I think REFMAC will generate anappropriate SSBOND entry in the pdb for
you if you run it from the GUI with Review restraintsoption
Eleanor
On 10/20/2010 08:40 PM, Seema Mittal wrote:
Hi All,
I have engineered intra-molecular disulfide bond in my protein monomer.
The protein functions as a
Being lazy I would just do refinement with REFMAC and let it generate
the SigmaA values.. then try rebuilding with either buccaneer or
Arp/Warp.They willboth generate weighting terms based on the Rfactors.
Eleanor
On 10/21/2010 12:58 AM, Goragot Wisedchaisri wrote:
Hi,
I have helices that
as others have said, there are many cases where the actual symmetry is
lower than the apparent, because a small part of thesructure does not
obey the higher symmetry. This seems to have happened to you - an
inhibitor which has P21 symmetry in a structure with near P212121 symmetry..
In similar
I would expect such a difference with lowish resolution data.
Your model will be biased towards the restraints - ie the geometry
willbe good, but there is bearly enough observations to fit the
actualmodel properly. eg - it will be hard to position solvent, and to
recognise any deviaions from
On 08/20/2010 05:50 PM, Charles W. Carter, Jr wrote:
Is there a program that will read in a pdb coordinate file and re-order the
side chain atoms in each residue according to a standard order?
I've a program that compares two files for the same structure, but requires
that the order of the
Oh cynic!
Eleanor
On 10/27/2010 09:01 PM, Simon Kolstoe wrote:
Surely the best model is the one that the referees for your paper are
happy with?
I have found referees to impose seemingly random and arbitrary standards
that sometime require a lot of effort to comply with but result in
little
This iseasy to do
Reindex 2h,k,l then the cell will double; the FreeR will stay with the
reflection, and you can use those FreeRs to append to your new data in
the scala/truncate GUI.
All the unset ones (2h+1,k,l) willbe given new FreeRs and the old ones
transferred.
Eleanor
in On
The way I do this is to use mtz2various which reads the SHELX output and
(I hope) copes with its various idiosymcrasies, producing an mtz file
with H k l I SigI FreeR
This can then be fed to the ctruncate GUI
You need - to request
Ensure unique data... Copy FreeR from another mtz file
Then
I suggested mtz2various for taking SHELX input which is nonsense - it
actually goes the way..
Eleanor
On 10/29/2010 01:05 PM, Phil Evans wrote:
The normal use of [c]truncate is to take intensities from Scala, so it wouldn't
expect FreeR flags in the file.
I suppose this should be added for
CAD and Kevins phasematch correctly change phases etc when you change
symmetry operator.
I cant think that this is the job for pointless.. it is responsible
for intensities, and surely only needs to use a merged file to decide on
the appropriate choice of axes - eg getting your new PG3 data
On 11/02/2010 02:36 PM, Buz Barstow wrote:
Dear All,
I'm looking for a software program to produce, given a 3D atomic structure of a
molecule, a linear map showing the surface accessibility of residues in a
protein structure.
Would any one know of a program that can produce this sort of map.
I think it is far safer to run CAD with 9 files,
then again with the output file as the first input, plus 8 more etc etc
etc..
This isnt something you want to do very often
Eleanor
On 11/03/2010 06:01 PM, Ian Tickle wrote:
I have a version wten is it?
hich I modified a while back to handle
Well - I usually use the COOT ncs map generation first.
You place waters into good peaks in the 3 fold averaged map -say it is A
B C - check that there are reasonable peaks in the other rotated maps -
then once the waters are generated for A, fit those coordinates A to B
and save them, then A
If you want to shift the coordinates, just use a superposition program.
If you want to know the exact shift to best match phases you need to CAD
together phases calculated from each model, then use PhaseComparison
(reflection utility) That will tell you the shft, and whether there is
an
Have you tried
csymmatch -pdbin-ref one.pdb -pdbin two.pdb
That will move chains to match asfar as possible, using sym ops and
allowedorigin shifts to generate the best fit.
