Re: [ccp4bb] pH dependent conformational change

[AMIT]

Hi
   Intrinsic fluorescence may be used to monitor such change qualitatively.
Another option is red-edge excitation flourescence technique may work if
there are suitable fluorophores (W or F) on the each of the two domains
changing solvent accessibility upon rigid body motion.

Amit.

On Mon, Dec 6, 2010 at 11:56 PM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:

> Well, I just got word that the protein is ~100kD anyway, so I think
> the HSQC is out the window anyway!
>
> Jacob
>
> On Mon, Dec 6, 2010 at 12:16 PM, Roopa Thapar 
> wrote:
> >
> >
> > I agree that the experiment is a good one and can easily be done, but
> without assignments I think the interpretation could be ambiguous.
> >
> > pH dependent chemical shift perturbations could occur far removed from
> the linker (either due to a conformational change or the change in chemical
> environment around the amide nucleus)
> > and without any information about which residues are shifting it may be
> difficult to conclude that these perturbations are due to a change in domain
> orientation rather than other subtle
> > pH dependent effects.
> >
> > If there are no perturbations, then of course one can conclude little or
> no conformational changes occur.  The magnitude of the perturbation would
> depend on how extensive the conformational change is.
> >
> > One could specifically label the protein with 15N-labeled amino acids
> that are particularly unique to the linker - this would simplify the
> spectrum and the data may be easier to interpret.
> >
> > It is a good experiment to try however.
> >
> >
> > Roopa
> >
> >
> >
> > 
> > From: Jacob Keller [j-kell...@fsm.northwestern.edu]
> > Sent: Monday, December 06, 2010 12:54 PM
> > To: Roopa Thapar
> > Cc: CCP4BB@jiscmail.ac.uk
> > Subject: Re: [ccp4bb] pH dependent conformational change
> >
> > Even without assignments, wouldn't a dramatic shift be seen in the
> > interacting residues? Also, I suggested the method because it is
> > pretty easy, probably doable in a week...
> >
> > Jacob
> >
> > On Mon, Dec 6, 2010 at 11:24 AM, Roopa Thapar 
> wrote:
> >> If there are backbone NMR assignments available then, definately a pH
> titration using HSQCs would give site specific information.  These are easy
> experiments if someone can help you set them up.
> >> The perturbations should map to the inter-domain interface.
> >>
> >> If there are no assignments for the protein, spectral changes in
> response to pH would be harder to interpret.  You could try FRET by
> introducing two probes - one in each domain.
> >>
> >> Roopa
> >>
> >> 
> >> From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Jacob
> Keller [j-kell...@fsm.northwestern.edu]
> >> Sent: Monday, December 06, 2010 12:15 PM
> >> To: CCP4BB@JISCMAIL.AC.UK
> >> Subject: Re: [ccp4bb] pH dependent conformational change
> >>
> >> Wouldn't a HSQC of 15N-labeled protein be a relatively easy yes/no
> experiment? Maybe it would not be incredibly definitive?
> >>
> >> Jacob
> >>
> >>
> >> On Mon, Dec 6, 2010 at 11:10 AM, Mischa Machius  > wrote:
> >> Daniel,
> >>
> >> You'll probably have to monitor pH changes through size changes of your
> protein, provided the structural changes will indeed cause size changes.
> >>
> >> You said "easy", so that probably rules out Small-Angle X-Ray Scattering
> (SAXS), but that would be the highest-resolution method. You can try static
> and dynamic light scattering, analytical ultracentrifugation and
> fluorescence anisotropy. If you are really lucky, size exclusion
> chromatography might work too.
> >>
> >> And then there are the "difficult" ways...
> >>
> >> MM
> >>
> >>
> >>
> >>
> >> On Dec 6, 2010, at 11:59 AM, Daniel Jin wrote:
> >>
> >>
> >> Dear CCP4 colleagues,
> >>
> >>
> >>
> >> We have a protein that is composed of two domains connected by a short
> peptide linker. We have some indirect evidence showing that the two domains
> may somehow move against each other when exposed to different pH. It is
> unlikely to have any obvious secondary structure change since each domain
> behaves like a rigid body. I am wondering whether there is any “easy” way,
> biochemically or biophysically, to monitor the conformational changes in
> solution. Many thanks.
> >>
> >>
> >>
> >> As far as I know most of the pH sensing stories are linked to histidine
> residue. Can you point me to any references that show a different pH sensing
> mechanism (other than His)? Thanks.
> >>
> >>
> >>
> >> Best,
> >>
> >> Daniel
> >>
> >>
> >>
> >> ---
> >> Mischa Machius, PhD
> >> Director, Center for Structural Biology
> >> Assoc. Professor, Dept. of Pharmacology
> >> Member, Lineberger Comprehensive Cancer Center
> >> University of North Carolina
> >> 4079 Genetic Medicine
> >> CB#7365
> >> 120 Mason Farm Road
> >> Chapel Hill, NC 27599-7365, U.S.A.
> >> t

