[ccp4bb] inverse beam integration/scaling protocol

[Francis E Reyes]

Hi all

Is there a walkthru/tutorial for processing inverse beam images with  
imosflm/scala? Googling  a few things didn't get me anywhere.



Thanks!
F

-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

[ccp4bb] Postdoctoral position Greifswald/Germany

[palm]

Dear All,

In the group of Winfried Hinrichs a postdoctoral position is available 
for initially 3 years.
The position involves research and teaching. Knowledge in German is 
not mandatory but is helpful. You need at least enough to read the 
official posting of the university regarding this position:

http://www.uni-greifswald.de/informieren/stellenausschreibung/oeffentlich/wissenschaftliches-personal/institut-fuer-biochemie-nr-11b3.html

Applications should be sent to Winfried Hinrichs 
(hinri...@uni-greifswald.de) before January 25th, 2011, questions also 
to him or to me (p...@uni-greifswald.de).
See also our homepage (http://www.chemie.uni-greifswald.de/~biochem/) 
for information on the group and research.


Posting in behalf of Prof. Hinrichs,
 good luck Gottfried Palm

[ccp4bb] Neutron Protein Crystallography Call for Proposals

[Paul Langan]

PROTEIN CRYSTALLOGRAPHY STATION AT LANSCE -- CALL FOR PROPOSALS

for Run Cycle Beginning the June 2011

You are invited to apply for beam time on the neutron Protein 
Crystallography Station (PCS) at the Los Alamos Neutron Science Center. The 
deadline for submitting proposals is 6:00 p.m. (1800) Mountain Standard 
Time on Wednesday, March 16, 2011.  Any proposals submitted after the due 
date will not be reviewed by the Program Advisory Committees and must be 
resubmitted for the following run cycle.  Rapid access proposals may be 
submitted at any time, but require compelling evidence of sufficient 
scientific urgency to justify special scheduling.


The PCS is a high performance neutron protein crystallography beam line 
funded by the Office of Biological and Environmental Research of the U.S. 
Department of Energy. Users of the PCS have access to free neutron 
beam-time, free perdeuration services and also support for data reduction 
and structure analysis.


For more technical information about the PCS and experimental requirements 
you are encouraged to contact Zoe Fisher (505) 
665-4105  zfis...@lanl.gov or Paul Langan (505) 
665 8125, langan_p...@lanl.gov


Proposal Guidance and Submission
==
Proposals must be submitted through the LANSCE website. Only proposals
submitted on-line will be accepted.  To access the proposal submission 
site, log onto
the LANSCE home page (http://lansce.lanl.gov).  On 
this page click the link located on
the left "Lujan Center' first call. This will take you to the on-line 
submission system.



Detailed instructions for preparing the proposals can be found on the proposal
submission sites under "Step-by-Step Guide to Submitting an Online Proposal."

Should you have any questions or require assistance, please contact the 
Lujan Center User Office Administrator:  by e-mail at 
l...@lanl.gov or by telephone at


(505) 667-5649.

Re: [ccp4bb] Counting of geometrical restraints?

[Ian Tickle]

Hi Pete

Not sure what you mean by 'which parameters'.  We're talking here
about the total parameter _count_ and its effect on the statistics,
i.e. R factors etc.  You can't relate a specific parameter to a
specific restraint.  The statistics behave in exactly the same way as
they would if you did actually reduce the number of parameters (and
they certainly don't behave in the same way as they would if you
increased the number of observations).  That's why I call it the
'effective' no of parameters.  In any case I don't think
transformation of constraints to parameters is straightforward at all!
 For example if you constrain all the y co-ordinate parameters to sum
to zero by adding an extra equation which y parameter are you
'removing'?  Obviously you can remove a parameter explicitly by
expressing it in terms of the others, but that's not the only way (or
even the best way) of solving a constrained optimisation problem.  A
better way is usually to _add_ constraint equations using Lagrange
multipliers without changing the parameters, then there's no 1-to-1
relationship between constraints and parameters.

Cheers

-- Ian

On Tue, Feb 1, 2011 at 3:56 PM, Pete Meyer  wrote:
> Ian,
>
>> Now it's still true that Ncon reduces Npar but it's no longer true
>> that Ncon increases Nobs.
>
> This seems counter-intuitive enough for me to ask a stupid question: which
> parameters are being removed in restrained refinement?
>
> For constraints this seems straightforward (transformation of >1 parameters
> to 1 parameter); but the same logic doesn't appear to apply to restraints
> (at least, I can't figure out how it would).
>
> Pete
>

Re: [ccp4bb] contour map

[Adam Ralph]

Dear Leila,

   The CCP4 program FFT, which generates 3D maps from reflection data
can also produce projections. Use the keyword PROJECTION. It will only
give projections down an axis but if the X-ray SG is trigonal then you
will be OK. Another CCP4 prog MAPSLICER can be used to view the map.

Adam



On Mon, 31 Jan 2011, Leila Foroughi wrote:

> I'm currently trying to compare single crystal X-ray data for a protein
crystal with previously published electron miscroscopy data. I would really
like to be able to take my electron density map (from X-ray) and view it as a
2D projection of 3D space (essentially a contour map). The attached is an
example of the type of electron density map I'm trying to mimic. Does anyone
have any suggestions on what software I could use to do this?
>
> Image Source: J Mol. Biol. (1975) 94, 425-440.
>
> Thanks,
> Leila
>

Re: [ccp4bb] Counting of geometrical restraints?

[Pete Meyer]

Ian,


Now it's still true that Ncon reduces Npar but it's no longer true
that Ncon increases Nobs.


This seems counter-intuitive enough for me to ask a stupid question: 
which parameters are being removed in restrained refinement?


For constraints this seems straightforward (transformation of >1 
parameters to 1 parameter); but the same logic doesn't appear to apply 
to restraints (at least, I can't figure out how it would).


Pete

Re: [ccp4bb] contour map

[Nicholas M Glykos]

Hi Leila,

What feels like two centuries ago, we had written a program that would 
read a ccp4 map and produce a postscript plot containing both contours and 
a dithered grayscale representation of the map. This is useful for complex 
projections like the one shown in [1]. The program (mcps) is still 
available via our pages ([2]), it even has documentation ([3]), but the 
ready-made executables are really old (and the old timers will certainly 
smile hearing that the tarball contains executables for irix, osf and 
solaris, but sorry, no VMS :-))  Having said that, the circa 2001 linux 
executable appears to run flawlesly under ubuntu 10.04, but as always YMMV.


Nicholas


[1] http://utopia.duth.gr/~glykos/mcps_graph.html
[2] http://utopia.duth.gr/~glykos/other.html
[3] http://utopia.duth.gr/~glykos/mcps.html


-- 


  Dr Nicholas M. Glykos, Department of Molecular Biology
 and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/