Eleanor
On 11/18/2010 12:26 PM, Ian Tickle wrote:
OK now I understand. I couldn't find the script 'origin.com' you
It is a program Kevin Cowtan wrote - here is the info you get when you
try to run it..
E
[c...@roo mariaH]$ csymmatch
BFONT COLOR='#FF'!--SUMMARY_BEGIN--
html !-- CCP4 HTML LOGFILE --
hr
pre
###
SSM - see superpose task under Coordinate utilities.
This matches secondary structure and gives RMSD for CAs - inceredibly
useful program..
Eleanor
On 11/19/2010 10:55 PM, Srivastava, Dhiraj (MU-Student) wrote:
Hi All
does anyone know any software that can calculate and print out
Can you see the hydrogens in the maps when they are excluded from the
phasing? There is little hope of refining them independently if you cant
see discrete peaks for them.
Eleanor
On 11/23/2010 05:18 AM, Kenneth Satyshur wrote:
Sirs:
We are attempting to refine hydrogens on a ligand (which
I have rarely worked with such data, but when we did, we always kept to
the riding hydroge positions in for refinement. You can check the
important ones by calculating sfs without them and seeing how well they
fit the map. For important residues like ASPS in catalytic triads that
can be very
Yes - I think there is a button on the GUI to click?
Eleanor
On 11/24/2010 01:58 AM, Huiying Li wrote:
Another question on RMSD:
I have two structures of the same protein superposed with the LSQ
Superpose in Coot by matching the first ~100 residues of the N-terminal
domain. Now I'd like to
,
Huiying
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
email: h...@uci.edu
On Wed, 24 Nov 2010, Eleanor Dodson wrote:
Yes - I think
Are you sure that the mtz file you are refining against has spacegroup
C2221 in the header? Phaser can test C222 and C2221 but when you start
refinement you need to be sure the data header is correct.
Another possible bug - is the model elongated in any way - they
sometimes need surface
We did something like this with esprit.
You get the sequence alignments from Psiblast or whatever you fancy,
then edit in the structural alignment into the txt file it generates.
Messy but successful..
Eleanor
On 12/01/2010 03:44 PM, Gerard DVD Kleywegt wrote:
This was one of the things that
Easiest to follow the documentation..
http://www.ccp4.ac.uk/dist/html/dm_ncs_averaging.html
You get the matrices most easily by mapping A to B A to C etc using
lsqkab if you want to average over the A molecule..
Eleanor
On 12/01/2010 05:41 PM, Francis E Reyes wrote:
Hi all
I'm trying to
On 12/07/2010 09:38 PM, Arnon Lavie wrote:
Hi there:
The situation: We are facing difficult molecular replacement: we believe
we have two molecules in the ASU, but phaser/molrep find only one. Using
the electron density calculated using this single molecule, we have
manually placed the 2nd
As far as I know there are no repulsions restraints applied if the sum
of the atoms occupancies is =1.0. If one atom is fully occupied. and
another partial then there will be a restraint.
Eleanor
On 12/08/2010 04:45 PM, Keitaro Yamashita wrote:
Dear Ed,
These tables were reported by
Of course metal ions, So4 etc often lie on special positions - the
insulin hexamer is generated around Zn atoms on the 3-fold axis.
Eleanor
On 12/09/2010 01:29 PM, Ian Tickle wrote:
Of course it's always possible for an asymmetric molecule (or part of
a molecule, such as a side-chain) to lie
That gap isnt surprising given your resolution - indeed anything smaller
could be suspicious! eg symmetry equivalent reflections labeled
differently..
Eleanor
On 12/10/2010 11:17 AM, Petr Kolenko wrote:
Dear colleagues,
I appreciate any help, or any suggestion with my difficult data. Many
compar does this providing the sequence is the same.
amd you can get lsqkab to give you the full list but only i think for
those atoms you overlap..
eleanor
On 12/29/2010 01:52 PM, Michael Swan wrote:
Dear all,
I am having a bit of trouble finding a program to do an rmsd calculation and
give
Hmm - there are some hydrogens which are simply not fixable from
chemistry, or electron density at low (ie 1.5A!) resolution - any of us
who have looked in vain for them can testify to that - and I cant think
that it is good to add in scatterers when you dont know where they are.
