Re: [ccp4bb] how many stuck datasets are actually twinned?

[Peter Zwart]

This usually leads to a mad 
chase through all possible space groups, twinning refinements, etc. and, 
in my experience, often results in a lot of time being spent for no 
significant improvements.


If one has a model to refine, it is actually very straightforward to 
test all possible merohedral twin laws for a given unit cell and space 
group. phenix has a 'jiffy' called mmtbx.twin_map_utils (in the cctbx 
actually) that carries out anisotropic and bulk solvent scaling together 
with the refinement of the twin fraction for a fixed model. This can 
give a very quick indication which twin law results in the best twin 
fraction if you have a model.


If your space group is too high (and doesn't have any twin laws) it is a 
trivial matter to expand the data to a lower point group and try that. 
Currently not automated in phenix, but easy to do by hand with some 
cctbx tools. The same goes for MR, expanding to a lower symmetry and 
trying that is straightforward and relatively easy to automate.


Sometimes however, people get confused. I once saw a case where a person 
wasn't able to a beautiful Se-SAD structure with a certain software 
package and decided that the space group was too low. Merging the data 
in a lower SG did allow that particular software to find the sites and 
phase it. The symmetry was however too low. Using different resolution 
cut offs or other packages did result in a successful structure 
solution. The wrong symmetry structure is still in the PDB unless it has 
been redeposited.


In the end, I guess one should try everything possible and likely, 
starting with the most plausible and easy solution. Automation makes a 
lot of things easy (and sometimes even fast) so in the future we might 
not even have to bother about the plausible bit.


HTH

Peter

[ccp4bb]

[Peter Zwart]

hmmm...

is this the beginning of a potential endless loop of emails?

P


David W Borhani wrote:

Hi, David Borhani is no longer with Abbott. Please resend your email to:

[EMAIL PROTECTED]

Re: [ccp4bb] phasing power ofatoms

[Peter Zwart]

Hi all,

It is good to keep in mind that


  2*[ <|Iplus - Imin|> / < Imean > ]
\approx
[ < (|Iplus - Imin|) / Imean > ]


  i.e.

  / is NOT equal to 



In fact,  might be closer to what one is interested in from an 
experimental point of view, as that talks about 'average signal' rather 
than the 'signal average'.


Also, when reporting these ratios, it is important to stipulate what is 
reported. Some flavours are:

< |dI| >/
< |dI|/I >
< |dF| > 
< |dF|/F >
< dF^2 >^1/2 / ^1/2
.
.
. etc etc etc

They are all related of course, but all have slightly different values.

In the end, what matters is data quality anyway. Having good Bijvoet 
ratios on paper doesn't help much if you don't have good data.


Some thoughts on these issues can be found in Acta Cryst. (2005). D61, 
1437–1448 and references therein. The simulation tool described in this 
paper is available on request.



HTH

Peter





--
Peter Zwart
Beamline Scientist,
Physical Biosciences Division
Berkeley Center for Structural Biology

Building 6, Room 2134
Tel: 510-486-4214, Fax: 510-486-5664
http://bcsb.lbl.gov

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 6R2100
Berkeley, CA 94720, USA.
--

Re: [ccp4bb] twin fraction varies between crystals?

[Peter Zwart]

Hi Mark,

Estimating twin fractions is best done on the basis of refining it with 
a model. This can be done with phenix.refine or other programs like 
shelx or CNS.


The ML estimate ofd the twin fraction relies on the correctness of the 
sigmas. The 0.02 is actually the lower limit the ML procedure will 
produce, I should fix that/be more clear when reporting the results I guess.


The fact that the twin fractions vary this much is not surprising I 
think. I guess this depends on the type of twinning (contact vs 
penetration), although I am not sure about this.


Peter






Mark Mayer wrote:
For cases where people have had merohedral twinning, did the twin fraction vary substantially 
between individual crystals grown under indentical conditions? I have no prior experience with 
merohedral twinning, and was surprised to see that the twin fraction varied substantially as detailed 
below, and that by screening we were able to get untwinned xtals. 

The project started with a weak home data set for which the twin fraction was 0.478, and which 
scaled in both H3 and H32. We just came back from APS with data sets from another three crystals, 
for which the ML twin fraction, estimated using phenix.xtriage with scalepack merged intensities as 
input, varied from 0.335, 0.219 and 0.02. The latter is refining very nicely, in H3 and will not scale in 
H32. 


Thanks - Mark

Re: [ccp4bb] MolRep with Phaser using a partial existing solution

[Peter Zwart]

Hi Jay,

Maybe try to use the the rhombohedral setting (space group R32:R, with 
unit cell 229,229,229,81,81,81 ) rather than the hexagonal one used now. 
Depending on the fft algorithm used to compute structure factors for 
your partial model, this can save you a chuck off memory/time.


You can reindex the data and change the model relatively straightforward 
reflecting the new set of basis vectors.


Cheers

Peter








Jay Thompson wrote:
The cell is quite big.  300 x 300 x 450 A, 90, 90, 120 (R32).  I'm using 
the entire resolution range at the moment, but I've just set up another 
job with a reduced resolution range.  So we'll see how this goes.  I 
only get this error message when I do a run with Phaser with this 
partial known solution fixed.  It also does the rotation function fine, 
but fails at the translation.  Any other suggestions or comments would 
be greatly appreciated!  Thanks


Jay

On 5/17/07, *Tim Grune* <[EMAIL PROTECTED] 
> wrote:


Hi,

what resolution range do you use? You can try reducing it a little.
How big is your cell?
Tim

On Friday 18 May 2007 13:46, Jay Thompson wrote:
 > Hi,
 >
 > Thanks for the suggestions and quick reply.  Suggestions work great!
 >
 > But I have another problem and looking back at the ccp4bb, I see that
 > Elenor had a similar problem late last year.  The error message is as
 > follows:
 >
 >
 > 
 > --
 > OUT OF MEMORY ERROR: St9bad_alloc
 > --
 > 
 >
 > 
 > 
 > EXIT STATUS: FAILURE
 > 
 >
 > CPU Time: 0 days 0 hrs 19 mins 53.80 secs (1193.80 secs)
 > Finished: Thu May 17 20:28:14 2007
 >
 > 
 > 
 >
 > The only suggestion from the ccp4bb threads that I could see was
to try
 > running it on a different computer with more memory.  I've tried
running
 > the job on two different Mac G5 and I get the same error
message.  The
 > computers that I have are pretty new and have 2 GB of SDRAM.  I'm
surprised
 > that I have a memory problem.  I'm also using the Phaser 1.3.3 (I'm
 > assuming this is the latest version).  Thanks for all your help, in
 > advance.
 >
 > Jay
 >
 > On 5/17/07, Jay Thompson <[EMAIL PROTECTED]
> wrote:
 > > Hi,
 > >
 > > I have a question with molecular replacement using Phaser.  I'm
trying to
 > > solve a complex and I have a partial molecular replacement solution
 > > solved using another program.  This solution is correct and
makes up ~50%
 > > of the entire complex.  I wanted to fix this solution and
search for
 > > another small fragment of the complex using Phaser.  I've been
reading
 > > the Phaser manual and it seems that I cannot input a pdb with this
 > > partial solution and tell the program to fix this molecule.  It
seems
 > > that fixed solutions can be only input by putting in its Euler
angles and
 > > fractional coordinate
 > > translations.  Is this correct that I cannot input a pdb and
fix it?  If
 > > I cannot do this, then is there a quick way to identify the
euler angles
 > > and coordinate translations for Phaser.
 > >
 > > Thanks a lot!!
 > >
 > > Jay

--
Tim Grune
Australian Synchrotron
800 Blackburn Road
Clayton, VIC 3168
Australia

Re: [ccp4bb] Simultaneous PHENIX and CCP4 burp

[Peter Zwart]

The ccp4 gui has an option that allows one to specify which executable
to run. I allways forget how to get there.


From the phenix gui there is no problem, it uses the absolute path for

executables, and (as far as I know) phaser is invoked from within
python.

Most interesting mmtbx and iotbx commands can be accessed as
phenix.something. We also have things like phenix.solve,
phenix.resolve and phenix.reduce, which setup all the enviromental
variables +etc when you run it.
Furthermore, any executable in phenix can be executed as
phenix.something_XXX
where XXX is a version number. This works for phaser as well.
try
phaser_1.26b
and see what happens.

HTH

Peter







2007/5/23, Frank von Delft <[EMAIL PROTECTED]>:

Hi, surprisingly I've not seen this question on either BB -- or else nobody
have both packages installed simultaneously (surely not)





Both ccp4 and phenix have a version of Phaser (v1.3.3 and v2 respectively).
Each is (?) incompatible with the other's GUI, yet in a simultaneous
install, only one can be on the PATH.
 a) Are the executables very different?  (v1.3.3 and v2.0 for ccp4 and
phaser respectively.)  v2 has an older release date...
 b) How can one fix the path to make both executables available to the
shell?
 c) The same problem affects mmtbx and cctbx etc.


Shouldn't the ccp4 versions maybe get different names?

phx.

Re: [ccp4bb] DANO from PDB

[Peter Zwart]

Hi Santosh,

Here is an alternative to methods mentioned earlier. If you get the 
latest version of the cctbx or cci_apps (from www.phenix-online.org) you 
will find a new application named phenix.xmanip (or mmtbx.xmanip if you 
only download the cctbx).


xmanip has some useful features, one of them is that one can provide 
pieces of python code to the interface that will be executed. You have 
full access to all cctbx methods available.


Please find below an example parameter file that perform structure 
factor calculation (in less than 90 lines of code and input) that 
includes elements with f" and f' not being equal to zero (you have to 
set the values of f" and f' yourself rather then rely on lookup tables 
by wavelength) and allows you to set bulk solvent parameters such as 
ksol, bsol and the overall anisotropic B of the data (B_cart).


Save the text below (between the hash-es in a file named params.def , 
change the unit cell and sg parameters, the input pdb file and f" and f' 
value dictionary to suit your needs:

( like
fp_dict  = { "S": 0, "C": 0   }
fdp_dict = { "S": 0, "C": 2.8 }
for instance }

You can fool around with solvent density, solvent B, overall scale 
factor and overall anisotropic B value and resolution (d_min).


Then run

phenix.xmanip params.def

and get a file named xmanip.mtz that will contain your error free data.
If you want, you can add uniform or Gaussian errors yourself.

Since xmanip is fairly new, you will find a bug in the current release 
that somehow appears when you do not read in any external xray data. 
This happens however right after the mtz file in question has been 
written out. This will be fixed in the forthcoming release (soonish).


Let me know if anything is unclear or if you have trouble running it.

HTH

Peter Zwart


###

xmanip {
  input {
unit_cell =  "80.127   80.127   71.582  90.00  90.00 120.00"
space_group = R3:H
model {
  file_name = tst.pdb
}
  }
  parameters {
action = reindex manipulate_pdb *manipulate_miller
manipulate_miller {
  task = get_dano get_diso lsq_scale sfcalc *custom None
  output_label_root = "Imock"
  custom{
code = """
#---
# This you can change if desired
#

# Dictionary for fp and fpp values
fp_dict  = { "Zn": -0.189 }
fdp_dict = { "Zn":  4.898 }

# final resolution of the data
d_min= 2.0

# anisotropic B value
b_cart = [ 0, 0, 0, 0, 0, 0 ]

# solvent parameters
k_sol = 0.35
b_sol = 45.0

# overall scale
k_overall  = 1.0


#---
# below this point, things should be more or less okai
#

from mmtbx import f_model
from cctbx.xray import observation_types

#loop over all scatterers in the xray structure
#print >> out, dir(xray_structure)
scatterers = xray_structure.scatterers()
for atom in scatterers.as_1d():
  if fp_dict.has_key( atom.element_symbol() ):
atom.fp = fp_dict[ atom.element_symbol() ]
  if fdp_dict.has_key( atom.element_symbol() ):
atom.fdp = fdp_dict[ atom.element_symbol() ]
#the changes have been made to fp and fdp

#Now we have to do some trickery to get some fobs with bulk solvent
#contribution ...

#First make a 'fake' set of f_obs
fake_f_obs = abs(xray_structure.structure_factors(
   d_min  = d_min,
   anomalous_flag = True ).f_calc())
# make a 'fake' set of free flags
fake_free_flags = fake_f_obs.generate_r_free_flags(fraction = 0.1,
   max_free = )
fmodel = f_model.manager( xray_structure   = xray_structure,
  r_free_flags = fake_free_flags,
  target_name  = "ls_wunit_k1",
  f_obs= fake_f_obs,
  b_cart   = b_cart,
  k_sol= k_sol,
  b_sol= b_sol,
  overall_scale= k_overall )
# now get the final values of F+ and F-.
# Note the abs to get amplitudes only
result = abs( fmodel.f_model() ).set_observation_type( 
observation_types.amplitude() )

# you want make this into intensities?
result = result.f_as_f_sq()
# lets leave the intensities alone for now, and just make 'mock' sigmas
# to statisfy certain programs.
# Don't forget to set the observation type!
sigmas =  result.data()/100.0
result = result.customized_copy(data = result.data(), 
sigmas=sigmas).set_observation_type(result)

#By default, a parameter named result is passed back to the xmanip
#routines and will be written to the final mtz file

"""
  }
}
  }
  output {
logfile = "xmanip.log"
hklout = &

[ccp4bb]

[Peter Zwart]

I suggest you go back to your images and see what is going on during indexing.
You might want to check for certain unexplained peaks to could be an
indication of reticular-non merohedral twinning: you have 30 58 118 90
90 90. If you take two unit cells and stick them on top of eachother,
you will have a block with dimensions 60 58 118 90 90 90, which is
allmost equal to a P422 symmetry. This could be difficult to handle in
refinement, although not impossible in shelxl.

Other options could be that
1. Your space group is not P212121 but is P2x2y2z. Try all of them.
The truncate NZ plot could be messed up due to data quality.
2. Your spacegroup is P2x11, P12x1 or P112x and you have twinning
possibly combined with pseudo symmetry. Processyour data in all
spacegroups or process it in xtraige and look at the R-values for
various P21 choices.

You might have to solve the structure in each and every space group
and see if one of them does work out.


HTH

Peter





2007/6/8, Marius Schmidt <[EMAIL PROTECTED]>:

Dear Experts,
I have a strange problem.
Recently, we have collected some data on some myoglobin
derivative. Crystals were quite twinned and we had to
cut a leavlet out of a bundle of crystals.
Crystal scattered to 2.6 A. Apparent space group
P212121 with paramters [in A]: 30 58 and 118.
One single mol-rep solution was found with
sig to noise of rotation: 17
sig to noise of transl:   15
In two dimensions molecules pack nicely (see attached
image vowi34.gif) in the other direction there is much to much
space between the layers of molecules that one could
envision proper crystal packing (see other image vowi32.gif).
And indeed: refinement stops with R-cryst/R-free ~34/42 [%]
with some spurious e-density outside the molecule which does
not look like water.
Matthew coefficient: 2.8 with one mol per asy unit.
I tried to find another MR solution with the first
one fixed and I failed (signal to noise of the best
Rot and Trans solutions around 3).
What could be the problem? I always thought that
twinning cannot be the reason in P212121. Density
distributions (from truncate) however seem to indicate
some degree of twinning although this might also be
a problem of data processing (data are quite weak).
Maybe some of you have encountered similar problems and
know how to solve them. Any hint very much wellcome.

Marius

Re: [ccp4bb] Old High B-Factor Issue

[Peter Zwart]

Detwinning data and refining against detwinned data is not the best
thing to do, especially when you realise that detwinning data with
twin fraction larger than 45% is done using model information in CNS:
the detwinned data you get out is not experimental anymore.
Subsequently, you cannot trust your R and Rfree statistics as you
would normally and any 'improvement' you see in your free R or your
maps, might be due to the 'detwinning'

Have you tried using TLS refinement in combination with twin refinement?

Peter











2007/6/9, Gregg Crichlow <[EMAIL PROTECTED]>:





Dear CCP4 Readers,

Quite some time ago, before the CCP4BB changed its server, I
posted the following inquiry concerning high B-factors in a protein-DNA
complex from a twinned crystal in which most of the DNA was not visible.



