Ed,
When denzo integrates the frame it thinks that the step size is 0.5
deg./frame, when it is zero. Denzo compensates for this by adjusting
CRYST ROTX by -0.5 deg/frame. The change in CRYST ROT X is taken by
scalepack as a crystal slippage. Scalepack may have difficulty adding
partials from 1000 frames, given that the FORTRAN programs's array sizes
are fixed. Even scalepackvirus could have trouble, as this is a most
abnormal data collection.
The denzo keywords are:
OSCILLATION START 0
OSCILLATION STEP 0.001
OSCILLATION RANGE 0.5
also fixing the mosaicity may help
To avoid the Scalepack problems try:
{do not use the ADD PARTIALS keyword}
do not POSTREFINE either
Ed, if you just want to combine the images into a single image file, you
could modify the program we use to add MacScience or Quantum4 "still"
images. This is a highly useful way of improving statistics from very
small crystals with weak home sources. We have been able to index some
exceptionally small crystals this way. Crystals so small that you might
not even consider shooting them on a normal beamline. Let me know and
I'll send you the code.
Hope that this helps,
Mark
On Tue, 2010-02-23 at 08:57 -0600, Ed Pozharski wrote:
> Mark,
>
> denzo integrates frames just fine, it's the *scaling* that crashes.
>
> Ed.
>
> On Tue, 2010-02-23 at 07:35 -0600, White, Mark wrote:
> > Ed,
> >
> > Check the DENZO manual. I am away from the office, so I do not have access
> > right now. I remember a DENZO Keyword such as STEP, which should solve
> > your problem.
> >
> > You will need to run denzo manually, or via a command line script.
> >
> > Good luck,
> > Mark
> >
> > ________________________________________
> > From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Ed Pozharski
> > [epozh...@umaryland.edu]
> > Sent: Monday, February 22, 2010 5:23 PM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] short step
> >
> > I want to process bunch of frames with extremely short step - i.e. these
> > are 0.5degree oscillations but crystal only rotates by 1 degree over
> > 1000 frames (I would have kept it at the same orientation if Rigaku
> > control software would allow zero step). Denzo can process the frames
> > all right, but scalepack chokes on it saying "Floating Exception". I
> > don't have much experience with mosflm, and it failed also.
> >
> > What I wonder is if this happens because both programs have some bug in
> > these unusual conditions or there is something fundamental that prevents
> > scaling such data?
> >
> > Cheers,
> >
> > Ed.
> >
> > --
> > Edwin Pozharski, PhD, Assistant Professor
> > University of Maryland, Baltimore
> > ----------------------------------------------
> > When the Way is forgotten duty and justice appear;
> > Then knowledge and wisdom are born along with hypocrisy.
> > When harmonious relationships dissolve then respect and devotion arise;
> > When a nation falls to chaos then loyalty and patriotism are born.
> > ------------------------------ / Lao Tse /
>
>
Yours sincerely,
Mark A. White, Ph.D.
Assistant Professor of Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics
X-ray Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Cell. (409) 539-9138
Fax. (409) 747-4745
mailto://wh...@xray.utmb.edu
http://xray.utmb.edu
http://xray.utmb.edu/~white