The ones
Well - REFMAC and I think other refinement programs simply read in an
atom with occupancy 0.00 and write it out again in exactly the same
place.. All refinement contributions for atoms both Xray and geometrical
are weighted by the atom occupancy so such an atom will not shift.
The assumption
Does anyone know where to look for an error when PHASER outputs this
message?
Eleanor
.
*
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT
2.1.4 ***
If your dataextends to 2A resolution I suggest you run Arp-Warp or
Buccaneer to rebuild the structure. At that resolution the automated
building programd can usually fix errors.
At the end use this option to get the new build back to overlap the original
csymmatch -pdbin-ref MR.pdb -pdbin
On 01/20/2011 01:44 PM, Shao-Yang Ku wrote:
Dear all,
Is there a way to specify (somewhat arbitrarily) a origin for any
molecular replacement package (in a polar space group) without resorting
to phased translation so that one could more easily compare results from
different MR runs?
Thanks,
I absolutely agree with Phil.
However I think it is very important NOT to remove systematic absences
before scala. There are many cases of mis-assigned space groups where
systematic absences are misleading - due to NC translation or bad
measurement or whatever
Eleanor
On 01/24/2011
Coot does this seamlessly..
Eleanor
SSM superpose A to B
NCS Maps will generate the map around A over B - or vice versa..
Eleanor
On 01/28/2011 06:15 PM, RONG hui Rong wrote:
Dear All,
I have the problem as follows, but I can not find the corresponding
solution. Can somebody give me some
Have you checked for twinning? Look at the plots after scala..
Eleanor
On 02/07/2011 10:49 AM, Md. Munan Shaik wrote:
Dear all,
I have a question regarding the refinement and density map.
My protein is 261 amino acids long and crystalize very nicely with very high
resolution . There is no
Yees - a translation of 0.5 along x means you must consider SGs P212121
and P2 21 21 since the absences will be present (at least at low
resolution) with either SG.
I dont know how good Phenix would be at distinguishing between z=0.233
and z=0.25
However even if the exact peak is at z0.25,
Are you sure these are real FP=0 or reflections which werent measured
but have been added for completeness of the h k l list.
The check is whether the SigF is also 0.00 - in that case they are
genuinely missing..
Eleanor
On 02/09/2011 11:34 PM, Ed Pozharski wrote:
I observe under some
On 02/15/2011 04:36 PM, vineet joshi wrote:
Dear CCP4ers,
Is there any specific way that can help me locate the interactions between
ligand (GTP) to any other residue in the protein(GTPase) using CONTACT. And
how do I run CONTACT for a number of .pdb files(around 650) in one single
step and
Well P4 isnt a subgroup of P43212 - you would need P43
MR programs will often let you test several spacegroups. See Phaser MR
or MOLREP - I would try that and choose the best
Eleanor
On 02/16/2011 02:48 PM, Ting-Wei Jiang wrote:
Dear experts,
Sorry for a simple question but confusing
Another cause of difficulty - nothing really to do with the spacegroup
selection - is when one copy of the model has much higher B factors than
others. Most MR searches assume that the copies contribute more or less
equally to scattering.
If you assign too high a symmetry this will make MR
On 02/17/2011 09:35 PM, Peter Grey wrote:
Dear CCP4 and XDS users,
I have a P21 case with some strange ratios in the cell dimensions : a, b=a,
c=1.5a, 90, 105, 90. The native patterson shows a strong peak (40% of
origin) at (x,0.5,0) indicating some pseudo symmetry. Such cell dimension
and
On 02/18/2011 07:42 AM, Vellieux Frederic wrote:
Arp Warp used to want a blank line between the MALDH title, and the
first line of the sequence..
