching sequences. If the
rotation looks like a symmetry
That is done I believe in mtz2various..
Eleanor
George M. Sheldrick wrote:
I would like to second Ian's bug report, and suggest one minor
improvement. Rather than multiplying I and sigI by 10, one could find
the largest intensity value I(max) and multiply all the I and sigI
values by (say)
Assign LABI I(+)= etc I(-) etc
OUTP SHELX
and I think you get what you want..
Eleanor
Nat Echols wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
A coworker recently solved a structure at high
This is possible but a bit of a pain.. - you need to make an mtz file,
convert it to the multi record format, go through a scala step to
reformat that then you get back to the mtz with
h k l Fmean Dano F+ F- Imean I+ I- all on one line..
I have such a script but it is not part of the
Congratulations - That is amazing - did you find both molecules even
though they differ?
Eleanor
William Scott wrote:
shameless-plugWe just solved a 142 nucleotide asymmetric unit of a novel
ribozyme structure using only A-form RNA helical fragments and phaser. I'm
trying to find some time to
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
Kevin Cowtan wrote:
Here's an updated version of cns2mtz. The new version automatically
Whatever you do it is good practice to do your first run of refinement as
Review Restraints
Under the Monitoring folder set the level to many (default medium)
and set the sigma cut off for chirals to 3.00 say to get a god list
Then run the job and you will get a list of violations of restraints
yang li wrote:
Hi:
Now I need to input a heavy atom pdb file in the ccp4 interface, does
ccp4 has a special format for all the programs in the package? I used
heavy atom file from shelxd but it seemed not right. where can I get a
model of such pdb file? Thanks!
SHELX has its own
You can do that to some extent by scattering random atoms about and
calculating phases from them..
Then the centrics will be sensible.
That is how some direct methods programs get their random starting set
of phases..
Depends on how flat you want the starting map to be
Eleanor
David Briggs
You dont say the size of the protein but in fact errors in f' or f will
have very little effect. You can correct the SE formator if you like,
but even so in most cases if you call the MET MSE then you get holes
over the Se in difference maps which probably indicate partial conversion.
Frankly any
Well - it happens by default. Do not wantt to tighten the restraint?
Eleanor
Kristof Van Hecke wrote:
Dear,
I was wondering what is the best method for applying 'anti-bumping'
restraints in Refmac?
(e.g. for preventing some specific water molecules coming too close to
each other)
Many
This is a good point - I had thought that D would be very low for an
incomplete shell, but that doesnt seem to be true..
Garib - what do you think?
Eleanor
Petrus H Zwart wrote:
I typically process my data to a maximum I/sig near 1, and
completeness in
the highest resolution shell to 50% or
Qing Xie wrote:
Hi,
I'm trying to get the difference map by subtracting the native
electron density map from the complex electron density map. MAPMASK
has a function of ADD/MULT, but I don't know how to use it?
Any other ways to attack this problem in real space?
Thanks in advance,
Qing
1) Why do you think there is twinning? If you label a structure whose
true spacegroup is H32 as having SG H3, then some of the twinning
analyses report that this is consistent with perfect twinning..
I believe the graphs of the moments from TRUNCATE give a true indicator.
Ditto the latest
You dont say how you solved this, but usually now the solution methods
should give the correct hand, providing you indexed the data correctly
and did not muddle up hkl and -h,-k,-l measurements!
Fromm the heavy atom search you cant tell the hand so both x,y,z in P32
and -x,-y,-z in P31 will
Superb picture - thankyou - will add it to the lab gallery!
Eleanor
William Scott wrote:
Hey, dude, thanks for writing!
I could swear (so to speak) You sat next to me on an 11 hour airplane
flight not too long ago and tried to strike up a similar conversation. I
apologize for being too
I think the SD-CE is pointing the wrong way. And they look much too close.
I would rotate them and re-refine
Eleanor
PS - any noise on the 3 fold axis will be multiplied by a factor of 3
Ethayathulla Abdulsamath wrote:
Dear all
I am doing one structure at 2.6A resolution where I found
In cases like this I use the S atoms to calibrate the peak height.
Of course it isnt definitive a) it is near the noise level, and b) peak
height is very dependent on B factor..
But the ratio might distinguish between an atom with an f of 1.3 or f=2.8
Eleanor
David Briggs wrote:
Dear all.
I
This is unlikely to be the result of the method you used to solve the
structure.
It is probably due to you having some NCS related reflections in the
free set and some not.