[ccp4bb] MX Post-Doc postion at Diamond

[Martin Walsh]

Dear all, we have a vacancy for a postdoc within the MX group at Diamond. Full 
details can be found at 
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0584-TH.html. Interested 
candidates can contact me directly by email for further details on research 
project associated with the post

 

Martin

 

PDRA, Beamline I04-1 Diamond

Diamond Light Source is a new synchrotron and a leading scientific facility of 
its type in the world. Located on the Harwell Science and Innovation Campus in 
South Oxfordshire, we host facilities supporting cutting edge research in all 
fields of science.

 

We are looking for a highly motivated and experienced crystallographer at the 
Post Doctoral Research Associate level to join the I04-1 beamline within the 
Macromolecular crystallography village at Diamond. I04-1 is a fixed wavelength 
(0.92 Å) insertion device beamline dedicated to macromolecular crystallography 
(MX) and complements the other four currently operating MX beamlines at 
Diamond. I04-1 provides a high flux X-ray beam for macromolecular structure 
determination by the Single Anomalous Diffraction (SAD) or Molecular 
replacement (MR) methods. A state of the art automated endstation consisting of 
a MD2 microdiffractometer, a Pilatus 2M hybrid pixel array detector and a CATS 
robot for automated sample handling is integrated into a automated data 
reduction pipeline that provides users with a high-throughput crystallography 
platform.

 

Research will be focused on structural studies of a multifunctional bacterial 
uptake system that is required for critical mechanisms of bacterial survival in 
the human.

Re: [ccp4bb] salt or protein crystals?

[Artem Evdokimov]

Looks like diffraction off of tiny small-molecule crystals to me.

Artem

On Tue, Dec 7, 2010 at 8:14 AM, xiuwen zhang  wrote:

> Dear Colleagues,
>
> Currently we got several very tiny crystals. After exposuring a cluster
> of crystals one hour in home source, we could find some weak diffraction
> spots. As the spots are too few for indexing, I am not quite sure whether
> these tiny crystals are salt crystals or protein crystals. I appreciate your
> experience on similar case.
>
>Attached files are two diffraction images at 0 and 90 degree. Thank you
> very much for your kind help.
>
> Cheers,
> Xiuwen

Re: [ccp4bb] pH dependent conformational change

[Daniel Bonsor]

I would like to point out that HSQC could still be applied even in such a large 
protein. TROSY-HSQC has been successful in improving peaks in spectra of large 
protein. Typically the sample would need to be deuterated to see the full 
effect of TROSY, but even a partial deuteration can improve signal.  We have 
run TROSY-spectra of a complex (75kDa) with no deuteration and that spectrum is 
much better than a normal HSQC spectrum.

Dan

Re: [ccp4bb] salt or protein crystals?

[David Briggs]

I agree - looks like small molecular diffraction.

Try increasing delta-phi to catch more of the lattice to confirm - I
often do a 5º image or two with the detector pushed as close as
possible to check for salt diffraction when screening.

The lack of low res (~15-20Å) spots around the beamstop is another
"smoking gun".