Not sure if that still holds.
Eleanor
a Hi Careina,
Just an example of a pir file which I just generated (using Bart Hazes
program mcfman):
Yes - you are.
-
There are some extra steps.
Download pdbs and mtz files
csymmmatch -pdbin-ref 1.pdb -pdbin 2.pdb -origin-hand -pdbout 2-to-1.pdb
That checks they are on same origin and symmetry equivalent.
refmac for 1.pdb
refmac for 2-to-1.pdb
cad to merge two refmac outputs.
You will
I think you have been caught by a new REFMAC feature which tries to
design its own TLS groups including linked H2Os and ligands.
Check your tls output records and see what it has clustered into a group..
I am not sure how to disable this - at times I want to override any
automatic
On 03/03/2011 06:13 AM, Ting-Wei Jiang wrote:
Dear all experts,
I'm trying to calculate R-value (and free R) specifically which is between
data and the modified structure(refined by myself without help from any
program).I've looked the program for calculating a long while.Actually,I
found one
No - and I dont think it is accepted practice now either..
I often use I/SigI 1.5 for refinement..
Look at your Rfactor plots from REFMAC - if they look reasonable at
higher resolution use the data
Eleanor
On 03/03/2011 11:29 AM, Roberto Battistutta wrote:
Dear all,
I got a reviewer
On 03/12/2011 05:29 AM, Vandu Murugan wrote:
Dear all,
Recently I collected a data for my 20Kda protein in C2 space group, and
ran SFcheck in ccp4 suite. It is giving an indication for
pseudo-translation as 'Pseudo-translation is detected: 17.6%
Pseudo-translation vector: 0.000
I guess the only real choice is P2 21 21 or P21 21 21 - the absences
alng h00 could be a result of the pseudo-translation.
I cant explain the score - maybe there is something in the documentation?
But I am afraid after refinement in P212121 the resultant model is sure
to give the best score
I have found it erratic, and sometimes terribly slow, but that may be
due to local network problems..
But it was working last week..
Eleanor
On 03/26/2011 05:28 PM, Miri Hirshberg wrote:
Sat., March 26th 2011
EBI
Dear Dan,
I've just checked (Sat. 17:25 British times), and uploading my
Well - I usually work in confunction with the graphics, so you can look
at the regions which differ.
I start with the rms difference. If that is 2, I think there are
significant changes. So then you have to decide what Q you are asking,
and why. Is it that you want to use a model for
Yes - that is true.
Any crystal might be split, and give diffraction with overlapping
lattices- ie show non-merohedral twinning. If you are lucky/careful you
might only get a few spots which overlap after integration of one of the
lattices- not enough to be detected as twinning from the
That translation is interesting - R3 indexed as hexagonal has a
crystallographic translation of 0.667 0.333 0.333, so this one
indicated by SFCHECK is related.
The twinning is not very severe so it should refine OK from the PHASER
solution.
Is that so?
Eleanor
On 04/08/2011 05:50 AM,
On 04/08/2011 12:17 PM, krishan wrote:
Dear CCP4BB members,
We are using a script written in python to generate symmetry mates for a
given pdb file using PYMOL. After generating symmetry mates we want to
combine all the symmetry molecules in a single PDB file with all the chains
having
On 04/08/2011 05:19 PM, Cale Dakwar wrote:
Hello all,
Given a PDB file of a newly solved protein structure, what is the standard
procedure for assigning regions of secondary structure? And by this I mean
to ask, how does one decide which residues form beta strands, which alpha
helices, and so
On 04/13/2011 09:18 PM, REX PALMER wrote:
Dear All
What is the best program to use for comparing two protein structures which are
very similar both structurally and wrt aa sequence? ie to get the rms
deviations both generally and in selected regions.
Rex Palmer
Birkbeck College
Using CCP4
Hmm - I use this quite a bit.
ifier.