First consider the direction of your 4 fold - could you have a higher
symmetry space group?
Eleanor
Vineet Gaur wrote:
Such high R values usually mean there are many many very weak relections..
You havent kept in the h+k+l = 2n+1 reflections have you?
Do a native Patterson check too to make sure there are not other
translations which might distort the data
Eleanor
Yi Xue wrote:
Dear all:
I have a
Use COOT to do NCS averaging then look at the maps of B onto A a well as
the averaged one to see where differences might be.
Eleanor
Paul Paukstelis wrote:
I'm working on a 4.5-A structure with 4-fold NCS. I've generated a SA
composite omit map and all the protomers look pretty good, but with
You say you have only found one of at least 3 copies?
Why not continue and find the other 2 before starting refinement? Phaser
will do that automatically if you ask for 3 molecules..
Refinement of structural fragments is always tricky..
Eleanor
Yi Xue wrote:
Dear all:
I have a dataset
Well - it is extremely likely that the peptide is partially occupied and
the occupancy may well be 0.5..
But at this resolution you are going to have great difficulty deciding
whether you should have
Occ=1.0 B = 130
Occ = 0.5 B = 100
Occ = 0.33 B = ??? 80???
As your Rfactors show it
I believe if you go to the CCP4 main page you can find:
http://www.ccp4.ac.uk/courses/procs.html
1991) Isomorphous replacement and anomalous scattering. DL/SCI/R32.
Contents Available.
http://www.ccp4.ac.uk/courses/pastprocs/dl_sci_r32.html
Eleanor
Bernhard Rupp wrote:
Dear All,
I failed
Well - A and B are meant to be flags to show there are 2 conformations
of a particular unit. sp they arent appropriate here and may be muddling
things up.
On the other hand you shouldnt get any repulsion between pairs of atoms
whose added occupancy is = to 1.0
Is that always the case for
Dirk Kostrewa wrote:
Dear CCP4ers,
I try to refine a protein structure with a Mg2+ bound. In the
REFMAC5.2 dictionary, I only found a neutral Mg and several (strange)
entries of different water-coordinated Mg2+ with some predefined water
naming that I don't want to use. I would just like to
Nalam, Madhavi wrote:
Hello:
I am planning to cite the following references (which are given in the
CCP4 program references) for TLS refinement.
* B.Howlin, S.A.Butler, D.S.Moss, G.W.Harris and H.P.C.Driessen,
TLSANL: TLS parameter analysis program for segmented
MOLECULE: 27.449 -14.779 52.855
CENTROID OF REFERENCE MOLECULE:(fractional)0.165 -0.149 0.324
Distance between CENTROIDS : 181.751
Direction cosines of vector between CENTROIDS: -0.634 0.721 -0.281
Eleanor Dodson
Nian Huang wrote:
Dear all
It is a bit clunky - you can use siperpose molecules - fit residues to
fit a selected range (1-40; 60-100 say) and write out a complete fitted
pdb file. Then you could use a VERY old program
compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb)
and it will match all pairs with the
Bernhard Rupp wrote:
Dear Coders,
Do I see this correctly that crossec.lib
is the XSECT.DAT file from Don Cromer's FPRIME
program? If so, has there ever been an update?
Mine is from some reel tape I got from him long ago
when I ported the code...seems to be the same.
Thx, br
High symmetry for me means F432 .. no particular problem in H32
And of course the more molecules to find in the asymmetric unit the more
difficult it is..
But the general rule is
Rotation function harder the higher the symmetry - more likely to have
overlap between crystal symmetry and NCS
Nian Huang wrote:
Hi, all,
I met some crystal structures with disordered active sites. Soaking
common ligands can not make it become ordered. I am wondering what
people generally do in such situation.
Thanks,
Nian Huang
Swear?!
This is quite common - the usual tricks may work - Sulphate ,
Detwinning without a known structure, and such a high twin factor must
be very unreliable .
If you have only IT1 and IT2, the detwin algorithm gives I1 = (TF*It1
+ (1-TF)*IT2) / (1-2*TF)
(Maybe signs wrong there!) Since (1-2*TF) is almost 0, this is pretty
inaccurate..
But if you
I dont know but I would check whether there is some residual P422 info
somewhere..
Eleanor
Jan Abendroth wrote:
Hi mosflm experts,
last week's problem with mosflm solved, another one appearing.
Scala fails with the error message below.
These are ~10AA data. Scala finishes in p422, however
There are several scenarios and it is hard to generalise.