HTH

Dave


David C. Briggs PhD
Father, Structural Biologist and Sceptic

University of Manchester E-mail:
david.c.bri...@manchester.ac.uk

http://manchester.academia.edu/DavidBriggs (v.sensible)
http://xtaldave.wordpress.com/ (sensible)
http://xtaldave.posterous.com/ (less sensible)
Twitter: @xtaldave
Skype: DocDCB




On 7 December 2010 14:14, xiuwen zhang  wrote:
> Dear Colleagues,
>
>     Currently we got several very tiny crystals. After exposuring a cluster
> of crystals one hour in home source, we could find some weak diffraction
> spots. As the spots are too few for indexing, I am not quite sure whether
> these tiny crystals are salt crystals or protein crystals. I appreciate your
> experience on similar case.
>
>    Attached files are two diffraction images at 0 and 90 degree. Thank you
> very much for your kind help.
>
> Cheers,
> Xiuwen

[ccp4bb] BM14 Beamtime Call for Feb-March 2011.

[hassan belrhali]

Dear colleagues,



Since January 2010, the BM14 MAD MX beamline at the ESRF (Grenoble, France)

is providing beamtime for both European and Indian MX communities after a

smooth transition from the UK MRC-EMBL tandem to the actual

EMBL-ESRF-India consortium.



The beamline is fully opened now for EU-member state and EU-associated state
users[1].

Scientists are encouraged to submit proposals via the web-based eProposal
interface [2]

on http://www.bm14.eu (“Apply for Beamtime”).



A European reviewer panel, chaired by Dr. Pedro Matias (ITQB, Lisbon,
Portugal),

will process the proposals and beamtime will be provided for the

February – March 2011 period.



*Deadline for proposal submissions*: *31st of December 2010.*



Limited travel and accommodation support from the ELISA EU grant will be

provided to selected users.



*Beamline major features:*

-  7 to 18 keV energy range with a brand new ESRF monochromator

-  Rayonix 225 CCD detector

-  MD2 Microdiffractometer with mini-Kappa goniometer head

-  Robotic Sample changer (SPINE sample holders)

-  Ultra-low resolution beamstop (down to 300 Å data recordable)

-  Very high resolution data collection conditions (~ 0.6 Å data
recordable)

-  Crystal Humidity Control Device (HC1) for improving sample
diffraction

(*
http://www.embl-grenoble.fr/groups/instr/humidifier_page1.html*)**

-  Remote data collection

-   Substantial user support during data collections



Best regards,

Hassan Belrhali (*belrhali-at-embl.fr*).



*PS: this call is independent from Indian and ESRF calls.*



[1]* EU-associated state*: Switzerland, Israel, Norway, Iceland and
Liechtenstein

Turkey, Croatia, the Former Yugoslav Republic of Macedonia and Serbia,

Albania and Montenegro, Bosnia & Herzegovina (source EC: FP7 Third Country
Agreements)



[2] *eProposal platform:* kindly donated by UK MRC

Re: [ccp4bb] salt or protein crystals?

[Nian Huang]

Definitely small molecule crystals. You might want to push the
detector closer and use better cryo solution for further confirmation.

Nian

On Tue, Dec 7, 2010 at 8:14 AM, xiuwen zhang  wrote:
> Dear Colleagues,
>
>     Currently we got several very tiny crystals. After exposuring a cluster
> of crystals one hour in home source, we could find some weak diffraction
> spots. As the spots are too few for indexing, I am not quite sure whether
> these tiny crystals are salt crystals or protein crystals. I appreciate your
> experience on similar case.
>
>    Attached files are two diffraction images at 0 and 90 degree. Thank you
> very much for your kind help.
>
> Cheers,
> Xiuwen

[ccp4bb] brute force MR

[Arnon Lavie]

Hi there:

The situation: We are facing difficult molecular replacement: we believe 
we have two molecules in the ASU, but phaser/molrep find only one. Using 
the electron density calculated using this single molecule, we have 
manually placed  the 2nd molecule, albeit not good enough for rigid body 
refinement.


Our strategy: We are looking for a program to do a 3 dimensional search 
around the current position of the 2nd molecule. Maybe one that 
calculates R-factor at the different positions, to allow to identify the 
correct one. ...


Does anyone know of such a program, or an alternative approach?