Dear CCP4BB:

We have a protein-DNA complex from a twinned crystal (space group P31). I
detwinned the data and refined the structure to 2.1 A with Rfree=28.8%
before adding water and nucleotides. We can only observe density for two of
the 25 nucleotides. I noticed that the B-factors are very high (around 50-60
A^2). Not many water molecules can be added using a 80 A^2 cutoff. We
determined the structure of the unbound protein, and the B-factors are
almost as high. I tried fixing the B-factors at 20, but Rfree increased to
30.9%. Is this indicative of an error that can be fixed? Thank you.



I do apologize for the delay in the follow-up. I thank everyone who
responded. The real problem was not the B-factors, of course, but the
incomplete DNA density. The various replies I received in essence mentioned
that (1) high B-factors are not necessarily a problem, (2) I should not
refine against de-twinned data, and (3) try density modification to be able
to see more of the structure. Unfortunately, the density modification
suggestion did not work with respect to improving the map, and refining
against twinned data had not appeared to be useful. It turned out that
de-twinning the data was the best way to proceed, judging by R/R-free
statistics, although this was not supposed to be as good as working with the
twinned data using the twinning fraction. I remember noting in the CNS
tutorial that using twinned data may not work well if the twinning fraction
is greater than 0.4, which it was in our case (about 0.49). Maybe that was
the problem. In the end, I used the data de-twinned in CNS as if it were a
perfect twin. Nonetheless, the high B-factors seem to be real. Although the
Wilson B-factor is high, maybe I was just hoping that this was due to the
DNA, not so much protein, and that sharpening the protein B-factors would
improve the map. This did not work. However, after handling the data the way
we did and now obtaining reasonable statistics, at least now I can be more
confident that the electron density for the nucleotides that we do see are
real. I thank everyone for their input.



Gregg





***
 Gregg Crichlow
 Dept. of Pharmacology
 Yale University
 P.O. Box 208066
 New Haven, CT 06520-8066
 ***

Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

[Peter Zwart]

I don't think that there is a program available to do what you want, but


What about APEX2 from Bruker?

P

Re: [ccp4bb] Twinning in C2 ?

[Peter Zwart]

Hi Demetres,

not sure if this is going to be usefull, but here I go.

Your native has a twin law that and your cell is pseudo C222. The
mutant is not. pseudo merohedral twinning is not handled well by the
twin server you derscribe as it relies on lookup tables.


There is no obvious 'perfect' relation between two unit cells. The
ratio between the two unit cell volumes is about 1.8 and a sublattice
of your native cell that comes close to the lattice of your mutant
does exist. iotbx.explore_metric_symmetry tries to find you  possible
relations. It uses niggli settings though and the output is not very
user (or even developer) friendly:

--
Mutant niggli cell :  32.3  81.8  90.1  76.8  79.7  78.6
Native niggli cell :   33.1  53.2  73.4  90.3  90.0 108.1

   /   100  \
matrix :  M =  |   021  |
   \   001  /

(matrix M acts on the real space basis vectors of the Native niggli cell)

Additional Niggli transform:  x-y,-y-z,y
Additional similarity transform:  x,y,z
Resulting unit cell :   33.1  90.5  90.9  67.8  79.5  79.5
Deviations :-2.5 -10.6  -0.8   8.9   0.2  -0.8
Deviations for unit cell lengths are listed in %.
Angular deviations are listed in degrees.
--

Details of what the matrix M means is found in
http://www.ccp4.ac.uk/newsletters/newsletter44/articles/explore_metric_symmetry.html


It is too early for me to understand if the pseudo translation you see
at (1/2,0,1/2) is related to the transfomration shown above, but if
you multiply this translation in C2, you do end up with a smaller unit
cell. why don't you try this:

run xtriage (a latest version) on your mutant data and see what the
patterson analyses tells you what it thinks the unit cell is if the
patterson peak were a true crystallographic operator.
Take that unit cell and compare it to your native
(iotbx.explore_metric_symmetry might be usefull).

Again, I am not sure that a relation is there, but if it is real, you
can get the coordinates for your mutant structure almost directly from
your native structure.

The relations one sees can be deceiving though, it could be
crystallographic numerology.

Cheers

Peter








2007/7/13, Demetres D. Leonidas <[EMAIL PROTECTED]>:

Dear all,

we have encountered a problem in solving one mutant structure. The
mutant protein crystallizes in the same space group as the native (C2)
but the unit cell dimensions are different. These for the native
structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 160.4 32.3
107.0 90 125.7 90. As a result the mutant structure has  four molecules
in the asymmetric unit while the native had two. When we run molecular
replacement all programs (CNS, molrep, and amore) find only two
molecules. Phaser finds four but when we try to refine the Rfree does
not drop below 0.44 if we use four molecules and 0.53 if we only use two
no matter how well we built the molecule and regardless of any addition
of water molecules (the resolution of the data is 2.1). The interesting
thing is that in the electron density map we can clearly see density for
a substrate analog that was included in the crystallization media. Do
you thing  that we have a case of twinning here ? We have to mention
that Tod Yates served did not indicate any perfect merohedral twinning
(partial merohedral twinning for this space group is not possible).

We would appreciate any comments

Many thanks

Demetres

--
Demetres D. Leonidas, Ph.D.
Structural Biology & Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
 +30 210 7273895 (lab)
Fax. +30 210 7273831
E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==

Re: [ccp4bb] phenix mtz to ccp4 mtz conversion

[Peter Zwart]

Use truncate to convert I-obs to F-obs. No format change is needed.


Peter


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
I-obs
SIGI-obs
R-free-flags

I can't seem to get it to work.  I am using Import, it runs, spits out 
a new mtz, and then Refmac complains about the labels.  What is the 
easiest way (ie what program in ccp4 and usig what parameters).


Thanks,
John Bruning

Re: [ccp4bb] density histogram

[Peter Zwart]

Hi Bernard, it this is relatively easy. Copy this text:


#phil __ON__
xmanip {
 input {
   xray_data {
 file_name = porin.mtz
 labels = FOFCWT
 name = map_coef
 write_out =False
   }
 }
 parameters {
   action = *manipulate_miller
   manipulate_miller {
 task = *custom
 custom{
   code = """
import math
map = map_coef.fft_map().real_map_unpadded()
data = map.as_1d()
mean = flex.mean( data )
std = flex.mean( data*data-mean*mean)
std = math.sqrt( std )
data = (data-mean)/std
histo = flex.histogram(data,n_slots=30)
histo.show()
"""
 }
   }
 }
}
#phil __END__





into something called rupp.def
Change the input mtz file and input labels into whatever you need/have .
Make sure you have downloaded the latest version of phenix, cci_apps or 
the cctbx.

Then run

mmtbx.xmanip rupp.def

to get a histogram printed out:

-4.3615799 - -3.917308: 81
-3.917308 - -3.4730361: 408
-3.4730361 - -3.0287643: 1965
-3.0287643 - -2.5844924: 9006
-2.5844924 - -2.1402205: 28548
-2.1402205 - -1.6959486: 77763
-1.6959486 - -1.2516767: 186741
-1.2516767 - -0.80740483: 386079
-0.80740483 - -0.36313295: 634365
-0.36313295 - 0.08113894: 785736
0.08113894 - 0.52541082: 698574
0.52541082 - 0.96968271: 451065
0.96968271 - 1.4139546: 221478
1.4139546 - 1.8582265: 96711
1.8582265 - 2.3024984: 52725
2.3024984 - 2.7467702: 35046
2.7467702 - 3.1910421: 25470
3.1910421 - 3.635314: 18111
3.635314 - 4.0795859: 10530
4.0795859 - 4.5238578: 6165
4.5238578 - 4.9681297: 3366
4.9681297 - 5.4124016: 1476
5.4124016 - 5.8566734: 630
5.8566734 - 6.3009453: 252
6.3009453 - 6.7452172: 108
6.7452172 - 7.1894891: 36
7.1894891 - 7.633761: 18
7.633761 - 8.0780329: 9
8.0780329 - 8.5223048: 9
8.5223048 - 8.9665766: 9



Some background: xmanip has a 'custom' function that allows you to push 
in snippets of python code that deal with models or reflection files.  
The custom code I wrote is fairly simple as you can see. It saves you 
the overhead of writing an interface that deals with reading in data etc 
etc.

in the above text, the code that does the histogram stuff is:

import math
map = map_coef.fft_map().real_map_unpadded()
data = map.as_1d()
mean = flex.mean( data )
std = flex.mean( data*data-mean*mean)
std = math.sqrt( std )
data = (data-mean)/std
histo = flex.histogram(data,n_slots=30)
histo.show()

It should be obvious what is going on.
Other parts of rupp.def deal only with reading in the data and telling 
the jiffy what to do.


HTH

Peter









Bernhard Rupp wrote:


2007/8/2, Bernhard Rupp <[EMAIL PROTECTED]>:
  

Dear All -

before I code ahead - is there a simple program/script available where 
I can read in a map and it gives me a basic 1d density histogram (or 
the tabular data at least) in return?


Thx, br
-
Bernhard Rupp
http://www.ruppweb.org/
-
It is not your aptitude but your attitude that determines your 
altitude.

-

Re: [ccp4bb] High Rfac/Rfree for a 1.6A reso structure

[Peter Zwart]

Hi Elisabetta

Your unit cell is pseudo F222, with twin law (-h,-k,h+k+l):

iotbx.explore_metric_symmetry --unit_cell="47.7533.6191.04
90.000 103.635  90.000" --space_group=C2

(output below)

Did you rule out twinning?
Try runing phenix.xtriage for some intensity stats and/or
phenix.refine for lsq twin refinement  and see where the twin fraction
goes.

Contact me personally if you need help or if you are not sure how to run things.

HTH

Peter


A summary of the constructed point group graph object is given below


--
Input crystal symmetry
--
Unit cell:  (47.75, 33.609, 91.046, 90.0,
103.635001, 90.0)
Unit cell volume:  141990.310662
Space group:  C 1 2 1


--
Lattice symmetry deduction
--
Niggli cell:  (29.196295141678505, 29.196295141678505,
90.088423129339745, 94.902521424695664, 97.427868096943868,
109.71853700070298)
Niggli cell volume:  70995.1553311
Niggli transformed input symmetry:  C 1 2 1 (x+y,-x+y+z,z)
Symmetry of Niggli cell:  F 2 2 2 (x-y+z,x+y+z,2*z)


All pointgroups that are both a subgroup of the lattice symmetry and
a supergroup of the Niggli transformed input symmetry wil now be listed,
as well as their minimal supergroups/maximal subgroups and symmetry
operators that generate them.
For each pointgroup, a list of compatible spacegroups will be listed.
Care is taken that there are no sysmetatic absence violation with the
provided input spacegroup.


Vertices and their edges


Point group   F 2 2 2 (x-y+z,x+y+z,2*z)   is a maximal subgroup of :
  * None

Point group   C 1 2 1 (x+y,-x+y+z,z)   is a maximal subgroup of :
  * F 2 2 2 (x-y+z,x+y+z,2*z)



-
Transforming point groups
-

>From C 1 2 1 (x+y,-x+y+z,z)   to  F 2 2 2 (x-y+z,x+y+z,2*z)  using :
  *  -h,-k,h+k+l



--
Compatible spacegroups
--

Spacegroups compatible with a specified point group
**and** with the systematic absenses specified by the
input space group, are listed below.

Spacegroup candidates in point group F 2 2 2 (x-y+z,x+y+z,2*z):
  * F 2 2 2  33.61 47.75 177.01 90.00 90.00 90.00

Spacegroup candidates in point group C 1 2 1 (x+y,-x+y+z,z):
  * C 1 2 1  47.75 33.61 92.30 90.00 106.55 90.00


2007/8/17, Sabini, Elisabetta <[EMAIL PROTECTED]>:
> Dear all,
>
> I have a structure at 1.6A. At the end of refinement the Rfactor and Rfree
> are quite high (23/29.6%). Here are some info:
>
> Morphology of crystals: large but thin plates (150 x 400 x 20 microns)
> Number of residues: 160 (2 x 80); 103 water molecules
> Space group: C2
> Unit Cell: 47.7533.6191.04  90.000 103.635  90.000
>
> Data is a merge of a low resolution and high resolution sweep. The
> correlation between the two data sets is:
>
>  DATA SETS  NUMBER OF COMMON  CORRELATION   RATIO OF COMMON   B-FACTOR
>   #i   #j REFLECTIONS BETWEEN i,j  INTENSITIES (i/j)  BETWEEN i,j
>
> 124049   0.9731.0002 0.0001
>
> I include the data collection and refinement statistics in the attachment.
>
> Can you please suggest to me possible reasons for the high Rfact and Rfree?
>
> Thanks,
>
> Elisabetta.
>
> --
> Elisabetta Sabini, Ph.D.
> Research Assistant Professor
> University of Illinois at Chicago
> Department of Biochemistry and Molecular Genetics
> Molecular Biology Research Building, Rm. 1108
> 900 South Ashland Avenue
> Chicago, IL 60607
> U.S.A.
>
> Tel: (312) 996-6299
> Fax: (312) 355-4535
> E-mail: [EMAIL PROTECTED]
>
>

Re: [ccp4bb] Strange diffraction images

[Peter Zwart]

> As a side note, Xtriage
> doesn't think things are twinned as was suggested for one some of the other
> diffraction patterns discussed earlier today.

Hi Todd,

Detection of twinning in the presence of pseudo translations / and or
NCS parallel to the twin law is difficult and using model based
techniques (RvsR statistic) could be usefull.

Furthermore, I would like to point to Acta D 63, 926-930 with some
pointers to literature regaring other 'weird' pathologies.


HTH

Peter

Re: [ccp4bb] small molecule refinement GUI for Mac

[Peter Zwart]

What about the very nice OLEX2 gui?

http://www.dimas.dur.ac.uk/olex

Groet,

Peter

2007/8/31, William Scott <[EMAIL PROTECTED]>:
> gfortran -o platon platon.f xdrvr.c -lX11 -L/usr/X11R6/lib  does the trick.
>
>  export NETEXE="open"
>
> lets you use your default web browser.
>
> That's one fugly interface.
>
>
> Miller, Mitchell D. wrote:
> > What about Ton Spek's Platon / System-S package?
> > http://www.cryst.chem.uu.nl/platon/pl00.html
> > It does not have precompiled mac OSX binaries (only
> > linux and windows), but it does have source code
> > and instructions for compiling under unix and states
> > that it will compile without changes under macOSX.
> > It is free for academics.
> >
> > Regards,
> > Mitch
> >
> >
> > 
> >
> > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
> > Kristof Van Hecke
> > Sent: Friday, August 31, 2007 5:16 AM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] small molecule refinement GUI for Mac
> >
> >
> > Dear all,
> >
> > I'm looking for a small molecule refinement GUI for shelxl under Mac OSX
> > (commercially or non-commercially available).
> > Any suggestions are very welcome!
> >
> > Many thanks
> >
> > Sincerely
> >
> > Kristof
> >
> >
> >
> > --
> > Kristof Van Hecke, PhD
> > Biomoleculaire Architectuur
> > Celestijnenlaan 200 F
> > B-3001 Heverlee (Leuven)
> > Tel: +32(0)16327468
> > --
> >
> >
> >
> >
> >
> > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more
> > information.
> >
>

Re: [ccp4bb] Another twinning question

[Peter Zwart]

>
>   RRfree  Fract
> P6122   0.277  0.362
> P61 0.266  0.35
> P61 twin0.177  0.219  0.494
> P3112   0.27   0.352
> P3112 k,h,-l0.177  0.22   0.494
> P3112 -h,-k,l   0.177  0.22   0.494
> P3121   0.27   0.357
> P3121 -k,-h,-l  0.177  0.213  0.494
> P3121 -h,-k,l   0.177  0.213  0.494
>
> It seems I have for second time in a year a tetartohedral twinning in the
> space group P31.

I suggest that for all twin laws in each sg here you compute an R vs R
statistics and see what you get. For that, you need to have both Fobs
and Fcalc in the same file (which is easy enough using
phenix.twin_map_utils, it outputs obs_and_calc.mtz). A susbequent run
of xtriage where you will feed in both fobs and fcalc wil compute the
rvsr stats.