Certainties are:
1) The better your data the easier it is to see a ligand. At 3A it can
be hard to model a blob, but it is usually straightforward at 2A. It is
harder if your data is twinned etc..
2) There is a lot of unnecessary and
uniqueify this.mtz
this generates all indices to your high resln limit, adds freer and
outputs this-unique.mtz
Is this what you want?
Eleanor
James Pauff wrote:
Good day all,
What is the best means of getting a freeR column into
an existing mtz file? I've noticed the Edit MTZ
command bar
I certainly have used NCS restraints with ccp4-6.0.2
That doesnt help much though does it!
Eleanor
[EMAIL PROTECTED] wrote:
Date: Thu, 31 May 2007 14:57:03 +0100
From: Stephen Brian Carr [EMAIL PROTECTED]
To: ccp4bb@jiscmail.ac.uk
Subject: refmac crashes when ncs restraints are applied
Yes; a==b for P6i - prob. a typo..
B factors at 3.2A are hard to fix - it will depend on scaling convention
to some extent..
Can you download the data and re-run refinement for your own satisfaction.
If R ==Rfree for the complex then I suspect they did not transfer the
FreeR flags from the
Two things I think
1) I is a metal so you need to move the atom name 1 space to the left -
more like this:
ATOM 2838 O HOH W 102 6.018 39.720 31.127 1.00
21.43 O
ATOM 2839 I I B 1 19.956 22.770 18.597 1.00
30.00 I
And the monomer library
Santosh Panjikar wrote:
Hi all,
Does anybody have a program which can calculate anomalous differences or
F+ and F- from a refined structure at given wavelength and resolution ?
Thanks
Santosh
Santosh Panjikar, Ph.D. [EMAIL PROTECTED]
Staff Scientist
EMBL Hamburg outstation
These are B factors RELATIVE to your TLS parameters.
You need to run tlsanl to get back to something comparable to the
individual B factors..
Eleanor
CRAIG MCELROY wrote:
Hi all,
I'm working on the structure of a heterodimer phased by molecular replacement
using data to 2.9 angstroms. After
I suspect you can use the Reflection utilities
Convert to mtz
and ask for mmCIF input - this is meant to be mmCIF compliant.. I think?
Eleanor
U Sam wrote:
Hi
I would like to create ccp4 format 2fo-fc and fo-fc map from .fcf file
created in shelex.
I can load .fcf file in coot to see the
There is a CAD option to apply a scale and B factor to any set of data,
and an FFT option to apply a scale and B factor to any column in the map.
Check the documentation for whether you need SCALE 1 -10.0 or SCALE 1
+10.0 !
Eleanor
Jeff Lee wrote:
Hi,
I have a question for everyone. I
Craig McElroy wrote:
Hi all,
I'm refining a structure in refmac and for some reason it does not
seem to constrain bond lengths so when I look at the structure after
refinement many of the bonds are broken (i.e. too long). I know that
you can add distance restraints in the geometric restraint
Is COOT complaining because the SHELX output PDB has no spacegroup?
If you run pdbset xyzin shelx.pdb xyzout shelx1.pdb
SPAC P21 ( say)
end
it will add the SG to the CRYST1 card
Eleanor
Eleanor
Paul Emsley wrote:
Thanks George,
Yes, COOT can open fcf.file and make beautiful maps. But I
Coot has an expert mode which allows you to customise your FFT to some
extent - you will need to turn the fcf file into an mtz file, but that
is easy.. ( See reflection utilities)
And then you can use the great flexibility of the FFT routines to
generate a map to read into COOT.
Eleanor
I understand this surprising feature now ..
The atomic density is being smeared by the BADD 100 to cover a volume
3A from the atomic centre. (3.2A to be more precise..)
But the limit on the map sections to be included in the inverse fft is
calculated without that BADD - in fact you use the
There is a lot of confusion about this!
You can call it R3:H ( indexed with a=b and gamma = 120)
This is also called H 3 in the PDB deposition and the CCP4 symmetry
libraries.
(But for the CCP4 library - it checks the axes and angles to decide
whether this is using the H ( or hexagonal)
This sort of information is summarised on the MSDpisa site
http://www.ebi.ac.uk/msd/
Eleanor
U Sam wrote:
In this connection I like to know how symmetry (in degrees and
translation) is calculated between two or more molecules in the
asymmetric unit (A.U.).
Suppose if I download a PDB then
Look at http://www.ccp4.ac.uk/dist/html/twinning.html for introduction..