Thanks.

Arnon

--
***
Arnon Lavie, Professor
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1108 (M/C 669)
Chicago, IL 60607
U.S.A.
 Tel:(312) 355-5029
 Fax:(312) 355-4535
 E-mail: la...@uic.edu
 http://www.uic.edu/labs/lavie/
***

Re: [ccp4bb] brute force MR

[Bosch, Juergen]

Just a thought:
shave off parts of your model1, which you think might cause a clash perhaps, 
essentially keeping a core in place, then rerun molrep using model1 as fixed 
and search for a second. If you are successful, then SSM superimpose your 
complete model onto both and see what you have to fix the problem.

Jürgen

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/

On Dec 7, 2010, at 4:38 PM, Arnon Lavie wrote:

Hi there:

The situation: We are facing difficult molecular replacement: we believe
we have two molecules in the ASU, but phaser/molrep find only one. Using
the electron density calculated using this single molecule, we have
manually placed  the 2nd molecule, albeit not good enough for rigid body
refinement.

Our strategy: We are looking for a program to do a 3 dimensional search
around the current position of the 2nd molecule. Maybe one that
calculates R-factor at the different positions, to allow to identify the
correct one. ...

Does anyone know of such a program, or an alternative approach?

Thanks.

Arnon

--
***
Arnon Lavie, Professor
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1108 (M/C 669)
Chicago, IL 60607
U.S.A.
 Tel:(312) 355-5029
 Fax:(312) 355-4535
 E-mail: la...@uic.edu
 http://www.uic.edu/labs/lavie/
***

Re: [ccp4bb] brute force MR

[Nian Huang]

Try this, assuming you have good data. Use one molecule you got to do
refinement (rigid body or restraint refinement with tight restraint)
and phase the map.  Then do a phased map molecular replacement. You
might want only use the core of your protein to do the molecular
replacement search to avoid the clashing problem. It worked once for
me even the map was very bad.

Nian

On Tue, Dec 7, 2010 at 3:38 PM, Arnon Lavie  wrote:
> Hi there:
>
> The situation: We are facing difficult molecular replacement: we believe we
> have two molecules in the ASU, but phaser/molrep find only one. Using the
> electron density calculated using this single molecule, we have manually
> placed  the 2nd molecule, albeit not good enough for rigid body refinement.
>
> Our strategy: We are looking for a program to do a 3 dimensional search
> around the current position of the 2nd molecule. Maybe one that calculates
> R-factor at the different positions, to allow to identify the correct one.
> ...
>
> Does anyone know of such a program, or an alternative approach?
>
> Thanks.
>
> Arnon
>
> --
> ***
> Arnon Lavie, Professor
> Dept. of Biochemistry and Molecular Genetics
> University of Illinois at Chicago
> 900 S. Ashland Ave.
> Molecular Biology Research Building, Room 1108 (M/C 669)
> Chicago, IL 60607
> U.S.A.
>                             Tel:        (312) 355-5029
>                             Fax:        (312) 355-4535
>                             E-mail:     la...@uic.edu
>                             http://www.uic.edu/labs/lavie/
> ***
>

[ccp4bb] How to use XDS programme to process data collected at Q315r detector

[wu donghui]

Dear all,

Recently I collected several data sets at 13B1 Taiwan beamline with Q315r
detector. It's no problem to index these datasets using mosflm, but Rms
residual and weighted residual is high. Here I want to try XDS to play my
data. I downloaded a template example as below.

!*
! Example file XDS.INP for the ADSC Q105 CCD-detector
! Characters in a line to the right of an exclamation mark are comment.
!*
!NOTE: XDS can handle only "SMV" images of TYPE=unsigned_short.
!  Images are expected to be already corrected for spatial distortions.
!
!Standard settings for the ADSC Q105 that rarely need to be changed