Use the reference to the paper by Lebedev Vagin & murshudov as a
guideline to find out how to interpret these values.

algebraic detwinning results in maps that are less biased, but with
the twin fraction you describe, that is not possible. You could try
having a look at gradient maps of the LSQ target on F as produced by
phenix refine to see if it makes things better.

HTH

Peter

Re: [ccp4bb] Nearly perfect twinned data????

[Peter Zwart]

> As you see, distortion index table indicates I centered tetragonal, I
> centered orthorhombic, F centered orthorhombic, C centered monoclinic
> and triclinic as possible Bravais lattices.
>
>  Data processed in I centered tetragonal gives low Rmerge in all the
> possible space groups namely I4, I41, I422 and even I4122.  Other
> space groups in lower symmetry lattices also gave low R merge values
> (around 6% in most of the cases).

If it processes nicely in I422, it will also in subgroups of I422 (sub
as I4, I222, various choices of C2 and of course P1).

> Since we have not been able to obtain a solution in any of the space
> group from I centered tetragonal to triclinic (I4, I4122, I222, C2 and
> even P1) using Se-SAD, we decided to check the data for any intrinsic
> problem such as twinning.

Do you have any anomalous signal?


>
> Now my question is:
> -  Are data showing low Rmerge value in I4122 due to nearly perfect
> twin in space group I4?
>

That is possible, but seems unlikely.

> -  Why cumulative intensity distribution shows a normal pattern for
> the data where as Yeates server and SFcheck indicates nearly a perfect
> twin?  Why Yeates server and SFCheck shows different twin fraction and
> twin operator?

Twin fraction estimates rely on correlations between twin related
intensities. If you process yuor data in a spacegroup that is too low,
you will see that
1. You have twin laws available for your crystal symmetry
2. You have strong correlations between twin related reflections
In both cases, the cause is the that you have wrong symmetry.

Twinning analyses should take into account the presence of wrong
symmetry. If that is not done, question like this come up.

Furthermore, the yeates server unfortunately doesn't deal with pseudo
merohedral twinning.

The differences in twin operators is due to the crystal symmetry: the
operators listed are related by the symmetry of I4. The difference in
twin fraction is due to difference s in data cuts and resolution
limits I suppose.

I highly recommend using phenix.xtriage (for obvious reasons) to give
you a relatively clear picture of what is going on. Get it from the
latest phenix release. usage is straightforward.

> -  Is it possible to detwin this data and use it for structure solution?

I guess you first want to make sure that your experimental data has
any anomalous signal at all before your blame twinning to be the
reason that you cannot solve your structure.

HTH

P

Re: [ccp4bb] Twinning

[Peter Zwart]

try using phenix.refine and use TLS. it might help lowering Rfree (or
raising Rwork).

P




2007/10/23, john kryst <[EMAIL PROTECTED]>:
> Hi CCP4bb ,
>
>  Thanks for your suggestions... here is the summary of the
> structure...
>
> I am working in deletion and point mutants.  I have a mutant (P61 resoln
> 3.1A) with partial twinning with twinning fraction 0.28. Wilson b-factor is
> 50. The data collected in the home source with normal exposure time. The
> rmsd's of the refined structure  is 0.0081 (bonds) and 1.38672 (angles).
> Molprobity is score is 50 without any manual model building (just after the
> refinement).
>
> Since the structure is twinned new free R-flag has been chosen according to
> CNS make_cv_twin.inp. The b-factor has been flattened to 30. Then
> rigid-body_twin refinement followed by simulated annealing_twin is done
> (heating the structure up to 5000K with different initial velocity trials).
> The R and R free after this step is  18.35 and  27.22. Then i did
> bgroup_twin refinement which gave me  R and R free 17.06 25.63. Further
> model building and refinement tend to reduce the R and Rfee upto 15 and 23.
>
> I deleted some portion of the molecule and did refinement. But proper
> density appeared  after it.
>
> Please help me out.
>
> John
>
>

Re: [ccp4bb] Twinning

[Peter Zwart]

Hi Dirk,

Nice cross validation flags for twin refinement do obey the twin law:
if (h,k,l) is in the free set, then  (k, h, -l) should be as well.
Same is/should be true for work set btw.

In phenix, we generate test reflections that follow the lattice
symmetry (*). This means that even if you do not realise that your
data is potentially twinned (or has a wrong point group), you do not
end up biasing your test set. The actual reductionof a low symmetry
free set to high symmetry free set is a bit of 'art- and fly-work'
(kunst en vliegwerk) , but is doable.

The CNS "make_cv_twin.inp" script needs a specific twin law. In the
case where more then a single twin law is possible, taking them all
into account is not a bad idea.

Cheers

Peter



(*) check out:

http://phenix-online.org/cctbx_sources/cctbx/cctbx/miller.py

and look for the function

def denerate_r_free_flags_on_lattice_symmetry




2007/10/23, Dirk Kostrewa <[EMAIL PROTECTED]>:
> Hi John,
>
> if I understand the "make_cv_twin.inp" correctly, then this script takes
> care about separating reflections related by the twin law to avoid a
> potential bias of the Free-R set with twin-law-related reflections from the
> working set. At least, in the source of this script I read the comment: "{-
> make sure all twin related reflections are in the same set -}". If this is
> true, then you simply don't have to worry any further about your good
> R-factors, but enjoy a very well refined structure!
> Maybe, the authors of this CNS script could comment on this separation of
> reflections?
>
> Best regards,
>
> Dirk.
>
>
> Am 23.10.2007 um 15:32 schrieb john kryst:
>
> Hi CCP4bb ,
>
>  Thanks for your suggestions... here is the summary of the
> structure...
>
> I am working in deletion and point mutants.  I have a mutant (P61 resoln
> 3.1A) with partial twinning with twinning fraction 0.28. Wilson b-factor is
> 50. The data collected in the home source with normal exposure time. The
> rmsd's of the refined structure  is 0.0081 (bonds) and 1.38672 (angles).
> Molprobity is score is 50 without any manual model building (just after the
> refinement).
>
> Since the structure is twinned new free R-flag has been chosen according to
> CNS make_cv_twin.inp. The b-factor has been flattened to 30. Then
> rigid-body_twin refinement followed by simulated annealing_twin is done
> (heating the structure up to 5000K with different initial velocity trials).
> The R and R free after this step is  18.35 and  27.22. Then i did
> bgroup_twin refinement which gave me  R and R free 17.06 25.63. Further
> model building and refinement tend to reduce the R and Rfee upto 15 and 23.
>
> I deleted some portion of the molecule and did refinement. But proper
> density appeared  after it.
>
> Please help me out.
>
> John
>
>
>
> ***
> Dirk Kostrewa
> Gene Center, A 5.07
> Ludwig-Maximilians-University
> Feodor-Lynen-Str. 25
> 81377 Munich
> Germany
> Phone:  +49-89-2180-76845
> Fax:  +49-89-2180-76999
> E-mail: [EMAIL PROTECTED]
> ***
>
>

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

[Peter Zwart]

Wilson plots are not very informative for the detection of twinning.

The spikes you see in your Wilson plots,  could be due to ise ring
issues (both 3.89 and 2.24 A are at ice ring related d scapings.) The
very large mean intensity in those resolution shells could be due to
the fact that only  strong reflections were not rejected during data
processing.
Since there is only 1 spike per dataset and the completeness in those
shells is not shown, one canot be sure I guess.

The NZ plots or L-stats could be useful.

Cheers

Peter










2007/10/29, Iain Kerr <[EMAIL PROTECTED]>:
> Thanks very much for all the suggestions so far.
>
> While I am pursuing all the checks and balances for twinning here are
> the Wilson plots I forgot to attach before..I am not sure what is going
> on, especially in B !
>
> best,
> Iain
>
>
> >
> >
> > On Oct 25 2007, Iain Kerr wrote:
> >
> >> Dear all,
> >>
> >> I find myself posed with a rather interesting if somewhat confusing
> >> problem.
> >>
> >> Two crystals grown from the same conditions, let's call them A and B..
> >>
> >> A:
> >>
> >> Resolution 2.1A
> >> SpacegroupP4?
> >> Rmerge0.137 (0.324)
> >> Mean((I)/sd(I))   41.0  (17.8)
> >> Completeness 100   (100)
> >> Multiplicity53.6  (56.3)
> >>
> >> 4/mmm is clear from indexing...systematic absences show a clear 4
> >> fold screw-axis..Pointless gives the most likely as P4_1 22 (I'm not
> >> clear on how it distinguishes P4_1 22 and P4_3 22..)
> >>
> >> Molecular replacement in Phaser, checking all the possible
> >> spacegroups, gives two outstanding solutions
> >>
> >>  LLG   Z-score
> >> P4_3 22 1972   41 (1mol/asu)
> >> P4_3  3801   54 (2mols/asu, ASU too full warning !)
> >>
> >> Solutions in other spacegroups had negative LLGs and/or were rejected
> >> for poor packing...the P1 solutions have  LLGs of around -22000
> >>
> >> I rebuilt both solutions in ARP/wARP both giving Rfree ~32% and Rfac
> >> ~23%...rebuilding (most residues accounted for), adding ligands and
> >> water makes no difference.
> >>
> >> Different iterations of refinement/rebuilding eg. cutting resolution
> >> make no difference...the maps are really well defined and packing is
> >> very reasonable with no clashes in either spacegroup.
> >>
> >> B:
> >>
> >> Resolution 2.3A
> >> Spacegroup  C222?
> >> Rmerge0.187 (0.402)
> >> Mean((I)/sd(I))   11.8  (4.8)
> >> Completeness 99.4 (98.8)
> >> Multiplicity 6.8  (6.6)
> >>
> >> Mosflm:
> >>
> >> 11 144 mC   255.6164.3263.9790.0  90.3  76.1   C2
> >>  10 7 oC 90.69 90.74 124.09 90.3 90.7 89.7 C222,C2221
> >>   9   7tP63.9764.32   124.0990.7  90.3  90.0
> >> P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212
> >>   8   5   oP63.9764.32   124.0990.7  90.3  90.0
> >> P222,P2221,P21212,P212121
> >>   7   5  mP63.97   124.0964.3290.7  90.0  90.3   P2,P21
> >>   6   4  mC90.6990.74   124.0989.7  90.7  90.3  C2
> >>   5   4  mC90.6990.74   124.0990.3  90.7  89.7  C2
> >>   4   3  mP64.3263.97   124.0990.3  90.7  90.0   P2,P21
> >>   3   1  mP64.3263.97   124.0990.3  90.7  90.0   P2,P21
> >>   2   0   aP63.9764.32   124.0989.3  89.7  90.0   P1
> >>   1   0   aP63.9764.32   124.0990.7  90.3  90.0   P1
> >>
> >> This suggests pseudo-merohedral twinning to me...in C222/C222_1 ...a
> >> and b are almost equivalent,  so the 4/mmm symmetry would be apparent ?
> >>
> >> The Rmerge in 422 (19.6%) is only slightly higher than C222/C222_1
> >> systematic absences again suggest a 4 fold...the curves
> >> calculated from the cumulative intensity distribution suggest partial
> >> twinning (when inputting C222_1  into the 'old' server to calculate a
> >> twin fraction from the partial twin test it says there are no twin
> >> laws for that spacegroup...)
> >> _
> >> The outstanding solutions in Phaser this time are:
> >>
> >>   LLG Z-score
> >> P4_3 22 131735 (1mol/asu)
> >> C222_1 223746 (2mols/asu, ASU too full warning !)
> >>
> >> Rigid body refinement of the solutions give (C222_1 ) Rfree 43%, Rfac
> >> 42% and ( P4_3 22 ) Rfree 44%, Rfac 43%I'm thinking this is high
> >> and the maps from Phaser although fitting the placed molecules have
> >> poor connectivity (high Rmerge anything to do with this ?)
> >>
> >> Going back to crystal A it turns out the same C222/C222_1  is found
> >> but lower down in the list amongst the other solutions...
> >>
> >> I have attached the Wilson plots for both crystals...A has a large
> >> spike at high resolution (which is why I cut the data to 2.4A to try
> >> and improve refinement, to no avail) and B looks horrid !
> >>
> >> OK, I think that is all the information I have at 

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

[Peter Zwart]

> the Nz test says no twinning

and the intensity stats say this as well.

> but the Britton and H-plots give a twin fraction of
> 0.46-0.47 !

The britton and H test give an estimate of the twin fraction IF THE
DATA IS WOULD BE TWINNED. The fact it gives a non zero value does not
indicate the presence of twinning.


> the patterson analysis suggests weak translational
> pseudo-symmetry..could this be masking the detection of twinning in the Nz
> test ?

The peak is 5% of the origin. This is noise.

>  My first time using Phenix..am I interpreting these results correctly
> ?..the high twin fraction would certainly explain why I get a lot of really
> good MR solutions that don't refine...

Of course, the fact that the intensity stats do not indicate twinning
doesn't mean data is not twinned, so please go ahead in any lower
space group that you/PHASER/MOLREP feels comfortable with. make sure
however that the reduction you see in the R values are significant.
The RvsR stat can be helpfull as well (Lebedev et al, 2005(?)). It is
calculated when you supply an mtz file that contains Fcalc as well as
Fobs (use obs_lables=FOBS, calc_label=FMODEL or so). Also, check your
NCS operators and CA rmsd values when done with refinement to see if
they suggest any higher symmetry.

Peter



HTH

Peter

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

[Peter Zwart]

I am a big fan of the RvR statistic
(http://journals.iucr.org/d/issues/2006/01/00/ba5089/index.html)
This statistic is very usefull when a model is available.

When no model is present, the L test is nice as well and is relatively
robust in the presence of pseudo centring.

P





2007/10/31, Eleanor Dodson <[EMAIL PROTECTED]>:
> The cumulative intensity depends on correctly estimating weak
> reflections, so it is a bit vulnerable to the integration procedures.
>
> I prefer the 4th moment of E - 2nd moment of I. Providing there is no
> pseudo-translation they are pretty reliable indicators of twinning
>   Eleanor
>
> Bryan W. Lepore wrote:
> > On Mon, 29 Oct 2007, Iain Kerr wrote:
> >> The cumulative intensity distribution plot from crystal A did suggest
> >> partial twinning (attached, doesn't look too bad though..)
> >
> > notwithstanding other plots/statistics, does the cum. intens. dist.
> > plot (e.g. from truncate) really show a continuum from untwinned to
> > twinned?
> >
> > i.e, if the plots are 'overlapped in the middle', no question -
> > twinned. but, if the plots are 'a little off, but not in the middle'
> > can this result (alone) really mean the data is - as we want to say -
> > partially twinned?  i.e. is the plot robust only for the detection of
> > perfect twinning?
> >
> > -bryan
> >
> >
>

Re: [ccp4bb] XDS and overlaps

[Peter Zwart]

or use phenix, which is indifferent to format and asu choice.


P


2008/2/21, Michele Lunelli <[EMAIL PROTECTED]>:
> Simon Kolstoe wrote:
>
>  > I converted the resulting
>  > XDS_ASCII.HKL using xdsconv and then f2mtz ready for phaser and refmac.
>  >
>
>
> Sorry if this is obvious, but you should also run CAD after f2mtz, as reported
>  at the end of the log file XDSCONV.LP.
>
>
>  Michele
>

[ccp4bb] Beam Time at BCSB beamlines in Berkeley

[Peter Zwart]

=
Synchrotron Beam Time available for Macromolecular Crystallography
   at Berkeley Center for Structural Biology Beamlines
 (5.0.1, 5.0.2, 5.0.3, 8.2.1 and 8.2.2).

 The ALS is now accepting General User applications for May/June
=

The Berkeley Center for Structural Biology (BCSB) operates five
beamlines at the Advanced Light Source in Berkeley. Beamlines 5.0.1,
5.0.2 and 5.0.3 are equipped with the Berkeley Automounter system.
Beamline 8.2.2. has a Rigaku Actor sample mounter capable of handling
Rigaku, unipucks and ALS style pucks.