Eleanor
Li Sheng wrote:
Hi, Dear All,
How could I know whether a crystal was twin or not from it's
diffraction data?
Thanx in advance.
Sincerely,
Li
07-08-2007
Is this a SHELX data set where the FreeR is flagged as -1?
There seems to be a variety of methods ..
But if you read in the FreeR flag from SHELX and ask to have a FreeRflag
output the convert -t o - mtz script under Reflection data utilities
will output the SHELX value
Eleanor
Leonard
Yes there is a way to do something anyway.
Is your metal only linked to protein or are there extra atoms as part of
the metal?
If there is protein lins you need to make a LINK record in your PDB and
provide a dictionary description of your expected geometry.
If you have more details I can
John Pak wrote:
Hi all, I was hoping to receive some guidance on the following subject.
I'm refining a structure using REFMAC that shows all the symptoms of
radiation damage. Namely partially broken disulphide bonds and
decarboxylated Asp/Glu residues. I have an idea of how to handle the
You dont say whether the molecules in the native cell form a dimer - if
so I would search with that (you may need to turn off the packing search)
Or whether there is a pseudo translation vector in the mutant form..
Or what the data analysis graphs from TRUNCATE show - are they normal?
Eleanor
are getting
from molrep ?
many thanks
Demetres
P.S. I will summarize for the members of the list all the suggestions
I will get at the end
Eleanor Dodson wrote:
You dont say whether the molecules in the native cell form a dimer -
if so I would search with that (you may need to turn off
Do you mean you only have experimental data to 2.3A - if that is the
case I am afraid you cant force REFMAC to work to higher resolution.
Do you mean you just want SFS calculated to 2.2A ?
Eleanor
JOE CRYSTAL wrote:
Dear all,
I am refining a structure in Refmac at 2.3 A and I set
baverage xyzin prot.pdb
end
Will give you something of what you want..
Eleanor
fang sheng wrote:
Dear all,
The refmac output lists B-factor of each individual atom. But how can
I get the B-factor of each set of group, say, protein, ligand A, B,
and all 300 waters?
suzi
1) Combine your MAD 3A phases with the 1.7A native data and use DM or
Pirate to refine and extend the phase set.
2) Make sure your MR solution is on the same origin as the MAD phases.
You can calculate PHIC and FOM from MR solution, combinre with the MAD
phases and do an anomalous diference
First suggestion - use WEIGHT AUTO in REFMAC - you may have restrained
the geometry too tightly..
And have you tried TLS ?
And at what level do you see no density - remember sigma levels in
maps need to vary with B factor - very easy to achieve this with COOT..
Eleanor
JOE CRYSTAL wrote:
Q2
Copy the MAL entry into your own directory
cp $CLIBD/monomers/m/MALcif ./
Then correctt it in your directory
And assign LIBIN ./MAL.cif
The program will read your corrected version and ignore the distributed
one.
Q1
If you run REFMAC the GUI under review restraints, it will detect and
If you have used TLS the B factors listed for the residues are the
residual values AFTER the TLS is applied so they are correctly
restrained to be quite close - the differences in the molecules should
be expressed in the hard-to-visualise TLS parameters.
The first check is to run
TLSANL and
Are you using TLS? If so the B factors in the PDB file are relative to
the TLS parameters..
Or have you lost low resolution data - you can see that in many plots -
one in REFMAC gives F v Fcalc as a function of resolution?
If so you probably need to use SCALE SIMPLE - in gfact that is
REFMAC expects F not I so you need to convert the file..
You will need to run TRUNCATE to convert I to F or the GUI task under
Data processing
Eleanor
John Bruning wrote:
Hi,
I have an mtz file from Phenix I am trying to convert for use in
Refmac. The labels are currently:
H
K
L
It is hard to get a resonable estimate of Wilson B with 4.5A to 3A data,
but yes - if the crystal stops diffracting at 3A that seems reasonable to me
Eleanor
Michael Colaneri wrote:
Dear colleagues,
I have a B of 75A**2 from Wilson statistics 4.7 to 3 A res, good
straight line. Has anyone
The new pointless which is the underlying program for the Test
Alternate Indexing task from the CCP4-6.0.2 GUI works brilliantly for
matching 2 data sets.
However in P21212 if a not-equal b not-equal c it is hard to confuse them..
Like Tassos I think you should start your experiment by
Does your cell show pseudo symmetry or NCS translations?
Eleanor
Wu, Mousheng wrote:
hi, everyone!