 DETECTOR=ADSC  MINIMUM_VALID_PIXEL_VALUE=1  OVERLOAD= 65000
 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
 TRUSTED_REGION=0.0 1.05 !Relative radii limiting trusted detector region
!UNTRUSTED_RECTANGLE= 570 1920  1469 2048  ! rectangle: X1 X2   Y1 Y2
!UNTRUSTED_ELLIPSE= 910 11101010 1210  ! ellipse enclosed by X1 X2 Y1 Y2
!File name, access, format of dark-current (non-Xray background) image
!DARK_CURRENT_IMAGE=../images/blank.tif!hardly ever used

!MAXIMUM_NUMBER_OF_JOBS=4  !Speeds-up COLSPOT & INTEGRATE on a Linux-cluster
!MAXIMUM_NUMBER_OF_PROCESSORS=4!<33;ignored by single cpu version of xds
!MINUTE=0   !Maximum number of minutes to wait until data image must appears
!TEST=1 !Test flag. 1,2 additional diagnostics and images

!NX=number of fast pixels (along X); QX=length of a X-pixel (mm)
!NY=number of slow pixels (along Y); QY=length of a Y-pixel (mm)
!For the ADSC, the number of detector pixels and their sizes are
!obtained from the image header. It is therefore unnecessary to
!specify values for NX, NY, QX, QY.
!NX=2304 NY=2304 QX=0.0816 QY=0.0816   !ADSC Q4
!NX=2048 NY=2048 QX=0.0500 QY=0.0500   !ADSC Q105
!NX=2048 NY=2048 QX=0.1024 QY=0.1024   !ADSC Q210 at ESRF ID-29
!NX=4096 NY=4096 QX=0.051  QY=0.051!ADSC Q210r
!NX=3072 NY=3072 QX=0.10259 QY=0.10259 !ADSC Q315 at SSRL 9-2
!NX=6144 NY=6144 QX=0.0513 QY=0.0513   !ADSC Q315r at ESRF ID-29

!AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by
default

!== JOB CONTROL PARAMETERS
===
!JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT

!== GEOMETRICAL PARAMETERS
===
!ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2,
ORGY=NY/2
 ORGX=3072.0  ORGY=3072   !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2
 DETECTOR_DISTANCE= 480  !(mm)

 ROTATION_AXIS= 1.0  0.0 0.0
 OSCILLATION_RANGE=0.5!degrees (>0)

 X-RAY_WAVELENGTH=1.14   !Angstroem
 INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
 FRACTION_OF_POLARIZATION=0.90 !default=0.5 for unpolarized beam
 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0

!=== CRYSTAL PARAMETERS
=
 SPACE_GROUP_NUMBER=0  !0 for unknown crystals; cell constants are ignored.
 UNIT_CELL_CONSTANTS= 139.53   249.90   119.83  90.000 112.511 90.000

! You may specify here the x,y,z components for the unit cell vectors if
! known from a previous run using the same crystal in the same orientation
!UNIT_CELL_A-AXIS=
!UNIT_CELL_B-AXIS=
!UNIT_CELL_C-AXIS=

!Optional reindexing transformation to apply on reflection indices
!REIDX=   0  0 -1  0  0 -1  0  0 -1  0  0  0

!FRIEDEL'S_LAW=FALSE !Default is TRUE.




However indexed cell parameter for a b and c is small and error information
indicates that cell solution is not accurate.  I suspect that I need to
change some input parameters besides selection of ORGX=3072.0
ORGY=3072 when using XDS
as the template is for ADSC Q105.

Here I want to know if anyone has experience to use XDS to process data
collected at Q315r and what error I made for using this script.

Thank you very much for any suggestion.

Best regards,

Donghui

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[Jürgen Bosch]

Look into the header of your image file via more or run mosflm on one image and 
look at the output in the terminal window.