Beamlines 5.0.2, 5.0.3, 8.2.1 and 8.2.2 have large 3x3 Q315 or Q315r
CCD detectors. Beamlines 5.0.2, 8.2.1 and 8.2.2. are MAD stations, whereas
5.0.3 and 5.0.1 are fixed energy beamlines at the Se high energy
remote, suitable
for Se-SAD experiments. The beamlines generate between 1.5x10^11 and 8x10^11
photons per second of flux into a 100 micron collimator at 1.5 mrad divergence.
Please visit http://bcsb.lbl.gov/ for more details about the Center
and its beamlines.

If you'd like to apply for beamtime at these, or any other ALS
macromolecular crystallography beamlines, please submit a General
User proposal by March 15, 2008 in order to be considered for the
May-June schedules. To find out more, click on:

http://www-als.lbl.gov/als/quickguide/independinvest.html

We invite you to submit a proposal at:

http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize

You can also request access to any open beam time on the five BCSB
beamlines by e-mailing our scheduler at [EMAIL PROTECTED]

Any industrial or academic group interested in becoming part of the
Participating Research Team for beamlines 5.0.1 and 5.0.2 should contact
the Head of the BCSB (Paul Adams: [EMAIL PROTECTED], 510-486-4225).

(Please note that executed user agreements and proprietary fees, if
applicable, must be received at least five working days prior to
scheduled beam time.)

--
Peter Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron road,  Berkeley, CA-94720
Cell: +1 510 289 9246
Fax:  +1 510 486 5664

Re: [ccp4bb] Wilson B and Mean B factors

[Peter Zwart]

>
>
> I've never looked at this statistics before, so I'm a bit surprised
>

So am I !


> - I was expecting a larger discrepancy between Wilson B and average B at
> low resolution. Although this is probably because PHENIX uses Peter Zwart's
> likelihood-based Wilson B estimation (Peter - what's the reference?), which
> is supposed to be better.
>

The stability at lower resolutions is indeed due to the likelihood based
method that utilizes a reference curve ('standard wilson plot') as obtained
from the PDB.



The original idea came from Sasha Popov & Gleb Bourenkov, both the reference
curve idea as well as the likelihood target. It is in fact the same target
as used for refinement of anisotropic scale during refinement with the
important note that sigmaA = 0.

This is where the likelihood based wilson scaling comes from:

A.N. Popov and G.P. Bourenkov "Choice of data-collection parameters based on
statistic modeling" Acta Crystallogr. (2003). D59, 1145-1153


These are my notes:

http://www.ccp4.ac.uk/newsletters/newsletter42/articles/CCP4_2005_PHZ_RWGK_PDA.doc

HTH

Peter




>
> Pavel.
>
>
>
> On 7/1/10 12:52 AM, Dirk Kostrewa wrote:
>
>  Dear Murugan,
>
> at higher resolution, the Wilson plot captures mainly the contribution of
> atoms with lower B-factors which leads to a systematic underestimation of
> the true B-factor distribution. Accordingly, the average B-factor of refined
> structures tend to be higher then the Wilson B-factor, at least in my
> experience. In your case, it is the other way around. One possible problem
> could be, apart from the fit of the Wilson plot as James Holton suggested,
> that you have reflections at very low resolution with underestimated
> intensities due to cut overloads or measurement in the half-shadow of the
> beamstop. This would result in a too low overall B-factor for the model in
> order to try to fit the usually stronger low resolution reflections at the
> cost of the weaker high resolution data. One quick check of this hypothesis
> is to cut the low resolution at, say, 10 A instead of 50 A and run a
> test-refinement. If this results in more realistic model B-factors, you
> should have a closer look at the low resolution data and exclude the
> ill-measured ones.
>
> Best regards,
>
> Dirk.
>
> Am 30.06.10 19:31, schrieb Vandu Murugan:
>
> Dear all,
>  If one could find a difference of more than 15  between Wilson B
> factor of the data ( 55) and Mean B factor of the structure, (30) what could
> be the possible reasons?  I am seeing it in my structure.  Could someone
> tell me why it could be?? Thanks in advance.
>
> Yours faithfully,
> Murugan
>
>
>


-- 
-
P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:  http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
-

[ccp4bb] Beamtime at the ALS-BCSB beamlines

[Peter Zwart]

Dear All,

July 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal
cycle.

All Berkeley Center for Structural Biology(BCSB) beamlines are equipped
with ADSC Q315/Q315R detectors, automated sample changers and data
collection software enabling high-throughput crystal screening and data
collection.

Remote data collection is available on all BCSB beamlines, providing
the user with the full complement of sample visualization, sample
manipulation, beamline control, data acquisition and data analysis tools
exactly as they would see them if they were stationed at the beamline. The
main difference between local operation and remote operation, is the length
of the network cable!  This enhanced remote operation capability is coupled
with 22hr onsite support by BCSB staff who are able to assist immediately
with loading additional samples for remote users or troubleshoot any issues
that might arise. Remote users can furthermore be kept up-to-date on
changes in ring status via an SMS service (
http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Phone)
or via twitter (@AlsRingStatus).

Specific features are summarized below.


Beamlines 5.0.1, 5.0.2, 5.0.3:
--

Beamline 5.0.2 is equipped with a novel variable collimator allowing users
to adjust the beamsize continuously and on the fly between 25 and 100
micron, both horizontally and vertically. With a collimator setting of 30x30
micron, typical exposures are around 1 to 2 second.

The Berkeley Automounter sample handling system has a routine capacity of
96 samples (6 pucks). In a typical high-throughput screening mode, the
mount-to-mount time is around 2.5 minutes per sample, allowing users to
screen a full puck within 45 minutes.

The sector 5 beamline user stations are equipped with fully high-adjustable,
ergonomically friendly work stations.


Beamlines 8.2.1 and 8.2.2:
---

To facilitate studies on small crystals, a microdiffractometer was installed
in the beamline 8.2.1 endstation. The new equipment allows precise sample
positioning to within 2 microns, excellent sample viewing of very small
crystals, and an off-axis crystal positioningstage.

Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer
(Actor), allowing remote operations to now be a routine mode of access
for these beamlines.


Data analyses in the BCSB is facilitated by software maintained by sbgrid (
http://www.sbgrid.org).  A 16 core linux machine is available for our
users to process their data and solve/refine their structure.

An additional mode of access to the BCSB beamlines is through
the Collaborative Crystallography (CC) Program. Users apply for beamtime via
the general user program, and collaborate with an expert crystallographer
who will conduct the experiments and data reduction on behalf of the
researchers. Depending on the users, structure solution, model building and
refinement can be carried out as well.  Please contact
bcsbbeamt...@lbl.govfor more information.

Please visit http://bcsb.lbl.gov/ for more details about the Center and its
beamlines.

To find out more, click on:

http://www.als.lbl.gov/als/quickguide/independinvest.html

We invite you to submit a proposal at:

http://alsusweb.lbl.gov/

Scroll down to "Structural Biology beamines (includes protein SAXS)."

Click on "New Proposal."

If you have any questions or would like to request open beamtime,
please e-mail bcsbbeamt...@lbl.gov.

Please note that executed user agreements must be received by LBNL
prior to beamtime. Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.


-- 
-
P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:  http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
-

Re: [ccp4bb] Beamtime at the ALS-BCSB beamlines

[Peter Zwart]

Sorry for the clutter:  This is of course for the Aug/Sept cycle.

P

2010/7/12 Peter Zwart 

> Dear All,
>
> July 15, 2010 is the deadline for the March/April 2010 Rapid
> Access Proposal cycle.
>
> All Berkeley Center for Structural Biology(BCSB) beamlines are equipped
> with ADSC Q315/Q315R detectors, automated sample changers and data
> collection software enabling high-throughput crystal screening and data
> collection.
>
> Remote data collection is available on all BCSB beamlines, providing
> the user with the full complement of sample visualization, sample
> manipulation, beamline control, data acquisition and data analysis tools
> exactly as they would see them if they were stationed at the beamline. The
> main difference between local operation and remote operation, is the length
> of the network cable!  This enhanced remote operation capability is coupled
> with 22hr onsite support by BCSB staff who are able to assist immediately
> with loading additional samples for remote users or troubleshoot any issues
> that might arise. Remote users can furthermore be kept up-to-date on
> changes in ring status via an SMS service (
> http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Phone)
> or via twitter (@AlsRingStatus).
>
> Specific features are summarized below.
>
>
> Beamlines 5.0.1, 5.0.2, 5.0.3:
> --
>
> Beamline 5.0.2 is equipped with a novel variable collimator allowing users
> to adjust the beamsize continuously and on the fly between 25 and 100
> micron, both horizontally and vertically. With a collimator setting of 30x30
> micron, typical exposures are around 1 to 2 second.
>
> The Berkeley Automounter sample handling system has a routine capacity of
> 96 samples (6 pucks). In a typical high-throughput screening mode, the
> mount-to-mount time is around 2.5 minutes per sample, allowing users to
> screen a full puck within 45 minutes.
>
> The sector 5 beamline user stations are equipped with
> fully high-adjustable, ergonomically friendly work stations.
>
>
> Beamlines 8.2.1 and 8.2.2:
> ---
>
> To facilitate studies on small crystals, a microdiffractometer
> was installed in the beamline 8.2.1 endstation. The new equipment
> allows precise sample positioning to within 2 microns, excellent
> sample viewing of very small crystals, and an off-axis crystal
> positioningstage.
>
> Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer
> (Actor), allowing remote operations to now be a routine mode of access
> for these beamlines.
>
>
> Data analyses in the BCSB is facilitated by software maintained by sbgrid (
> http://www.sbgrid.org).  A 16 core linux machine is available for our
> users to process their data and solve/refine their structure.
>
> An additional mode of access to the BCSB beamlines is through
> the Collaborative Crystallography (CC) Program. Users apply for beamtime via
> the general user program, and collaborate with an expert crystallographer
> who will conduct the experiments and data reduction on behalf of the
> researchers. Depending on the users, structure solution, model building and
> refinement can be carried out as well.  Please contact
> bcsbbeamt...@lbl.gov for more information.
>
> Please visit http://bcsb.lbl.gov/ for more details about the Center and
> its beamlines.
>
> To find out more, click on:
>
> http://www.als.lbl.gov/als/quickguide/independinvest.html
>
> We invite you to submit a proposal at:
>
> http://alsusweb.lbl.gov/
>
> Scroll down to "Structural Biology beamines (includes protein SAXS)."
>
> Click on "New Proposal."
>
> If you have any questions or would like to request open beamtime,
> please e-mail bcsbbeamt...@lbl.gov.
>
> Please note that executed user agreements must be received by LBNL
> prior to beamtime. Proprietary fees, if applicable, must be received
> by LBNL at least five working days prior to scheduled beamtime.
>
>
> --
> -
> P.H. Zwart
> Research Scientist
> Berkeley Center for Structural Biology
> Lawrence Berkeley National Laboratories
> 1 Cyclotron Road, Berkeley, CA-94703, USA
> Cell: 510 289 9246
> BCSB:  http://bcsb.als.lbl.gov
> PHENIX:   http://www.phenix-online.org
> SASTBX:  http://sastbx.als.lbl.gov
> -
>



-- 
-
P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:  http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
-

[ccp4bb] Beamtime at the ALS-BCSB beamlines

[Peter Zwart]

Dear All,

September 15, 2010 is the deadline for the November/December 2010
Rapid Access Proposal cycle.
All Berkeley Center for Structural Biology(BCSB) beamlines are
equipped with ADSC Q315/Q315R detectors, automated sample changers and
data collection software enabling high-throughput crystal screening
and data collection.
Remote data collection is available on all BCSB beamlines, providing
the user with the full complement of sample visualization, sample
manipulation, beamline control, data acquisition and data analysis
tools exactly as they would see them if they were stationed at the
beamline. The main difference between local operation and remote
operation, is the length of the network cable!  This enhanced remote
operation capability is coupled with *22hr onsite support* by BCSB
staff who are able to assist immediately with loading additional
samples for remote users or troubleshoot any issues that might arise.
Remote users can furthermore be kept up-to-date on changes in ring
status via an SMS service
(http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Phone)
or via twitter (@AlsRingStatus).
Specific features are summarized below.

Beamlines 5.0.1, 5.0.2, 5.0.3:
--
Beamline 5.0.2 is equipped with a novel variable collimator allowing
users to adjust the beamsize continuously and on the fly between 25
and 100 micron, both horizontally and vertically. With a collimator
setting of 30x30 micron, typical exposures are around 1 to 2 second.
The Berkeley Automounter sample handling system has a routine capacity
of 96 samples (6 pucks). In a typical high-throughput screening mode,
the mount-to-mount time is around 2.5 minutes per sample, allowing
users to screen a full puck within 45 minutes. The sector 5 beamline
user stations are equipped with fully high-adjustable, ergonomically
friendly work stations.

Beamlines 8.2.1 and 8.2.2:
---

To facilitate studies on small crystals, a microdiffractometer was
installed in the beamline 8.2.1 endstation. The new equipment allows
precise sample positioning to within 2 microns, excellent sample
viewing of very small crystals, and an off-axis crystal
positioningstage. Both beamlines 8.2.1 and 8.2.2 feature a Rigaku
sample changer (Actor), allowing remote operations to now be a routine
mode of access for these beamlines.

Data analyses in the BCSB is facilitated by software maintained by
sbgrid (http://www.sbgrid.org).  A 16 core linux machine is available
for our users to process their data and solve/refine their structure.
An additional mode of access to the BCSB beamlines is through the
Collaborative Crystallography (CC) Program. Users apply for beamtime
via the general user program, and collaborate with an expert
crystallographer who will conduct the experiments and data reduction
on behalf of the researchers. Depending on the users, structure
solution, model building and refinement can be carried out as well.
Please contact bcsbbeamt...@lbl.gov for more information.

Please visit http://bcsb.lbl.gov/ for more details about the Center
and its beamlines.
To find out more, click on:
http://www.als.lbl.gov/als/quickguide/independinvest.html
We invite you to submit a proposal at:
http://alsusweb.lbl.gov/
Scroll down to "Structural Biology beamines (includes protein SAXS)."
Click on "New Proposal."
If you have any questions or would like to request open beamtime,
please e-mail bcsbbeamt...@lbl.gov.
Please note that executed user agreements must be received by LBNL
prior to beamtime. Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.

--
-
P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
-

Re: [ccp4bb] twinned?

[Peter Zwart]

Hi Bart,

important are the dimensions of the reduced cell.
in this case his uc params are 99 167 125 90 90 90. parameters of the
niggli cell are
97, 97, 125, 90.0, 90.0, 118 which is pseudo hexagonal.