You cant start Autoamore for a particular model until that has been
entered into the model database - the first Q you are asked from the GUI
is Which model? But you can certainly close the model database once
you have entered the model name with a unique
I dont know - it works for me..
That is under Fedora x
Eleanor
mtz2various HKLIN ./ins_pig_zn_T2_hex-unique_refmac1.mtz HKLOUT
./ins_pig_zn_T2_hex-unique_refmac1.hkl
OUTPUT CNS
labin FP=FP SIGFP=SDFP PHIB=PHIC FREE=FreeR_flag
end
On 04/27/2011 07:26 PM, Kelly Daughtry wrote:
Yes, you
I guess one way would be to seperate coordinates..
But doesnt overlapmap do that by default?
Eleanor
On 04/21/2011 10:25 PM, Maher Alayyoubi wrote:
Hi Everybody, I posted a question earlier on the bulletin regarding
how to calculate the map correlation coefficient using Overlapamp or
any
This may be too late to be of use, but as one of the authors of the
sfall/overlapmap system..
sfall does generate a coded map which flags every grid point with a
unique ID of the nearest atom, ie one which is unique providing there
are not too many atoms - it is adequate for most molecules
On 05/11/2011 10:30 AM, ka...@ssl.serc.iisc.ernet.in wrote:
Dear users,
I have refined a structure in R3 with cadmium bound to it, which
was present in the crystallization condition. There are 2 chains
in the asu. The structure is twinned. R and Rfree is around 22% and
28%. One of the
On 05/12/2011 08:13 PM, Fulvio Saccoccia wrote:
Dear ccp4 users,
I need to generate intensities from a model (.pdb). That is, I think that a
correct procedure could be to convert model to structure factor and then obtain
intensities squaring the SF.
Does anyone know how can I do?
Thanks in
If you have model coordinates for your CSA, I send those to the PRODRG
server and let it generate a REFMAC style dictionary.
You will need to make sure it is labelled as a peptide - cf the standatd
residue cif files to see how to do that..
Then you need to enter the LINKR record into the pdb
The default output for REFMAC
Missing Data: For those reflections where the FP are missing, mFo is set
equal to dFc. Hence the terms become FWT=dFC and DELFWT=0.0.
the Rfree reflections are counted as missing hence there shouldnt be
any bias intoroduced towards those Fobs assigned as free I
How very odd!
I have no ideas on the Zn phenonema - what do the R factor plots look
like against resolution - is there some aberrant reflection which was
part of the FreeR set? The theory is that excluding 5% of the data
should not affect the model seriously at all..
Re the 2nd point. Two
I havent used maprot for years. COOT does it very quickly and
automatically.
But it is tricky to get the matrices correct - can you give some more
details and I will try to help
Eleanor
On 05/27/2011 11:33 PM, Francis E Reyes wrote:
Hi all
I was just fiddling around with ncs and maps, so I
Use the GUI
Just feed the 2 sca files into pointless - choose one as the reference -
it really shouldnt match which..
pointless will check the indexing is consistent, then give you an output
file with the two sets merged and sorted together, with different batch
numbers assigned.
scala
On 06/03/2011 02:01 PM, Careina Edgooms wrote:
Dear ccp4 members
I have question about how to interpret polarrfn log. I wish to know if my
crystal display NCS. I am not sure how to interpret the file. I see it have two
peak, one is origin and the other is not that high to me. I have attach copy
I cant comment on the pictures - but to calculate an anom map -
if you have run REFMAC you will need to CAD together the refmac output
plus the Dano SIGdano in the data processed file
Use reflection utilies
Merge mtz files
then Map utilities
FFT - select anomalous
Fill in columns Dano
Reindex your data as -h -k l or h -k -l - this will automatically
change the cell to berta = 90.4
eleanor
On 06/08/2011 04:10 PM, Vellieux Frederic wrote:
Zhiyi Wei wrote:
Dear all,
I have a P2 derivative dataset with beta=89.6. I try to change the
beta to 90.4 to be consistent with
On 06/08/2011 07:19 PM, Shiva Bhowmik wrote:
Dear All,
I am working on a protein structure that yielded comparable diffraction
quality crystals from two different crystallization condition. One of the
crystallization condition conatins high conc. of salt pptant whereas the
oher one contains
First Q.