You'll get the pixelsize and you'll need to convert the beamcenter into pixels 
from mosflm. Keep in mind that beam X = orgy in xds and beam y is orgx
Plus the usual stuff lambda distance 2theta

Jürgen 

..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/

On Dec 7, 2010, at 22:03, wu donghui  wrote:

> Dear all,
> 
> Recently I collected several data sets at 13B1 Taiwan beamline with Q315r 
> detector. It's no problem to index these datasets using mosflm, but Rms 
> residual and weighted residual is high. Here I want to try XDS to play my 
> data. I downloaded a template example as below.
> 
> !*
> ! Example file XDS.INP for the ADSC Q105 CCD-detector 
> ! Characters in a line to the right of an exclamation mark are comment.
> !*
> !NOTE: XDS can handle only "SMV" images of TYPE=unsigned_short.
> !  Images are expected to be already corrected for spatial distortions.
> !
> !Standard settings for the ADSC Q105 that rarely need to be changed
> 
>  DETECTOR=ADSC  MINIMUM_VALID_PIXEL_VALUE=1  OVERLOAD= 65000
>  DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
>  DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
>  TRUSTED_REGION=0.0 1.05 !Relative radii limiting trusted detector region
> !UNTRUSTED_RECTANGLE= 570 1920  1469 2048  ! rectangle: X1 X2   Y1 Y2  
> !UNTRUSTED_ELLIPSE= 910 11101010 1210  ! ellipse enclosed by X1 X2 Y1 Y2
> !File name, access, format of dark-current (non-Xray background) image
> !DARK_CURRENT_IMAGE=../images/blank.tif!hardly ever used
> 
> !MAXIMUM_NUMBER_OF_JOBS=4  !Speeds-up COLSPOT & INTEGRATE on a Linux-cluster
> !MAXIMUM_NUMBER_OF_PROCESSORS=4!<33;ignored by single cpu version of xds
> !MINUTE=0   !Maximum number of minutes to wait until data image must appears
> !TEST=1 !Test flag. 1,2 additional diagnostics and images
> 
> !NX=number of fast pixels (along X); QX=length of a X-pixel (mm)
> !NY=number of slow pixels (along Y); QY=length of a Y-pixel (mm)
> !For the ADSC, the number of detector pixels and their sizes are
> !obtained from the image header. It is therefore unnecessary to
> !specify values for NX, NY, QX, QY.
> !NX=2304 NY=2304 QX=0.0816 QY=0.0816   !ADSC Q4
> !NX=2048 NY=2048 QX=0.0500 QY=0.0500   !ADSC Q105
> !NX=2048 NY=2048 QX=0.1024 QY=0.1024   !ADSC Q210 at ESRF ID-29
> !NX=4096 NY=4096 QX=0.051  QY=0.051!ADSC Q210r
> !NX=3072 NY=3072 QX=0.10259 QY=0.10259 !ADSC Q315 at SSRL 9-2
> !NX=6144 NY=6144 QX=0.0513 QY=0.0513   !ADSC Q315r at ESRF ID-29
> 
> !AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by default
> 
> !== JOB CONTROL PARAMETERS ===
> !JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT
> 
> !== GEOMETRICAL PARAMETERS ===
> !ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2
>  ORGX=3072.0  ORGY=3072   !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2
>  DETECTOR_DISTANCE= 480  !(mm)
> 
>  ROTATION_AXIS= 1.0  0.0 0.0
>  OSCILLATION_RANGE=0.5!degrees (>0)
> 
>  X-RAY_WAVELENGTH=1.14   !Angstroem
>  INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
>  FRACTION_OF_POLARIZATION=0.90 !default=0.5 for unpolarized beam
>  POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0
> 
> !=== CRYSTAL PARAMETERS =
>  SPACE_GROUP_NUMBER=0  !0 for unknown crystals; cell constants are ignored.
>  UNIT_CELL_CONSTANTS= 139.53   249.90   119.83  90.000 112.511 90.000
> 
> ! You may specify here the x,y,z components for the unit cell vectors if
> ! known from a previous run using the same crystal in the same orientation
> !UNIT_CELL_A-AXIS=
> !UNIT_CELL_B-AXIS=
> !UNIT_CELL_C-AXIS=
> 
> !Optional reindexing transformation to apply on reflection indices
> !REIDX=   0  0 -1  0  0 -1  0  0 -1  0  0  0
> 
> !FRIEDEL'S_LAW=FALSE !Default is TRUE.
> 
> 
> 
> 
> However indexed cell parameter for a b and c is small and error information 
> indicates that cell solution is not accurate.  I suspect that I need to 
> change some input parameters besides selection of ORGX=3072.0  ORGY=3072 when 
> using XDS as the template is for ADSC Q105.
> 
> Here I want to know if anyone has experience to use XDS to process data 
> collected at Q315r and what error I made for using this script. 
> 
> Thank you very much for any suggestion.
> 
> Best regards,
> 
> Donghui

Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector

[Konstantin v. Korotkov]

Donghui,

there are several ways to get ORGX ORGY parameters. As Juergen suggested, 
you could use the numbers from the header or Mosflm output.