[running xtriage would give this info, including an L-test and other
various tests]

HTH

P





2008/4/3, Bart Hazes <[EMAIL PROTECTED]>:
> I just realized that this is an orthorhombic C222(1) space group. I didn't
> check it up but unless two of the cell-dimensions are nearly identical I
> think merohedral twinning is not possible for this space group, because the
> symmetry of the unit cell shape is not higher than the symmetry of the space
> group.
>
>  Bart
>
>
>  Eleanor Dodson wrote:
>
> > 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. There is a reference to the L test: J. Padilla & T. O. Yeates. A
> statistic for local intensity differences: robustness to anisotropy and
> pseudo-centering and utility for detecting twinning. /Acta Crystallogr./
> *D59*, 1124-30, 2003.
> S
> They suggest using neighbouring reflections pairs to test .   This can often
> overcome the problem associated with pseudo-translation. However it is quite
> sensitive to data quality.
> > See http://nihserver.mbi.ucla.edu/pystats/
> >
> >  Eleanor
> >
> >
> > Bart Hazes wrote:
> >
> >
> > > Hi Qiang,
> > >
> > > A normal data set has a unimodal intensity distribution with a
> predictable shape. When there is twinning the distribution remains unimodal
> but becomes sharper and this is picked up in the twinning analysis. When
> there is pseudo-translational symmetry, as you indicate you have, then the
> intensity distribution becomes bimodal with one set of reflections
> systematically strengthened and another systematically weakened. This makes
> the whole distribution broader, just the opposite of what twinning does, and
> therefore shows up as "negative twinning" in the analysis.
> > >
> > > Bart
> > >
> > > Qiang Chen wrote:
> > >
> > >
> > > > Hi all,
> > > >
> > > > The data I am working on has a strong translation vector. The space
> group
> > > > is C2221 and resolution is 2.3 angstrom. There are two molecules per
> AU
> > > > with a pseudo-2-fold axis.
> > > > On the cumulative intensity distribution plot, the theor and obser
> curves
> > > > totally do not overlap. I did "detect_twinning" from CNS, and there is
> the
> > > > result:
> > > >
> > > >  <|I|^2>/(<|I|>)^2  = 3.2236 (2.0   for untwinned, 1.5   for twinned)
> > > >  (<|F|>)^2/<|F|^2>  = 0.6937 (0.785 for untwinned, 0.865 for twinned)
> > > > Does the result mean my data is not twinned?
> > > >
> > > > Any suggestion will be highly appreciated.
> > > > Thank you!
> > > >
> > > > The information transmitted in this electronic communication is
> intended only
> > > > for the person or entity to whom it is addressed and may contain
> confidential
> > > > and/or privileged material. Any review, retransmission, dissemination
> or other
> > > > use of or taking of any action in reliance upon this information by
> persons or
> > > > entities other than the intended recipient is prohibited. If you
> received this
> > > > information in error, please contact the Compliance HelpLine at
> 800-856-1983 and
> > > > properly dispose of this information.
> > > >
> > > >
> > > >
> > >
> > >
> > >
> >
> >
> >
>
>
>  --
>
> ==
>
>  Bart Hazes (Assistant Professor)
>  Dept. of Medical Microbiology & Immunology
>  University of Alberta
>  1-15 Medical Sciences Building
>  Edmonton, Alberta
>  Canada, T6G 2H7
>  phone:  1-780-492-0042
>  fax:1-780-492-7521
>
> ==
>


-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] space group problem

[Peter Zwart]

Take your c2 cell, go to niggli setting, double the c axis. apply
transform (-x+z,y-z,-z). now you end up with your P2 cell in the
niggli setting.  you might have stromng pseudo translational symmetry
(or your unit cell is too big)



phenix.explore_metric_symmetry --unit_cell=145,44,67,90,110.5,90
--space_group=C2 --other_unit_cell=67,44,136,90,96,90
--other_space_group=p2




.
.
.
.
.


Unit cell comparison


The unit cells will be compared. The smallest niggli cell,
will be used as a (semi-flexible) lego-block to see if it
can construct the larger Niggli cell.



Crystal symmetries in supplied setting

Target crystal symmetry:
Unit cell: (67, 44, 136, 90, 96, 90)
Space group: P 1 2 1 (No. 3)
Building block crystal symmetry:
Unit cell: (145, 44, 67, 90, 110.5, 90)
Space group: C 1 2 1 (No. 5)

Crystal symmetries in Niggli setting

Target crystal symmetry:
Unit cell: (44, 67, 136, 96, 90, 90)
Space group: P 2 1 1 (No. 3)
Building block (lego cell) crystal symmetry:
Unit cell: (44, 67, 75.7644, 109.58, 106.88, 90)
Space group: C 1 2 1 (x+y,z,2*x) (No. 5)

Volume ratio between target and lego cell:  1.99

Cartesian basis (column) vectors of lego cell:
  /  44.0   0.0 -22.0 \
  |   0.0  67.0 -25.4 |
  \   0.0   0.0  67.9 /

Cartesian basis (column) vectors of target cell:
  /  44.0   0.0   0.0 \
  |   0.0  67.0 -14.2 |
  \   0.0   0.0 135.3 /

A total of8 matrices in the hermite normal form have been generated.
The volume changes they cause lie between2 and1.

Trying all matrices

   1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0
   . * . . . . . .
 Listing all possible solutions

Solution1
--
Target unit cell :  44.0  67.0 136.0  96.0  90.0  90.0
Lego cell : 44.0  67.0  75.8 109.6 106.9  90.0

/   100  \
matrix :  M =  |   010  |
\   002  /

Additional Niggli transform:  -x+z,y-z,-z
Additional similarity transform:  x,y,z
Resulting unit cell :   44.0  67.0 136.8  96.8  90.0  90.0
Deviations : 0.0   0.0  -0.6  -0.8  -0.0  -0.0
Deviations for unit cell lengths are listed in %.
Angular deviations are listed in degrees.


--



2008/5/1 Junyu Xiao <[EMAIL PROTECTED]>:
>  Hi all,
>
> We run into an interesting space group problem. The same diffraction image
> can be either indexed into space group C2, with a=145, b=44, c=67, and
> beta=110.5; or space group P2 (should be P21 after scaling), with a=67,
> b=44, c=136, and beta=96.8. Both are refined ok during index. These two must
> somehow be related. Can anyone give some comments on that?
>
> Thanks a lot,
> Junyu
>
>
> =
> Junyu Xiao
> Department of Biological Chemistry,
> University of Michigan
>
> Lab address:
> 3163 Life Sciences Institute,
> University of Michigan,
> 210 Washtenaw Avenue
> Ann Arbor, MI, 48109-2216
> Phone: 734-615-2078
> ==
>
>
>
>



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
-

Re: [ccp4bb] space group problem

[Peter Zwart]

Clemens is right of course. If you ignore the lattice centring in C2,
the cells are the same.

I was however under the impression that auto-indexing goes via the
primitive cell. Which makes the two solutions unique.
Ignoring the possible lattice translation in P2 will show up in a
Patterson function (at 1/2,1/2,0 i think) . The lattice translation
might of course be a pseudo translation. In the C2 case, you would
miss weak reflections if P2 would be the right answer.


P





2008/5/1 Clemens Vonrhein <[EMAIL PROTECTED]>:
> Dear Junyu,
>
>  it looks to me like you encounter a classical monoclinic feature: one
>  can index monoclinic always in two ways
>
>
>  origin
>|
>V
>
>A' -- A
>   \   /\   /
>\ /  \ /
> \   /\   /
>  \ /  \ /
>   \   /\   /
>\ /  \ /
> \   /\   /
>  \ /  \ /
>   //
>
>  C  C'
>
>  One cell (A,B,C) has B coming towards you and the other (A',B',C') has
>  B' pointing away from you. The two axes A and A' have identical length
>  as have B and B'. But C' is the diagonal in the AC-plane.
>
>  In your case you can just swap the A and C axis of the C2 (to follow
>  the above picture) and then calculate the C' (diagonal) to 136.8.
>
>  So to summarize: these are identical cells - just different choice
>  of axes (and nothing to do with the C2 versus P2 choice ... I think).
>
>  Cheers
>
>  Clemens
>
>
>
>
>  On Thu, May 01, 2008 at 12:03:16PM -0400, Junyu Xiao wrote:
>  > Hi all,
>  >
>  > We run into an interesting space group problem. The same diffraction
>  > image can be either indexed into space group C2, with a=145, b=44,
>  > c=67, and beta=110.5; or space group P2 (should be P21 after
>  > scaling), with a=67, b=44, c=136, and beta=96.8. Both are refined ok
>  > during index. These two must somehow be related. Can anyone give some
>  > comments on that?
>  >
>  > Thanks a lot,
>  > Junyu
>  >
>  > =
>  > Junyu Xiao
>  > Department of Biological Chemistry,
>  > University of Michigan
>  >
>  > Lab address:
>  > 3163 Life Sciences Institute,
>  > University of Michigan,
>  > 210 Washtenaw Avenue
>  > Ann Arbor, MI, 48109-2216
>  > Phone: 734-615-2078
>  > ==
>  >
>  >
>  >
>
>  --
>
>  ***
>  * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
>  *
>  *  Global Phasing Ltd.
>  *  Sheraton House, Castle Park
>  *  Cambridge CB3 0AX, UK
>  *--
>  * BUSTER Development Group  (http://www.globalphasing.com)
>  ***
>



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
-

[ccp4bb] Beamtime available; Deadline for applications : May 15.

[Peter Zwart]

Dear All,

The Berkeley Center for Structural Biology (BCSB) has recently completed
a major upgrade of the Sector 5.0 beamline optics. A five- to tenfold
improvement in available flux has been achieved  at the side-station beamlines
(5.0.1 and 5.0.3), which now generate 1.5x10^11 photons per second at 0.97
Angstrom. This wavelength is slightly above the Se K edge making them ideal for
performing Se SAD experiments.

The performance of 5.0.2 (a tunable beamline) has improved by a factor of
3 to 4. It now generates a peak flux of 8x10^11 photons per second
under typical
user operations. The upgrade has also extended the energy range of
5.0.2 to 16 keV, enabling the routine use of shorter wavelengths and
anomalously scattering elements
such as bromine.

All the BCSB beamlines have robotic sample changers. The sector 5 beamlines are
equiped  with Berkeley Automounters (BAMs). The tuneable beamlines 8.2.1 and
8.2.2 are now equiped with Actor sample changers. Please visit
http://bcsb.lbl.gov/
for more details about the Center and its beamlines.

If you'd like to take advantage of the upgrades to these BCSB beamlines,
submit a General User proposal by May 15, 2008 in order to be
considered for the July-August schedules at the Advanced Light Source.
To find out more, click on:

http://www-als.lbl.gov/als/quickguide/independinvest.html

We invite you to submit a proposal at:

http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize.

If you have any questions or would like to request open beamtime,
please e-mailing [EMAIL PROTECTED]

(Please note that executed user agreements must be received by LBNL
prior to beamtime.  Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.)

Regards

Peter Zwart

-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

[ccp4bb] ALS user meeting

[Peter Zwart]

Dear All,

I would like to draw your attention to this years ALS user meeting,
held from October 13-15. In particular, the workshop titled
"Recent advances in the automation of protein crystallography" might
be of interest to the protein crystallographic community.
The workshop consists of a series of short talks and a hands-on
session in which various developers and beamline staff will
demo latest developments on their beamlines.

Scheduled speakers include:
 Gyorgy Snell (Takeda SD)
 Aina Cohen (SSRL)
 Jay Nix (ALS beamline 4.2.2)
 Babu Pothineni ( GMCA cat, APS)

Scheduled Demonstrations are (tentative titles only) :
 *  Efficient screening and data collection using Mini & WebIce (Bl. 5.0.n)
      Peter Zwart, John Taylor & Nick Sauter
* Data collection @ 4.2.2
  Jay Nix
* SSRL & Webice
  Aina Cohen
* Automated structure solution with PHENIX
  P. Afonine
* Elves & 8.3.1
  J. Holton

Detailed workshop information can be found at
http://bcsb.als.lbl.gov/wiki/index.php/ALS2008_Workshop

Other workshops of interest held during the ALS user meeting can be found here:
http://www-als.lbl.gov/als/usermtg/workshops.html

Registration is now open for all participants:
http://www-als.lbl.gov/als/usermtg/index.html

Greetings

Peter Zwart


-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
-

[ccp4bb] Dry shippers

[Peter Zwart]

Dear all,

Due to the presence of residual liquid nitrogen in dry shippers
'steaming' out of a tipped-over dewar on a Fedex dock, we (PX-ers in
the ALS) have been placed under some scrutiny with regards to
dry-shipping dewars. In particular, I am interested in how people
empty their dewars/pucks/vials and prepare them for dry-shipment and
how they and/or their shipping department checks if the dewars are
empty indeed.

Cheers

Peter Zwart

-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
-

[ccp4bb] Summary: Dry shippers

[Peter Zwart]

Dear All,

Thanks for the response.

For those of you interested, the extra cost associated with shipping
'wet' is about 35 USD within the US, and about 50 to 100 dollar
internationally. Extra paperwork and labels are needed when shipping
wet.  One of our users recommends shipping wet, especially
internationally. in the case that something does go wrong (customs,
dewar lost), your samples should still be okay.

The best procedure for preparing a dewar for dry shipping seems to be
the as described by Steve Ginell:

  all shipping dewars are turned upside down until all LN2 drains out,
this is repeated 2-3x times to remove the residual caught in the top.



Summary:

-
At APS/SBC sector 19 all shipping dewars are turned upside down until
all LN2 drains out, this is repeated 2-3x times to remove the residual
caught in the top. With this method there is no free LN2 remaining in
the dewars to leak out. During the upside down tipping the dewars must
not be bumped. The ANL shipping Department has been instructed to
verify that the dewars are empty of LN2 by turning them upside down
prior to shipping. When pucks are not used we caution all users to
place vials securely in the dewars using canes with tabs or placing
the bottom of one against the top of another and using plastic
sleeves, to prevent the pins from being dislodged from the vials.
-

-
We tip them out thoroughly ahead of time and by the time the Dewars ship
there's never any liquid in them. () if you absolutely MUST have
the vessel to be entirely dry it
is adviseable to empty the Dewar and wait 5-10 hours before shipping it.
-


-
Personally I drain the dewars before filling (...) Then I fill the
dewar with canes and make two attempts to tip/angle the dewar to drain
off nitrogen without losing the vials. (...) There is one group in our
department that likes (or liked) to ship "dry" dewars as "liquid"
(with all the paperwork and hassle that you can imagine) because they
had the same experience that you describe (...)
-


-
SSRL always ships them back full. We even had our shipper temporarily
denied by FedEx because we forgot to
remove the ssrl label specifying that there is liquid nitrogen inside.
So in theory one can arrange to ship dewars *with* liquid nitrogen.
We usually just tilt the shipper (we have Taylor-Wharton CX100) at
roughly 150 degrees polar angle with respect to its upright position
and
hold it like that until no liquid is coming out.  We never had a
problem with FedEx.
-


-
I always used to just fill the shipper w/ LN2, and declare it
Dangerous Goods. Never any trouble, save one time in Birmingham (AL),
the FedEx person at the office intentionally tipped shipper 90
degrees, even though it was marked DG, Keep Upright, etc. !!
Naturally, they got scared by all the "steam" and hissing! I went down
the the FedEx office, and easily convinced them not to tip it (after
all, it was marked DG!), and all was then OK. I guess the goal of
"dry" shipping is to save the DG costs. On this I cannot comment,
other than one potentially good, but ruined crystal to me is worth
more than DG shipping costs (which, as I recall, only add ~$100-200).
-----




Thanks a lot.

Peter Zwart

[ccp4bb] PX beamtime application deadline Sept 1st!

[Peter Zwart]

Dear All,

The deadline for general user proposals for PX beamtime at the ALS is
comming up soon! At the BCSB, we have 5 beamlines for which you can
apply for beamtime. At the Berkeley Center for Structural Biology
(BCSB) we have recently completed a number of upgrades:

Sector 8:  Recent improvements include:

* A high-accuracy microdiffractometer on BL 8.2.1, allowing for
centering and viewing of very small crystals
* Robot automounters which can increase the screening throughput
at the beamlines, and will allow for the implementation of remote data
collection
* A new large format (315mm active surface area) CCD detector on
BL 8.2.1, facilitating data collection on large unit cell crystals

Sector 5:  Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons
per second at 0.97 Angstrom. This wavelength is slightly above the Se
K edge making them ideal for performing Se SAD experiments. Beamline
5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons
per second, and the energy range of 5.0.2 has been extended to 17 keV,
enabling the routine use of shorter wavelengths and anomalously
scattering elements such as bromine.

Please visit http://bcsb.lbl.gov/ for more details about the Center
and its beamlines.

If you'd like to apply for Oct/Nov/Dec beamtime at the Advanced Light
Source, please submit a General User proposal by September 1, 2008.

To find out more, click on:

http://www-als.lbl.gov/als/quickguide/independinvest.html

We invite you to submit a proposal at:

http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize.

If you have any questions or would like to request open beamtime,
please e-mail [EMAIL PROTECTED]

(Please note that executed user agreements must be received by LBNL
prior to beamtime.  Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.)


-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
-

[ccp4bb] PX beamtime application deadline Sept 3rd!

[Peter Zwart]

Dear All,

The deadline for user proposals for PX beamtime at the ALS has been
extended to September 3, 5pm pacific time.

See my previous email for details.