Checking the refined structure in detail..
This is personal.
Basic - run REFMAC with monitor many - that lists really bad bonds,
chirality, symmetry clashes etc, but frankly by the time you are at
R=20% there shouldnt be many of those..
You need to be sure you have described any CIS
It helps to keep the same water naming convention in all the complexes.
distang is a slow tool but it will list all contacts to a given set of
atomic radii. I use that output a lot to check on interesting contacts..
But in the end it boils down to thoughtful book-keeping..
Eleanor
On
It looks like a rhombehedral data set with small deviations from the
exact H3 symmetry to give the weak spots.
The standard H3 setting has origins at (0,0,0) (1/3, 2/3, 2/3) and
(2/3,1/3,1/3) so to get your translation vector to match the
conventional H3 one, you will have to reindex the P321
On 06/24/2011 08:50 AM, mullapudi edukondalu wrote:
Dear Members,
I have my first data set on one of my protein crystals, that diffract to
2.7 A, and the space group is I222. According to Mathews coefficient, there
should be 4 molecules in the asymmetric unit. But, when I run molecular
Well - it isnt surprising that all your geometry is good at the start.
You have fitted a refined structure against a a different crystal form,
so the first geometry report relates to your starting model which will
not be the true model which fits your new data.
Refinement has to push that
On 06/29/2011 10:22 PM, Paul Lindblom wrote:
Hi everybody,
can anybody tell me how crystal contacts are defined? Are there good and bad
crystal contacts? They are the most important interactions with impact on
the crystal quality, but they are not of covalent nature, aren´t they?
With best
Well - you have a problem of chain IDS,
but pdbset xyzin asymm.pdb xyzout whole-cell.pdb
symgen P212121 (say)
end
will generate a whole unit cell,
then
pdbset xyzin whole-cell.pdb xyzout whole-cell-+100
symgen x+1,y,z
end
etc
will move that unitcell.pdb
You would have to put them all
Can you send a bit of the input file and the command script generated by
the GUI
Eleanor
On 07/02/2011 07:48 AM, Sudhir Kumar wrote:
Dear all
I am trying to convert a scaled file (scaled using Automar) to mtz butit is
showing follwoing error
:
#CCP4I TERMINATION STATUS 0 Error from script
This is a problem not properly addressed - if you generate your
FreeRflags in the highest possible Laue group for a system - eg P6/mmm
if you SG is trigonal, then add these to the lower symmetry reflection
list you are safe. It really should be done at the pointless stage but
it isnt..
Here
On 07/04/2011 04:24 PM, ruheng wrote:
Dear all,
Recently we are working on an archaebacteria protein which was expressed and
purified from E.coli by conventional procedures. After we solved the
structure, we found that there is an extra density in one of the argninine as
shown in the
There are tools out there that calculate such a map.
REVISE is one - I guess i is in the list of CCP4 programs.
i often do both maps independently and look at them for common peaks
The trouble is that dispersive differences are often less reliable than
the anomalous ones..
Eleanor
If there is no indication of twinning and your Rmerge is sensible then
it is probably point group P222
Run pointless - that gives you the quality of each of the 2 folds sepera
tely..
Deciding on the spacegroup is a bit trickier.
That depends on absences along h00 0k0 and 00l, and if there
On 07/09/2011 03:49 AM, weifeng wrote:
Dear All,
There are 8 moleculars in an asymmetry unit, but only one molecular should be
rebulit, what can I do ?
Thanks a lot!
Wei Feng
Use coot - average maps over your best molecule, rebuild that - save
There are 2 rogue reflections in a data set I have here. How can I
eliminate them?
I thought sftools did this but i cant seem to get the syntax right.