I am struggling with my crystal structure in a very big unit cell. my protein is about 16KDa. probably there are about 20 molecules in the asymmetric unit. I tried to use molecular replacement
I think the error is in BALBES - there is a peak I guess at 0.95 0 0.01
but it must be too close to the origin to be a translation vector from
one molecule to another.
There are reasons for such peaks - sometimes spurious large terms in the
data..
but they dont usually represent true
Well - there will be a ripple, but is it there in the difference map as
well? that is meantto be less affected.
REFMAC5 claims to be able to refine some atoms anisotropically and
that would be a good place to start
Maybe you will need to read the documentation! There is some way of
Try submitting your coordinates to www.ebi.ac.uk/ msd and choose the
task MSDpisa
It gives you lots of info including that..
Eleanor
Sreeram Mahesh wrote:
Hi All!
I have found stacking interaction between aromatic residues of a
structure of an enzyme. does anybody knows any server
Well - this (expert??) would suggest using SCALE SIMPLE -
SCBULK is a fudge which has some theoretical justification if you have
measured very complete and accurate low resolution data, but seeing most
people havent done this it remains a fudge factor
The justification is related to average
Jie Liu wrote:
Dear CCP4ers:
Does anyone know an existing program to calculate the lateral
displacement---the vertical offset, measured as a fraction of the
the heptad repeat---of neighboring helices in coiled coils or helix
bundles, either parallel or antiparallel?
Your input is greatly
Well - I seem to get many things twice! Prob. my fault - and it fills
up my Deleted box..
Eleanor
Thomas Stout wrote:
Has anyone else noticed that they're only getting some of the postings
on the CCP4 mailing list?
Lately I've been noticing that I often see responses to queries, but
There might be many reasons..
Do you have a spacegroup with alternate indexing? If so the two crystals
may not be using the same convention.
See $CHTML/reindexing.html for more details.
Or is one data set a high resolution pass and one a low resolution pass?
Sometimes then there are
Xue-Yuan Pei wrote:
Dear ALL:
I am runging AMORE and get an error message:
AMORE: NSOL set too small
When I checked the document, I could not find the keyword to reset NSOL.
Any one can give a suggestion?
Regards,
xue
This is a program parameter - it means you are working with more
Can you combine the PHIC and FOM from each of your solutions, then do
the Phase comparison in Clipper utilities checking for alternate
origins? That gives a good indication of what is going on.
Do you have more than one molecule in the asymm unit? You can finish up
with A_phaser matching
ping sun wrote:
Thanks for your answer.
I guess I did not make it clear. I used the data file for refinement
which is also used for phasing (peak_anomalous.hkl).
Traditionally, people will reprocess the same set of data for
refinement (rescale it in hkl2000 without using the option
I just have to write out matrices:
CCP4 rotation matrix:
[R11 R12 R13] [x]
[R21 R22 R23] [y]where x y z are orthogonal coordinates relative
to fixed axes...
[R31 R32 R33] [z]
represents a rotation of ccordinates by first gamma then beta then alpha
as Phil says:
[R11 R12 R13]
[R21
Ditto - I am getting everything in duplicate
Eleanor
Andy Purkiss-Trew wrote:
Hi Ian and list,
I don't know about rejected postings, as I've not made any recently, but
I am getting two copies of each posting made and the second has gone
through the same server as below:
Received: from
test..
What does the matthews_coeff indicate? You would expect more water than
that, but maybe you have a low Matthews_coeff indicating little solvent?
maybe you have lost the low resolution data which makes it harder to
find water? Maybe you have refined with bulk solvent scaling -
sometimes that
Not enough information but some suggestions.
Are you sure the data is OK? Any sign of twinning? That is suspicious
if you cant decide between P43 and P43212
(Run SFCHECK on the amplitudes and try to understand output! )
Or send it and I will provide commentary.
Eleanor
Yanming Zhang
and rfactor?
Quoting Eleanor Dodson [EMAIL PROTECTED]:
The weighting in REFMAC is a function of SigmA ( plotted in log file).
For this example it will be nearly 1 for all resolutions ranges so
the weights are pretty constant. There is also a contribution from
the experimental sigma, which in this case
Refmac will not introduce a repulsion unless the sum of the occupancies
of the two neighbouring atoms id 1.00 . Is that the case for you? ( It
might list the close contacts - but shouldnt use them)
If you want a link between the ligand and something else though you must
label them both A or B
/%7Evanraaij/
On 16 Aug 2007, at 15:22, Randy J. Read wrote:
On Aug 16 2007, Eleanor Dodson wrote:
The weighting in REFMAC is a function of SigmA ( plotted in log file).