Thanks

Peter

2008/8/29 Peter Zwart <[EMAIL PROTECTED]>:
> Dear All,
>
> The deadline for general user proposals for PX beamtime at the ALS is
> comming up soon! At the BCSB, we have 5 beamlines for which you can
> apply for beamtime. At the Berkeley Center for Structural Biology
> (BCSB) we have recently completed a number of upgrades:
>
> Sector 8:  Recent improvements include:
>
>* A high-accuracy microdiffractometer on BL 8.2.1, allowing for
> centering and viewing of very small crystals
>* Robot automounters which can increase the screening throughput
> at the beamlines, and will allow for the implementation of remote data
> collection
>* A new large format (315mm active surface area) CCD detector on
> BL 8.2.1, facilitating data collection on large unit cell crystals
>
> Sector 5:  Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons
> per second at 0.97 Angstrom. This wavelength is slightly above the Se
> K edge making them ideal for performing Se SAD experiments. Beamline
> 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons
> per second, and the energy range of 5.0.2 has been extended to 17 keV,
> enabling the routine use of shorter wavelengths and anomalously
> scattering elements such as bromine.
>
> Please visit http://bcsb.lbl.gov/ for more details about the Center
> and its beamlines.
>
> If you'd like to apply for Oct/Nov/Dec beamtime at the Advanced Light
> Source, please submit a General User proposal by September 1, 2008.
>
> To find out more, click on:
>
> http://www-als.lbl.gov/als/quickguide/independinvest.html
>
> We invite you to submit a proposal at:
>
> http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize.
>
> If you have any questions or would like to request open beamtime,
> please e-mail [EMAIL PROTECTED]
>
> (Please note that executed user agreements must be received by LBNL
> prior to beamtime.  Proprietary fees, if applicable, must be received
> by LBNL at least five working days prior to scheduled beamtime.)
>
>
> --
> -
> P.H. Zwart
> Beamline Scientist
> Berkeley Center for Structural Biology
> Lawrence Berkeley National Laboratories
> 1 Cyclotron Road, Berkeley, CA-94703, USA
> Cell: 510 289 9246
> BCSB: http://bcsb.als.lbl.gov
> PHENIX: http://www.phenix-online.org
> CCTBX: http://cctbx.sf.net
> -
>



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
-

Re: [ccp4bb] truncate ignorance

[Peter Zwart]

>  I believe also that in an earlier posting Peter Zwart said he thought
>  that CNS doesn't take account of the Wilson distribution when doing its
>  version of the correction; if this is true (and I have no independent
>  evidence that it is since I'm not a CNS user), then the above argument
>  implies that the F's corrected by such a procedure will inevitably be
>  biased, though the damage done may well not be significant compared with
>  that done by using F's instead of I's in the first place.
>

Actually, this is an option in phenix.reflection_file_converter
(massage_intensities) and its use is discouraged by forcing the user
to use a multitude of keywords at the same time to perform this.

That said, I do use this option inside xtriage for space group
determination purposes. At the moment it is a quick hack, and
something more suitabvle to overcome current limitations is imminent.

P

Re: [ccp4bb] truncate ignorance

[Peter Zwart]

> However, when you
> need amplitudes, truncate is the way to go.


Better is to buy a detector that records amplitudes rather then intensities:

http://shelx.uni-ac.gwdg.de/SHELX/#FAQs%20smallmol

P

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

[Peter Zwart]

phenix.refine also might not (by default) use missing data in map calculation.
AFAIK, refmac fills in missing data with DFc. Phenix doesn't (maybe
this changed now).
When your high resolution shells are incomplete (like when using the
anisotropy server to perform elliptical data truncation, or etc etc),
I can imagine that the use of DFc can have considerable effect on the
looks of a map.

P







2008/9/28 Kevin Cowtan <[EMAIL PROTECTED]>:
> Another factor may be that phenix.refine does not make a full use of
> experimental phase information in its calculation of the error parameters -
> I've been discussing this with Peter, Randy and Ralph. I don't know that
> this is the cause, but I see inferior results when recycling  buccaneer with
> phenix.refine (although this is confounded by the fact that phenix.refine
> doesn't output the updated ABCD's. Having said that, neither does refmac,
> but it does give me something I can fudge. Both Garib and Pavel could toss
> me a bone here).
>
> A corollary is that phenix.refine may also not use the experimental phase
> information in its map coefficients - I simply assumed that it did, but that
> assumption may be unwarranted.
>
> Both of these factors would affect the quality of the maps when refining
> with experimental phasing (assuming a good modern phasing program). However
> if the difference is also present after MR, then you need to look elsewhere
> for an explanation.
>
> Kevin
>
> Dunten, Pete W. wrote:
>>
>>
>> I mentioned previously phenix.refine tosses your weak data if IMEAN,
>> SIGIMEAN are chosen during refinement.
>>
>>
>> I'm wondering if this omission of weak Fobs from the Fobs-Fcalc difference
>> map explains why the difference maps out of refmac seem to be more helpful
>> in showing where to move atoms.
>>
>> D. Crowfoot et al. in The Chemistry of Penicillin (1949) explain why this
>> might be so, and Stout & Jenson elaborate the argument.  Briefly, the
>> calculated phase will be closest to the phase of the vector difference Fcalc
>> – Fobs when |Fcalc| > |Fobs|.
>>
>> I leave it to the reader to try calculating some maps with and without the
>> weak Fobs in phenix.refine or refmac, and perhaps making some deliberate
>> rotamer errors, to see if using the complete data with weak Fobs helps.
>>
>



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] R32 data

[Peter Zwart]

Hi Josiah,

The primitive cell is what is important.  The primitive cells for C2
and R32:H are the same as the P1 cell you report:

(using  phenix.explore_metric_symmetry)

R32:H Niggli cell: (81.728198520053866, 81.728198520053866,
81.728198520053866, 84.166443879693517, 84.166443879693517,
84.166443879693517)
C2 Niggli cell: (81.5370006, 81.567520633215281,
81.567520633215281, 84.147871626167259, 84.163573178668059,
84.163573178668059)

Twinning, pseudo symmetry etc etc can all be possible, even if
intensity statistics indicate that things are fine.

P




2008/10/2 Josiah Obiero <[EMAIL PROTECTED]>:
> Dear all,
>
> I have set of data (~2.7A). After indexing, HKL2000 suggests a
> rhombohedral space group or C centered monoclinic space group. I tried
> molecular replacement with R32 ( 109.55 109.55 155.28 90.00 90.00
> 120.00) and C2 (121.092   109.31581.53790.00097.874
> 90.000) (both have good merging statistics), but did not get any
> solution. I also tried P1 ( 81.55381.52781.52384.202
> 84.13284.156) but did get any solution ( wt structure is known and
> the only difference with the wt structure is that the new structure is
> complexed with a smaller protein). I expect that there'll be some
> domain movement so searched for individual domains in phaser.
>
> The self rotation function in P1 showed both two fold and three fold
> peaks but they were both off the centre. The data does not appear to be
> twinned. I am curious to know if it is normal for cell dimensions to
> drastically vary from one space group to another. I am running out of
> ideas, could I be dealing with a wrong space group or pseudosymetry?
>
> Any suggestions would be appreciated.
>
> Thanks.
>
> Josiah.
>



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] foam dewar usage ?

[Peter Zwart]

> If they really do cost $160, your best bet might be to email your friendly 
> local synchrotron group and ask if they will make you something at a fraction 
> of the price ...

Or just pay up. 160 USD is not a lot when compared to other
consumables likes chemicals or crystal screens. The dewars last quite
a while.

P

[ccp4bb] postdoc position in LBNL

[Peter Zwart]

Dear All,

We would like to bring the following postdoctoral research position
to your attention.

Within Lawrence Berkeley Laboratory, we have an opening for a
postdoc to work on the development of new software for the analysis
of small angle X-ray scattering (SAXS) data.
The availability of user friendly, robust software analysis tools for
SAXS data is of growing importance as the biological community is
increasingly using SAXS as a standard method to analyze complex
biological systems. We are developing a new set of tools, including a
software library, for SAXS data analysis.

The successful candidate will have the opportunity to work with
experienced software developers in the field of biophysics and
interact with users and beamline staff on SAXS beamline 7.3.3 at the
Advanced Light Source (ALS) in Berkeley California.

Interested candidates can contact me (Peter Zwart, [EMAIL PROTECTED])
for more details, or visit the LBL job site at:  http://jobs.lbl.gov/

Sincerely,

Peter Zwart



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX:  http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] P21,C2, C2221

[Peter Zwart]

Hi,

Please note that there are 3 different spacegroups directly below
C222(1), namely

C 1 2 1  41.85 181.82 119.48 90.00 90.00 90.00
C 1 2 1  181.82 41.85 119.48 90.00 90.00 90.00
P 1 21 1  41.85 119.48 93.26 90.00 102.89 90.00

[ as obtained by phenix.explore_metric_symmetry --unit_cell="41.8500
119.4800   93.2600   90.  102.8880   90." --space_group=P21
--start_from_p1 ]

Note that the two choices of C2 are not equivalent; it looks like you
have missed a space group.

You can try to solve the structure in P1 and from an RvsR analyses
guess which choice is best. Contact me personally on help with that if
so desired.

Cheers

Peter


2008/11/7, Yuan, Hua <[EMAIL PROTECTED]>:
> Dear All,
>
>  I'm trying to decide the spacegroup between P21 and C2 and in need of
>  your help.
>  I have a data with the following possible cells:
>  P21: 41.8500  119.4800   93.2600   90.  102.8880   90.
>  C2: 181.8000   41.8400  119.5300   90.   90.0820   90.
>
>  The data is twinned (C2221 is always suggested by different programs
> without considering twinning).  Therefore twin refinement is carried on in
>  Phenix.refine, with twin law "h,-k,-h-l" for P21 and  "h,-k,-l" for
>  C2.  Both space groups give a reasonable but not so different R-free
>  close to 23% for a 2.3 angstrom data, and the resulted map is also OK
>  in both cases.  As it is with higher symmetry, maybe I should go with
>  C2. But there could be something I missed here, i.e. a pseudosymmetry
>  operator taken as crystallographic symmetry?  Any suggestions or
>  comments are highly appreciated!
>
>  Thanks,
>
>  Hua
>


-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

[ccp4bb] General user proposal deadline November 15

[Peter Zwart]

Dear All,

The deadline for general user proposals for PX beamtime at the ALS is
comming up soon! At the BCSB, we have 5 beamlines for which you can
apply for beamtime. At the Berkeley Center for Structural Biology
(BCSB) we have recently completed a number of upgrades:

Sector 8:  Recent improvements include:

* A high-accuracy microdiffractometer on BL 8.2.1, allowing for
   centering and viewing of very small crystals
* Robotic automounters which can increase the screening throughput
  at the beamlines, and allows for the implementation of remote data
  collection.
* A new large format (315mm active surface area) CCD detector on
  BL 8.2.1, facilitating data collection on large unit cell crystals

 Sector 5:  Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons
 per second at 0.97 Angstrom. This wavelength is slightly above the Se
 K edge making them ideal for performing Se SAD experiments. Beamline
 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons
 per second, and the energy range of 5.0.2 has been extended to 17 keV,
 enabling the routine use of shorter wavelengths and anomalously
 scattering elements such as bromine.
 Remote data collection for general users on sector 5 is currently
being tested for
 a limited number of users. Please contact beamline staff for details.

 Please visit http://bcsb.lbl.gov/ for more details about the Center
 and its beamlines.

 If you'd like to apply for next round of beamtime (Jan-Feb) at the
Advanced Light
Source, please submit a General User proposal by November 15, 2008.

 To find out more, click on:

 http://www-als.lbl.gov/als/quickguide/independinvest.html

 We invite you to submit a proposal at:

 http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml

If you have any questions or would like to request open beamtime,
please e-mail [EMAIL PROTECTED]

(Please note that executed user agreements must be received by LBNL
prior to beamtime.  Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.)

-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] General user proposal deadline November 15

[Peter Zwart]

Dear All,

The link I send earlier was incomplete:

http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize

Excuses,

Peter

2008/11/13, Peter Zwart <[EMAIL PROTECTED]>:
> Dear All,
>
>  The deadline for general user proposals for PX beamtime at the ALS is
>  comming up soon! At the BCSB, we have 5 beamlines for which you can
>  apply for beamtime. At the Berkeley Center for Structural Biology
>  (BCSB) we have recently completed a number of upgrades:
>
>  Sector 8:  Recent improvements include:
>
> * A high-accuracy microdiffractometer on BL 8.2.1, allowing for
>centering and viewing of very small crystals
> * Robotic automounters which can increase the screening throughput
>   at the beamlines, and allows for the implementation of remote data
>   collection.
> * A new large format (315mm active surface area) CCD detector on
>   BL 8.2.1, facilitating data collection on large unit cell crystals
>
>   Sector 5:  Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons
>   per second at 0.97 Angstrom. This wavelength is slightly above the Se
>   K edge making them ideal for performing Se SAD experiments. Beamline
>   5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons
>   per second, and the energy range of 5.0.2 has been extended to 17 keV,
>   enabling the routine use of shorter wavelengths and anomalously
>   scattering elements such as bromine.
>   Remote data collection for general users on sector 5 is currently
>  being tested for
>   a limited number of users. Please contact beamline staff for details.
>
>   Please visit http://bcsb.lbl.gov/ for more details about the Center
>   and its beamlines.
>
>   If you'd like to apply for next round of beamtime (Jan-Feb) at the
>  Advanced Light
>  Source, please submit a General User proposal by November 15, 2008.
>
>   To find out more, click on:
>
>   http://www-als.lbl.gov/als/quickguide/independinvest.html
>
>   We invite you to submit a proposal at:
>
>   http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml
>
>  If you have any questions or would like to request open beamtime,
>  please e-mail [EMAIL PROTECTED]
>
>  (Please note that executed user agreements must be received by LBNL
>  prior to beamtime.  Proprietary fees, if applicable, must be received
>  by LBNL at least five working days prior to scheduled beamtime.)
>
>  -
>  P.H. Zwart
>  Beamline Scientist
>  Berkeley Center for Structural Biology
>  Lawrence Berkeley National Laboratories
>  1 Cyclotron Road, Berkeley, CA-94703, USA
>  Cell: 510 289 9246
>  BCSB: http://bcsb.als.lbl.gov
>  PHENIX: http://www.phenix-online.org
>  CCTBX:  http://cctbx.sf.net
>  -
>


-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] indexing choice for C2

[Peter Zwart]

use MOSFLM, XDS or D*TREK

Peter


2008/12/13, James Whittle :
> Dear all,
>
>  I believe I've run across a case similar to that described recently in
> Zwart et al., Acta Cryst. (2008) D64, 99-107:
>
>  "Given the pseudosymmetric nature of the lattice (pseudo-rhombohedral), C2
> can be embedded in the higher symmetry lattice in three different ways (see
> Fig. 4), corresponding to the three orientations of the twofold axis in
> space group R32. The integration suite used to initially process the data
> only gave a single indexing choice for C2, which was unfortunately
> incorrect."
>
>  I've been using denzo/scalepack to process my data, which, as far as I can
> tell, only allows me one indexing choice for C2.
>
>  How can one do this integration using the other two indexing choices?
>
>  --James
>


-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

[ccp4bb] Deadline for ALS PX beamtime this Thursday, Jan 15.

[Peter Zwart]

Dear All,

The deadline for general user proposals for PX beamtime at the ALS is
coming up soon (Jan 15)! At the BCSB, we have 5 beamlines for which you can
apply for beamtime. At the Berkeley Center for Structural Biology
(BCSB) we have recently completed a number of upgrades:

Sector 8:  Recent improvements include:

   * A high-accuracy microdiffractometer on BL 8.2.1, allowing for
  centering and viewing of very small crystals
   * Robotic automounters which can increase the screening throughput
 at the beamlines, and allows for the implementation of remote data
 collection.
   * A new large format (315mm active surface area) CCD detector on
 BL 8.2.1, facilitating data collection on large unit cell crystals

 Sector 5:  Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons
 per second at 0.97 Angstrom. This wavelength is slightly above the Se
 K edge making them ideal for performing Se SAD experiments. Beamline
 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons
 per second, and the energy range of 5.0.2 has been extended to 17 keV,
 enabling the routine use of shorter wavelengths and anomalously
 scattering elements such as bromine.
 Remote data collection for general users on sector 5 is currently
 being tested for a limited number of users. Please contact beamline
staff for details.

 Please visit http://bcsb.lbl.gov/ for more details about the Center
 and its beamlines.

 If you'd like to apply for next round of beamtime (March-April) at the
 Advanced Light Source, please submit a General User proposal by
Januari 15, 2009.