Short of dumping the whole file, using an editor, then reconstructing it
I am stuck..
Eleanor
On 08/26/2011 10:18 AM, REX PALMER wrote:
Once waters have been located and refined is there a program that analyses
their positions
in terms of solvation shells?
Can the results be compared easily with those from related known
protein structures?
Rex Palmer
Dear John,
In a hexagonal crystal class the possible point groups are
P3 (only a 3-fold axis)
P321(3-fold plus 2-fold relating hkl and kh-l)
P312 (3-fold and 2-fold relating (hkl and -k,-h,-l)
P6 ( 6 fold axis only)
P622 (6-fold plus 2-fold relating hkl and k,h,-l)
pointless will tell you which
On 08/31/2011 01:32 AM, Yuri Pompeu wrote:
Quick newbie question,
After i get my output file from baverage containing the average b-factor and
rms by residues,
How can I calculate and display the average (and or mean) B-factors?
Is there a way of calculating it by protein, ligands and solvent
Like Jan, I find it very useful to sort out the clear cut cases.
Otherwise it is easy to get things wrong..
But isnt a buried surface area of 720 rather small for a stable
interface? If there is other confirming evidence like 2 diff space
groups then you feel more secure!!
On 09/01/2011
Hmm - Firstly: your final FC PHIC calculation are just wrong. I cant
tell why without more details - is the SG set correctly, because those
phases cannot reflect the SG symmetry.. Can you send the log file?
For the scaling against Fobs Qs. It looks to me as though you are using
values of Fobs
Yes - the RMS for the map is weighted by sin beta
Here is the comment:
C Mean RMS need to be weighted by sin beta, to allow for distortions
c in Eulerian space.
c On the last section, if beta = 90, the weight is 1/2 because of
c symmetry. Here we only need to test for last
Are you absolutely sure of the spacegroup?
Eleanor
On 09/13/2011 09:55 AM, #HEW KAI LI KELLY# wrote:
Hi,
I am facing some problems in solving my structure now, so I am wondering if
anyone is able to give me any tips and tricks on this matter.
My protein-DNA complex structure diffracted to
First the C2221 cell is a version of the hexagonal with the 2-fold axes
now aligned along the a=b 2-fold in the hexagonal.
But I dont think you can define NCS properly without some knowledge of
coordinates.
If you have enough anomalous scatterers that might allow you to get a
start.
Does
The cooot method is easiest, as long as you have model coordinates. Then
coot works out the transformation between molecule 1, 2, etc and
averages any map requested to cover molecule 1.
However if you dont have a model it is very tricky to get a proper
transformation matrix.
If you have
At this resolution you may/ should be able to find anamalous scatterers
using the anom signal from P and S. the SHELXC/D/(E) package is very
good at this!
Once you have the sites for the heavier atoms I would expect most direct
methods programs couild extend that sub-structure.
Certainly
You might like to look at this..
It tries to explain likely twinning possibilities in P21.
If you get C and P21, then probably a~=c - then Beta can have any
value.
C222 axes are then always possible with a* +c* , a*-c*, b* all
having angles ~ 90
Without twinning you wont get 222
On 09/29/2011 10:12 PM, Sam Arnosti wrote:
Hi every one
I have a problem with docking my ligand into the electron density map and make
the connections ( bonds ) with the protein.
It is a Lysine residue that makes a Schiff Base with a long chain aldehyde.
I do not know how to make the bonds
On 09/30/2011 08:01 AM, Yuri Pompeu wrote:
Hello everyone,
I am refining a structure to 2.4A with 2-fold NCS and twinned.
Maps look ok and Rfree is 0.27however as I start checking my validations I
notice that after refinemnt
my geomtry gets significantly worse. especially the rama plot.
Further Qs.
Do you have a noncryst translation parallel to the b axis (ctruncate
will list any such translation..)
If the b shift is 0.5 then the 0k0 absences will be present whether
the spacegroup is P2 or P21.
How many Xe sites do you expect? If there is only one then phasing is
more
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