For this example it will be nearly 1 for all resolutions ranges so
the weights are pretty constant. There is also
There are obvious ones like - incomplete structure etc, but have you
tried TLS? Sometimes this can dramaticaly improve the R factors.
You seem to have lost of lot of the low resolution data - could this
mean you had overloads which naybe could be rescued.. That can down
grade the maps a
I think Garib or Alexei must answer this and they are both on holiday
till the end of August
Eleanor
juergen J. Mueller wrote:
Dear all,
using refmac5 to provide H-atoms for a known protein structure the
distance between CYS-CG and HG is defined to 1.34 Ang. in CYS.cif.
This distance has been
ALMN will do this ..
It does not have a GUI - Gr
#!/bin/csh -f
#
almn \
hklin /y/people/ccp4/projects/insmon/ins_p1_1,55A-I422cell.mtz \
hklin2 /y/people/jean/Youshang/monomeric/datproc/*mtz eof
CROSS 15
resol 10 3
CRYSTAL FILE 1 ORTH 1
LABIN FILE 1 F=F_P1 SIGF=SIGF_P1
CRYSTAL FILE 2
ZO has a good point - it is a pain trying to get decent simulated
material - maybe there is an employment opportunity here?
Eleanor
Zbyszek Otwinowski wrote:
James Holton wrote:
How MUCH do you want to bet?
;)
Any amount, as long as we are taking about real diffraction images
Look at the MSDpisa page:
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
reached from http://www.ebi.ac.uk/msd/
It probably tells you much of what you wantt o know..
Eleanor
Mary Rorick wrote:
Hi,
I'm a evolution/genetics grad student trying to address protein
questions. I'd like to
If you have a high off origin peak at 0 0 0.5 you must have absences
along the 00l axis also consistent with
P63 22.
So you need to test both P6322 and P6 22
And is the tetramer generated by crystal symmetry or is the whole thing
in the asymmetric unit?
Eleanor
Jorge Iulek wrote:
Dear all,
Beware twinning tests with pseudo translation! Intensity stats are
distorted..
What does SFCHECK suggest? It pre-selects data for testing..
Eeanor
Green, Todd wrote:
I have a case that is similar to this, or at least visually similar by
diffraction pattern(ie. strong/weak intensities). I
Vu Thai wrote:
Hi,
I have a protein that binds nucleotides, and in my structure, it
appears that the binding pocket is partial occupied by ADP and AMP;
the beta phosphate of ADP is transfered to another molecule. I want
to refine the structure with both ADP and AMP modeled in the sight and
Within CCP4
SFCHECK and TRUNCATE provide an analysis
the PHENIX Xtriage is excellent..
See http://www.ccp4.ac.uk/dist/html/twinning.html
Eleanor
Jobichen Chacko wrote:
Dear All,
Can you please inform me the programs available to find whether a crystal is
twinned and also the data reduction
There are many alternate origins for different space groups..
However a somewhat arbitrary choice or origin was made for the first
listing of independent space groups, and it is simplest to accept the
established conventions.
If you shift the C2 origin from 0 0 0 to 1/4, 0 0 you generate
You need a LINK record in the PDB and a dictionary to describe the link.
If you run the job from the GUI with Review Restraints, the program
should write out a suitable dictionary to describe the link. Check the
distances etc to see if you agree with them. You then use the extended
pdb and
That is very very peculiar!
as far as I know REFMAC doesnt really care whether you call something
ATOM or HETATM .
I suspect the problem is either in the cif file describing the co-factor
- could the atom type fpr MO be set as N? or possibly in the PDB file -
is the Atom name displaced to
DM will produce its own mask if you provide the operators - the only
time you really need a mask is for cross-crystal averaging.
Eleanor
m zhang wrote:
Hi All,
I was trying to make a model-mask file for ncs-averaging in DM. I noticed that in CNS, the mask file has to be O-compressed. Does
I am not clear whether you want to apply NCS restraints to multiple
copies of the same ligand type.
That is easy - you just restrain Ligand CHAIN and residue number1
residue number 1 in the same way as for protein chains ( Presumably
residue number1 and residue number2 will be the same)
If
You need the atom name CA and CL moved one space to the left relative to
C O N etc..
And correct the atom type in cols 76?? from C to CL and CA ( again moved
one space to left)
Eleanor
Vineet Gaur wrote:
Hi all
i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing
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