 To find out more, click on:

 http://www-als.lbl.gov/als/quickguide/independinvest.html

 We invite you to submit a proposal at:

http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize


If you have any questions or would like to request open beamtime,
please e-mail bcsbbeamt...@lbl.gov.

(Please note that executed user agreements must be received by LBNL
prior to beamtime.  Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.)


-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

[ccp4bb] Beamtime proposal deadline for ALS GU time

[Peter Zwart]

The deadline for the may/June cycle of general user time for PX in the
ALS is coming up soon (This Sunday).


The Berkeley Center for Structural Biology (BCSB) has recently
completed a number of upgrades:

Sector 8:  Recent improvements include:

* A high-accuracy microdiffractometer on BL 8.2.1 allows for
centering and viewing of very small crystals;
* Robot automounters on BL8.2.1 and 8.2.2 are now fully
commissioned and the beamlines can be used remotely;
* A new large format (315mm active surface area) CCD detector on
BL 8.2.1 facilitates data collection on large unit cell crystals.

Sector 5:  Recent improvements include:

* Beamlines (5.0.1 and 5.0.3) now generate 1.5x1011 photons per
second at 0.97 Angstrom. This wavelength is slightly above the Se K
edge making them ideal for performing Se SAD experiments.
* Beamline 5.0.2 (the tunable beamline) generates a peak flux of
8x1011 photons per second, and the energy range of 5.0.2 has been
extended to 17 keV, enabling the routine use of shorter wavelengths
and anomalously scattering elements such as bromine.
* All sector 5 beamlines can be run remotely. The automated sample
mounter holds six pucks (96 sample in total). On weekdays, staff is
available 22 hours (out of 24) for puck changes and assistance.

Please visit http://bcsb.lbl.gov/ for more details about the Center
and its beamlines.

If you'd like to apply for May/June beamtime at the Advanced Light
Source, please submit a General User proposal by March 15, 2009.

To find out more, click on:
http://www-als.lbl.gov/als/quickguide/independinvest.html

We invite you to submit a proposal at:
http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize.

If you have any questions or would like to request open beamtime,
please e-mail bcsbbeamt...@lbl.gov.

[Please note that executed user agreements must be received by LBNL
prior to beamtime.  Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.]



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] Problems with phasing a protein (1300aa)

[Peter Zwart]

<|delta F|>/ *c \approx < |delta I|/ I > ,

with c somewhere between 2.5 and 3.

Bijvoet amplitude ratios seem always more pessimistic then they should be.

The 4 to 5% <|delta F|>/ would translate into a 10 to 12% expected
difference for individual intensities.


P

2009/3/20 Bernhard Rupp :
> What is not true?
>
> Also in your case the applet estimates an expected
> 4-5% signal which is quite doable with decent data.
>
> BR
>
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tommi
> Kajander
> Sent: Friday, March 20, 2009 3:43 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Problems with phasing a protein (1300aa)
>
> this cant be true,
> in the idea case (not Rmerge 15%, then again one can apply a resolution
> cutoff, perhaps, while this sounds like a very desperate case) the
> answer must be yes. didnt do the calculation right now (but it
> _should_ back this up)
> we for instance have solved a structure long time ago
> -- and this probably wasnt on the limit (well it was at the time but
> not anymore),  365 res x 8 in AU and 80 Se.
>
> at least looking at the SnB success list ("very" old list )
> http://www.hwi.buffalo.edu/SnB/SnBSuccesses.htm
> there are plenty of others.
>
> -tommi
>
> On Mar 20, 2009, at 10:53 PM, Bernhard Rupp wrote:
>
>> One can estimate this from
>>
>> http://www.ruppweb.org/new_comp/anomalous_scattering.htm
>>
>> and the answer as Jim says is no.
>>
>> BR
>> -Original Message-
>> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf
>> Of Jim
>> Pflugrath
>> Sent: Friday, March 20, 2009 1:08 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Problems with phasing a protein (1300aa)
>>
>> Well, what do you expect the anomalous signal contributed from your 45
>> seleniums in a perfect world to be when the asymmetric unit contains
>> 1300
>> aa?  Do you think a dataset with Rmerge of ~15% is good enough to
>> detect a
>> signal of even 2%?  (Note: I did not do the calculation, so I just
>> made up
>> the number of 2%.)
>>
>> Jim
>>
>>
>> On Fri, 20 Mar 2009, Kumar wrote:
>>
>>> Hello CCP4bb members,
>>>
>>> I have been trying to obtain phases for a protein which contain
>>> ~1300aa.
>> We
>>> have obtained native data to a resolution of 3.3A (Space group I222
>>> or
>>> I212121). But we are having tough time phasing it.
>>> ...
>>
>
> Tommi Kajander, Ph.D.
> Structural Biology and Biophysics
> Institute of Biotechnology
> University of Helsinki
> Viikinkaari 1
> (P.O. Box 65)
> 00014 Helsinki
> Finland
> p. +358-9-19158903
> tommi.kajan...@helsinki.fi
>



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] Problems with phasing a protein (1300aa)

[Peter Zwart]

> Sure, no while lines considered in the edge calc, for example.


That and (more important) that

2*abs(a-b)/(a+b) >  2*abs(sqrt(a)-sqrt(b))/(sqrt(a)+sqrt(b))

See  Acta Cryst. D61, 1437–1448.

(btw, while is overrated, use for and a break statement)

p

Re: [ccp4bb] Crick-Magdoff and anomalous

[Peter Zwart]

Hi,

>
> If we then require that the rms change in intensity be greater than the
> average noise, then we can write down the requirement:
> sigma(I_P) < rms(deltaI)
>
.
.
.
> I_P/sigma(I_P) > 1.3*sqrt(MW/N_H)/fpp

one can actually require that

abs(delta I) > 3 sigma(delta I)

Using  eq. 13 from Acta Cryst. D61, 1437–1448, and the same (sometimes
(very) questionable assumptions) James used, the magic factor 1.3
inflates to 2.0

I once wrote a jiffy that allows one to simulate FOM's for various
phasing + errors scenarios. I still have the code around, if someone
is interested.
Note that sometimes you cannot find sites, but with knowledge of the
sites itself, phasing + density modification would result in
interpretable maps (Acta Cryst. D60, 1085–1093).
Also, the distribution of errors is rather important. I suspect that
what matters in the end is that you have enough well-measured Bijvoet
pairs to get the substructure. An empirical analysis possibly could
shift the magic number  back to 1.3 ;-)

Cheers,

P


SAD Scientist ;-)






> So, after doing these substitutions and rearranging, we get:
>
> sigma(I_P)/I_P < sqrt(2*N_H/(MW/14))*fpp/7
> sigma(I_P)/I_P < 0.756*sqrt(N_H/MW)*fpp
>
> I_P/sigma(I_P) > 1.3*sqrt(MW/N_H)/fpp
>
> There are some obvious approximations here.  Probably the biggest is
> assuming that fpp = F_H.  In actual fact, anomalous differences "count
> double" since fpp contributes both to F+ and F-.  I think Peter Zwart
> pointed this out earlier.  There is also another sqrt(2) in the opposite
> direction because sigma(delta-I) is the quadrature sum of two sigma(I_P).
>  It also matters if you are interested in the rms anomalous difference or
> the mean absolute anomalous difference, as these are not the same thing.
>  Nonetheless, I think this last formula should be accurate to at worst a
> factor of two.
> In general, it is a good idea to have your signal be more than equal to
> noise, so I consider this formula a limit to be avoided rather than a goal
> to be met.  The skill and expertise required to solve the structure
> increases quite sharply as your I/sigma(I) approaches this limit, but you
> can always double I/sigma(I) by merging data from four crystals.  The latter
> is a better strategy.
>
> -James Holton
> MAD Scientist
>

Re: [ccp4bb] Reindexing Orthorhombic

[Peter Zwart]

when reindexing p212121 with -h,l,k, you get

P 21 21 21 (a+1/4,b-1/4,c-1/4)

so you should subtract 1/4 from x and add a quarter to y and z.
some tools in the cctbx are available that make this go easy
(reindexing and moving things back to a standard setting). Reruning
phaser might be the least painful option you have.

P


2009/4/17 James Stroud :
> Update:
>
> The pounding I am beginning to feel in my head is reminiscent of a pounding
> I felt while working in p43212 a while ago. I think this is an alternate
> origin issue. Now I just need to figure out how to redefine the origin.
>
> James
>
>
> On Apr 16, 2009, at 9:38 PM, James Stroud wrote:
>
>> Hello All,
>>
>> I have two crystals (that I'll call "data set 1" and "data set 2") that
>> seem to be isomorphic, but y and z are transposed between the two data sets.
>> Reindexing data set 2 with the operators
>>
>> h => -h
>> k => l
>> l => k
>>
>> makes the axes match data set 1, but running MR with the previous data set
>> 2 solution on the newly reindexed data set 2 yields a solution rotated 180
>> about z with respect to the data set 1 solution. What is the operation to
>> reindex such that real space is rotated 180 about z? These are in P212121.
>>
>> James
>



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

[ccp4bb] Beamtime proposal deadline for ALS GU time

[Peter Zwart]

May 15, 2009 is the deadline for the July-August Rapid Access Proposal
cycle.  Please note that the ALS will be shut down in September, 2009.
The deadline for applications of beamtime on the BCSB beamlines in the
ALS is today!


Other notable features include:

* A high-accuracy microdiffractometer on BL 8.2.1 allows for
centering and viewing of very small crystals;
* Robot automounters on BL8.2.1 and 8.2.2 are now fully commissioned.
* A new large format (315mm active surface area) CCD detector on
BL 8.2.1 facilitates data collection on large unit cell crystals.
* Beamlines 5.0.1 and 5.0.3 now generate 1.5x1011 photons per
second at 0.97 Angstrom. This wavelength is slightly above the Se K
edge making them ideal for performing Se SAD experiments.
* Beamline 5.0.2 (a tunable beamline) generates a peak flux of
8x1011 photons per second, and the energy range of 5.0.2 has been
extended to 17 keV, enabling the routine use of shorter wavelengths
and anomalously scattering elements such as bromine.

All  beamlines of the BCSB (5.0.1, 5.0.2, 5.0.3, 8.2.1 and 8.2.2) can
all be operated remotely. Please contact Peter Zwart (sector 5
beamlines) or Corie Ralston (sector 8 beamlines) for more information.


Please visit http://bcsb.lbl.gov/ for more details about the Center
and its beamlines.

To find out more, click on:
http://www.als.lbl.gov/als/quickguide/independinvest.html
Scroll down to "Structural Biology and SAXS."

We invite you to submit a proposal at:
http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize

If you'd like to apply for October-November-December beamtime at the
Advanced Light Source, please submit a General User proposal by August
15, 2009.

If you have any questions or would like to request open beamtime,
please e-mail bcsbbeamt...@lbl.gov.

Please note that executed user agreements must be received by LBNL
prior to beamtime.  Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.

Cheers,

Peter Zwart
-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

[ccp4bb] General User Proposal Deadline for PX/SAXS at the ALS: August 15, 2009

[Peter Zwart]

Dear All,

August 15, 2009 is the deadline for the October - December 2009 Rapid
Access Proposal cycle. (Please note that the ALS will be shut down
in September, 2009.)

Remote data collection is available on all beamlines at the Berkeley
Center for Structural Biology (BCSB). The NX remote desktop technology
provides the remote user with the full complement of sample
visualization, sample manipulation, beamline control, data acquisition
and data analysis tools exactly as they would see them if they were
stationed at the beamline. This enhanced remote operation capability
is coupled with 24hr onsite support by BCSB staff who are able to
assist immediately with loading additional samples for remote users or
troubleshoot any issues that might arise.

Beamlines 8.2.1 and 8.2.2:

Both beamlines are now fully remote capable, which means that users
are able control sample mounting, data collection and analysis from
their home labs. This has dramatically increased the efficiency of
data collection and significantly reduced the cost of protein
crystallography experiments, since users no longer have to travel to
the synchrotron.

To facilitate studies on small crystals, a microdiffractometer was
installed in the beamline 8.2.1 endstation. The new equipment allows
precise sample positioning to within 2 microns, excellent sample
viewing of very small crystals, and an off-axis crystal positioning
stage. As part of the beamline optics upgrades, a new toroidal
focusing mirror was purchased and installed in beamline 8.2.1; new
parabolic mirrors are currently being polished. When completed, the
new optics will increase the brightness of beamline 8.2.1 by a factor
of 4 to 5 and decrease the spot size to 30 microns, greatly
facilitating structure solution on large macromolecular complexes.

Beamlines 5.0.1, 5.0.2, 5.0.3:  On Sector 5, improvements to the
existing Berkeley Automounter sample handling system have dramatically
improved both total capacity and reliability.

Upgrades to the 5.0.1 and 5.0.3 monochromators have been completed.
The operational energy of both beamlines has been increased, taking
them above the Se K-edge and thus introducing a significant new Se SAD
capability for experiments on Se derivatized proteins. The new
monochromators also provide significantly better beam focus and
performance under the increased power loads of ALS topoff operation.
These improvements have been coupled with the introduction of enhanced
positional feedback, diagnostic tools, and auto-alignment systems for
the beamline components to improve the overall stability and quality
of the beam delivered to users.

Another mode of access to the BCSB beamlines is through the
Collaborative Crystallography (CC) Program. Users apply for beamtime
via the general user program, and collaborate with an expert
crystallographer who will conduct the experiments and data reduction
on behalf of the researchers. Depending on the users, structure
solution, model building and refinement can be carried out as well.

Please visit http://bcsb.lbl.gov/ for more details about the Center
and its beamlines.

To find out more, click on:
http://www.als.lbl.gov/als/quickguide/independinvest.html
Scroll down to "Structural Biology/Small Angle X-Ray Scattering (SAXS)."

We invite you to submit a proposal at:
http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize

If you'd like to apply for January-February 2010 beamtime at the
Advanced Light Source, please submit a General User proposal by
November 15, 2009.

If you have any questions or would like to request open beamtime,
please e-mail bcsbbeamt...@lbl.gov.

Please note that executed user agreements must be received by LBNL
prior to beamtime. Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.





-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] Summary for "Anisotropic Diffraction In Refinement" question

[Peter Zwart]

> Application of a elliptical resolution boundary is justified because the
> resolution boundary from common integration programs (Denzo and Mosflm for
> example) is spherical where diffraction for anisotropic data is ellipsoidal.
> A spherical boundary would result in the inclusion of numerous poorly
> measured reflections in the higher resolution shells which effectively makes
> these data more noisy. Imposing an ellipsoidal resolution boundary is
> equivalent to removing noise from the higher resolution bins and is simply
> the anisotropic equivalent of the normal resolution limit truncation.

Hi Justin,

Please be careful in interpreting maps from elliptically truncated
maps, there is a potential for introducing some bias. In Refmac (as
well and Phenix) maps are produced that fill in missing amplitudes
with DFcalc. When your mtz file contains only a small fraction of
miller indices in the highest (spherical) shell, all the missing
reflections will be assigned DFcalc. Depending on your anisotropy,
this can be a significant number of reflections.

I'm not sure how serious this issue is, but it might be worthwhile
checking the 'unfilled' maps as well (both phenix.refine and Refmac
allow you to compute these).

HTH

Peter

Re: [ccp4bb] Software for predicting potential disulfide cross-linking sites?

[Peter Zwart]

I remember this question (and the answer) from 11 years ago!

http://www.ysbl.york.ac.uk/ccp4bb/1998/msg00051.html

HTH

Peter



2009/9/30 Jie Liu :
> Dear All
>
> Does anyone know a software or web-server which can predict potential
> disulfide cross-linking sites?
>
> I have solved a crystal structure. Is there a software to read in the
> coordinates
> file and symmetry information and predict the potential contacting
> residues
> which I can then mutate to CYS in order to introduce an intermolecular
> disulfide bond to stabilize the biological assembly?
>
> Your input is greatly appreciated!
>
> Jie Liu
>



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

[ccp4bb] Dear friend!

[Peter Zwart]

Dear friend,
I want to share a wonderful thing with you.
I know a very good website:  http://www.kcnshop.com/
They mainly sell new and original electronic products. Now they are
promoting their products.
The promotion will keep for 45 days.
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Re: [ccp4bb] Question about merging of data from different crystals

[Peter Zwart]

>The way Phenix.refine refines a model with a high twin fraction is
different >(proportionality rules) which can introduce model bias, so your
model should >be pretty close to the end product. I recommend refining your
structure as >well as you can without inputting the twin law until the very
end.

Minor comment: Detwinning is not used in refinement: the target function
used is 'twin aware' and there is no need for dewtinning of data until you
actually want to look at the maps (water picking etc etc)

It is true indeed that when detwinning data using proportionality rules one
introduces some bias. The extend of this bias depends on the presence and
amount of pseudo rotational symmetry. When no pseudo rotational symmetry is
present, I suspect this bias to be high. When a lot of PRS is there, I
suspect the bias is less of an issue.

I hope that you have assigned your free set with phenix.refine. in that way,
you are certain that the symmetry of the free set follows the point group
symmetry of the lattice. This should avoid potential pitfalls Eleanor
mentioned.

HTH
P

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures

[Peter Zwart]

> He pretends to go to the synchrotron, comes back

Thats what I do all the time. Instead, I go to lane splitters /
jupiter for pizza and beer.


P

Re: [ccp4bb] H32 or R 3 2 :H

[Peter Zwart]

Hi Stephen,

> R32
> H32
> R32 :H

Correct. These are all hexagonal setting. As far as I know, the
hexagonal setting of R32 (R32:H) is the first one that comes up in the
ITvA as is listed a R32. The rhombohedral/primitive setting of R32
(R32:R) comes second in the ITvA, I guess the first setting takes
precedence. H32 is a pdb/ccp4ism.

In my cctbx-skewed view, it looks like this:

R32 ==  R32:H (== H32; not supported by the cctbx)

R32:R is the primitive setting of R32:H

Appending the setting to the space group makes life easier (no
ambiguities) and you can do more funky stuff if one has the
stomach/need to do so [like  "P212121 (a+b,a-b,c)" ].


HTHP

[ccp4bb] Beamtime at the ALS

[Peter Zwart]

Dear All,

January 15, 2010 is the deadline for the March/April 2010 Rapid Access
Proposal cycle.

All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with
ADSC Q315/Q315R detectors, automated sample changers and data collection
software enabling high-throughput crystal screening and data collection.

Remote data collection is available on all BCSB beamlines, providing the
user with the full complement of sample visualization, sample manipulation,
beamline control, data acquisition and data analysis tools exactly as
they would
see them if they were stationed at the beamline.  This enhanced remote
operation
capability is coupled with 22hr onsite support by BCSB staff who are able to
assist immediately with loading additional samples for remote users or
troubleshoot
any issues that might arise. Remote users can furthermore be kept
up-to-date on changes
in ring status via an SMS service
(http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Phone)

Specific features are summarized below.

Beamlines 8.2.1 and 8.2.2:

To facilitate studies on small crystals, a microdiffractometer was
installed in the beamline 8.2.1 endstation. The new equipment allows
precise sample positioning to within 2 microns, excellent sample
viewing of very small crystals, and an off-axis crystal positioning
stage.

Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer (Actor),
allowing remote operations to now be a routine mode of access for
these beamlines.

Beamlines 5.0.1, 5.0.2, 5.0.3:

The Berkeley Automounter sample handling system has a routine capacity of 96
samples (6 pucks). In a typical high-throughput screening mode, the
mount-to-mount time
is around 2.5 minutes per sample, allowing users to screen a full puck
within 45 minutes.

The sector 5 beamline user stations are equipped with fully
high-adjustable, ergonomically
friendly work stations.

Data analyses in the BCSB is facilitated by software maintained by sbgrid
(http://www.sbgrid.org).  A 16 core linux machine is available for our users
to process their data and solve/refine their structure.

An additional mode of access to the BCSB beamlines is through the
Collaborative Crystallography (CC) Program. Users apply for beamtime
via the general user program, and collaborate with an expert
crystallographer who will conduct the experiments and data reduction
on behalf of the researchers. Depending on the users, structure
solution, model building and refinement can be carried out as well.
Please contact bcsbbeamt...@lbl.gov for more information.

Please visit http://bcsb.lbl.gov/ for more details about the Center
and its beamlines.

To find out more, click on:
http://www.als.lbl.gov/als/quickguide/independinvest.html

We invite you to submit a proposal at:

http://alsusweb.lbl.gov/
Scroll down to "Structural Biology beamines (includes protein SAXS)."
Click on "New Proposal."
If you'd like to apply for May/June 2010 beamtime at the
Advanced Light Source, please submit a General User proposal by
March 15, 2010.

If you have any questions or would like to request open beamtime,
please e-mail bcsbbeamt...@lbl.gov.

Please note that executed user agreements must be received by LBNL
prior to beamtime. Proprietary fees, if applicable, must be received
by LBNL at least five working days prior to scheduled beamtime.


-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] reforigin on 2FKA

[Peter Zwart]

Hi,

If you go to

http://cci.lbl.gov/cctbx/explore_symmetry.html

fill out any space group (F432), and search for:

Additional generators of Euclidean normalizer


to get


  Number of structure-seminvariant vectors and moduli: 1
VectorModulus
(1, 0, 0) 2


The seminvariants for F432 are thus

(1/2, 0, 0)


so the only unique origin shift to consider here is (1/2,0,0).


The 1/4 solution do not arise in F432 as can be seen in
http://scripts.iucr.org/cgi-bin/paper?a10657 (table 4) as well.
Giacovazzo actually lists 1/2 1/2 1/2, which is symmetry equivalent to
1/2 0 0 (F centering).

In the cctbx, these seminvariants are derived from first principles
and do work as well when you have things in weird settings. One nice
application of doing this from first principles over using lookup
tables, is (for instance) finding "pseudo" origin shifts in the
presence translational NCS.

For instance the origin shifts in P21:

--
  Number of structure-seminvariant vectors and moduli: 3
VectorModulus
(1, 0, 0) 2
(0, 1, 0) 0  <-   continuous shift along y
(0, 0, 1) 2
  Inversion through a centre at: 0,0,0
--


and in P21 with added (pseudo) (x+1/2,y,z), one gets

--
Number of structure-seminvariant vectors and moduli: 3
VectorModulus
(1, 0, 0) 4
(0, 1, 0) 0
(0, 0, 1) 2
  Inversion through a centre at: 0,0,0
--


This indicates that you have an additional origin shift of (1/4,0,0)
when you have (x+1/2,y,z) as part of the symmetry. If (x+1/2,y,z) is a
'pseudo' operator, then the origin shift of (1/4,0,0) will be pseudo
as well. This can lead to interesting molecular replacement problems
(Andrey Lebedev has done some nice work there).


Cheers,

Peter




2010/1/27 James Holton :
> Francois Berenger wrote:
>>
>> It correspond to what is found at the end of James Holton's
>> origins.com script
>> http://bl831.als.lbl.gov/~jamesh/pickup/origins.com
>> so I guess it should be correct.
>
> Uhhh...
>>
>> He also says how he found them:
>> 
>> # TABLE OF ALLOWED ORIGIN SHIFTS
>> These origin shifts were determined emprirically using 100 randomly-placed
>> atoms
>> that were shifted around with pdbset and checked with SFALL for identical
>> amplitudes to the 0 0 0 origin.  They should be correct for the CCP4
>> convention
>> of symmetry. (I.E. R3 and R32 have hexagonal indexing)
>> 
>
> Okay, I just went back to my notes on this.  I should admit that in my
> completely brain-dead allowed-origin-shift search described above I
> originally found no "allowed" shifts for F432 (not sure why, but maybe
> because it was last on my list). Years later, I think it was Peter Zwart who
> pointed out to me that I was missing a few of what ought to be allowed
> origins.  As I recall, at least one of them passed my pdbset/sfall test, so
> I just assumed I must have done something wrong and added everything in the
> CCP4 document and ITC Vol B to the list.  For purposes of the origins.com
> script, I decided to err on the side of having it try things that may or may
> not work.  If it finds a match, then great!  Right?
>
> Perhaps this was not wise of me.  I just tried shifting the 2fka PDB file by
> "SHIFT FRAC 0.25 0.25 0.25" with pdbset and comparing the resulting Fs from
> sfall to those of the un-shifted PDB.  They are ~30% different.  It could be
> that this is a bug in sfall or pdbset (doubtful), but I would say that
> pragmatically, this is not an "allowed origin shift" for F432.  However,
> 0,0,0.5 and 0,0.5,0.5 and all the other half-cell combinations do work!
>  Guess I missed those!  I have now updated my origins.com script.  It
> appears that the allowed origin shifts for F432 and F23 are not the same, as
> I had previously thought.
>
>>
>>> plus of course the symmetry-equivalent origins generated from these 4 by
>>> the space-group centring (F) translations:
>>>
>>>     0.    0.5000    0.5000
>>>     0.5000    0.    0.5000
>>>     0.5000    0.5000    0.
>>
>> I can see these in syminfo.lib.
>>
>> However, from what you say, I understand that only 2x3 possible
>> origins with each coordinate being 0 or .5 should be accepted by
>> reforigin.
>> But in my test it accepted all 8 possible combinations of 0 and .5
>> that I artificially introduced in my translated test PDBs:
>>
>> m...@myps:2fka# grep Frac run.log | sort | uniq
>> Fractional origin shift:         0.   0.   0.
>> Fractional origin shift:         0.   0.   0.5000
>> Fractional origin shift:         0.   0.5000   0.
>> Fractional origin shift:         0.

Re: [ccp4bb] reforigin on 2FKA

[Peter Zwart]

eason
>> > > > to question since it comes from an excellent authority (Jorge
>> Navaza),
>> > > > the Cheshire space group and cell for both F222 and F23 is I
>> centred
>> > > > (Immm & Im3m resp) with cell lengths a/2, b/2, c/2.  This implies
>> the
>> > > > origin shift (1/4,1/4,1/4), and therefore by unit translations in
>> the
>> > > > Cheshire lattice (3/4,3/4,3/4) also, is a non-equivalent origin.
>> For
>> > > > F432 the Cheshire cell is the same as for F222 & F23 but the
>> Cheshire
>> > > > space group is primitive (Pm3m), which implies that (1/4,1/4,1/4)
>> is
>> > > > *not* an allowed origin shift, i.e. 'disallowed' in the sense that
>> you
>> > > > can't use the same SF calculation formula and still expect to get
>> the
>> > > > right answer: if you're willing to use a different formula
>> > > > then anything
>> > > > (including completely arbitrary origin shifts, i.e. as in P1) is
>> > > > allowed!
>> > > >
>> > > > So the one redeeming factor from all this is that reforigin at
>> least
>> > > > appears to give the right answer.
>> > > >
>> > > > Cheers
>> > > >
>> > > > -- Ian
>> > > >
>> > > > > -Original Message-
>> > > > > From: owner-ccp...@jiscmail.ac.uk
>> > > > > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton
>> > > > > Sent: 27 January 2010 21:35
>> > > > > To: Francois Berenger
>> > > > > Cc: CCP4BB@jiscmail.ac.uk
>> > > > > Subject: Re: [ccp4bb] reforigin on 2FKA
>> > > > >
>> > > > > Francois Berenger wrote:
>> > > > > > It correspond to what is found at the end of James Holton's
>> > > > > > origins.com script
>> > > > > > http://bl831.als.lbl.gov/~jamesh/pickup/origins.com
>> > > > > > so I guess it should be correct.
>> > > > > Uhhh...
>> > > > > >
>> > > > > > He also says how he found them:
>> > > > > > 
>> > > > > > # TABLE OF ALLOWED ORIGIN SHIFTS
>> > > > > > These origin shifts were determined emprirically using 100
>> > > > > > randomly-placed atoms
>> > > > > > that were shifted around with pdbset and checked with SFALL
>> > > > > for identical
>> > > > > > amplitudes to the 0 0 0 origin.  They should be correct for
>> > > > > the CCP4
>> > > > > > convention
>> > > > > > of symmetry. (I.E. R3 and R32 have hexagonal indexing)
>> > > > > > 
>> > > > > Okay, I just went back to my notes on this.  I should admit
>> > > > > that in my
>> > > > > completely brain-dead allowed-origin-shift search described
>> above I
>> > > > > originally found no "allowed" shifts for F432 (not sure why,
>> > > > > but maybe
>> > > > > because it was last on my list). Years later, I think it was
>> > > > > Peter Zwart
>> > > > > who pointed out to me that I was missing a few of what ought to
>> be
>> > > > > allowed origins.  As I recall, at least one of them passed my
>> > > > > pdbset/sfall test, so I just assumed I must have done
>> > > > something wrong
>> > > > > and added everything in the CCP4 document and ITC Vol B to
>> > > > the list.
>> > > > > For purposes of the origins.com script, I decided to err on
>> > > > > the side of
>> > > > > having it try things that may or may not work.  If it finds
>> > > > a match,
>> > > > > then great!  Right?
>> > > > >
>> > > > > Perhaps this was not wise of me.  I just tried shifting the
>> > > > 2fka PDB
>> > > > > file by "SHIFT FRAC 0.25 0.25 0.25" with pdbset and comparing
>> the
>> > > > > resulting Fs from sfall to those of the un-shifted PDB.  They
>> > > > > are ~30%
>> > > > > different.  It could be that this is a bug in sfall or pdbset
>> > > > > (doubtful), but I would say that pragmatically, this is not
>

Re: [ccp4bb] ALS or Uni Pucks

[Peter Zwart]

We have drawings available for both pucks and tools, freely available
for anybody to use:

http://bcsb.als.lbl.gov/wiki/index.php/Automounter#Technical_drawings_and_CAD_models_for_the_pucks_and_automounter_tools

At the moment, crystal positioning is the only supplier possible (they
will have the ALS puck as well AFAIK). If there is demonstrable demand
from the user community for these items, other vendors might have
interest as well. Systems like the Actor, BAM and Irelec CATS systems
can/should handle these pucks.

HTH

Peter




2010/4/9 Deena Oren :
> Does anyone know the status of Crystal Positioning? They are not responding
> to email or phone calls.
> Are they the only alternative to the late Peter Boyd?
> Deena
>
>
> Deena Abells Oren, PhD
> Manager, Structural Biology Resource Center
> Rockefeller University
> 1230 York Avenue, Box 295
> New York, NY 10065-6399
> phone: 212- 327-7429
> fax: 212-327-7389
>
>
>
>



-- 
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-

Re: [ccp4bb] General user proposal deadline May 15, 2010

[Peter Zwart]

Dear All,

Just a reminder that May 15, 2010 is the deadline for the July-August
2010 Rapid Access Proposal cycle for PX beamtime at the ALS. The BCSB
beamlines (5.0.1,5.0.2, 5.0.3, 8.2.1 & 8.2.2) can all be operated
remotely and are all equipped with ADSC Q315(R) detectors.  Beamlines
8.2.2, 8.2.1 and 5.0.2 are tuneable stations whereas 5.0.1 and 5.0.3
are fixed-wavelength beamlines. Control software for the beamlines
features an interface allowing ultra high-throughput screening,
automated annotation of diffraction quality and on the fly indexing
and collection strategy feedback.

The automounters in use on sector 5 support the unipuck and the ALS
puck (both commercially available at
http://www.crystalpositioningsystems.com). Beamlines 8.2.1 and 8.2.2.
support in addition to the uni- and ALS puck the Rigaku system
(http://www.rigaku.com/)

To submit a proposal, please go to the ALS website link listed below:
http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize

Thank you,
Stacey Ortega
510-495-2450

[ccp4bb] Postdoc position available in Berkeley

[Peter Zwart]

Dear All,

We have a postdoc position available at LBNL to work on the development of 
computational approaches for twinned crystallographic data. This is an exciting 
opportunity to address a relatively common phenomenon in crystallographic data 
analysis for which there are currently limited twinning-aware approaches. The 
aim is to develop tools that impact substructure solution, molecular 
replacement, density modification and structure refinement.

Click the link below for more info or contact me directly for more information.

https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480

Regards

Peter Zwart


-- 

P.H. Zwart
Staff Scientist
Molecular Biophysics and Integrated Bioimaging
Center for Advanced Mathematics for Energy Research Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
PHENIX:   http://www.phenix-online.org
CAMERA: http://camera.lbl.gov/
-


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