More information on the excellent XDS Wiki:
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Obtaining_ORGX_ORGY

Another option would be to run generate_XDS.INP script, which will get 
ORGX ORGY parameters from headers automatically:

http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP

If you know the spacegroup, define it with keyword SPACE_GROUP_NUMBER= 
(your script has 0).


HTH,
Konstantin

On Wed, 8 Dec 2010, wu donghui wrote:


Dear all,
Recently I collected several data sets at 13B1 Taiwan beamline with Q315r
detector. It's no problem to index these datasets using mosflm, but Rms
residual and weighted residual is high. Here I want to try XDS to play my
data. I downloaded a template example as below.

!
*
! Example file XDS.INP for the ADSC Q105 CCD-detector 
! Characters in a line to the right of an exclamation mark are comment.
!
*
!NOTE: XDS can handle only "SMV" images of TYPE=unsigned_short.
!      Images are expected to be already corrected for spatial
distortions.
!
!Standard settings for the ADSC Q105 that rarely need to be changed

 DETECTOR=ADSC  MINIMUM_VALID_PIXEL_VALUE=1  OVERLOAD= 65000
 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
 TRUSTED_REGION=0.0 1.05 !Relative radii limiting trusted detector region
!UNTRUSTED_RECTANGLE= 570 1920  1469 2048  ! rectangle: X1 X2   Y1 Y2  
!UNTRUSTED_ELLIPSE= 910 1110    1010 1210  ! ellipse enclosed by X1 X2 Y1
Y2
!File name, access, format of dark-current (non-Xray background) image
!DARK_CURRENT_IMAGE=../images/blank.tif    !hardly ever used

!MAXIMUM_NUMBER_OF_JOBS=4  !Speeds-up COLSPOT & INTEGRATE on a
Linux-cluster
!MAXIMUM_NUMBER_OF_PROCESSORS=4!<33;ignored by single cpu version of xds
!MINUTE=0   !Maximum number of minutes to wait until data image must
appears
!TEST=1     !Test flag. 1,2 additional diagnostics and images

!NX=number of fast pixels (along X); QX=length of a X-pixel (mm)
!NY=number of slow pixels (along Y); QY=length of a Y-pixel (mm)
!For the ADSC, the number of detector pixels and their sizes are
!obtained from the image header. It is therefore unnecessary to
!specify values for NX, NY, QX, QY.
!NX=2304 NY=2304 QX=0.0816 QY=0.0816   !ADSC Q4
!NX=2048 NY=2048 QX=0.0500 QY=0.0500   !ADSC Q105
!NX=2048 NY=2048 QX=0.1024 QY=0.1024   !ADSC Q210 at ESRF ID-29
!NX=4096 NY=4096 QX=0.051  QY=0.051    !ADSC Q210r
!NX=3072 NY=3072 QX=0.10259 QY=0.10259 !ADSC Q315 at SSRL 9-2
!NX=6144 NY=6144 QX=0.0513 QY=0.0513   !ADSC Q315r at ESRF ID-29

!AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by
default

!== JOB CONTROL PARAMETERS
===
!JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT

!== GEOMETRICAL PARAMETERS
===
!ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2,
ORGY=NY/2
 ORGX=3072.0  ORGY=3072   !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2
 DETECTOR_DISTANCE= 480  !(mm)

 ROTATION_AXIS= 1.0  0.0 0.0
 OSCILLATION_RANGE=0.5            !degrees (>0)

 X-RAY_WAVELENGTH=1.14           !Angstroem
 INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
 FRACTION_OF_POLARIZATION=0.90 !default=0.5 for unpolarized beam
 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0

!=== CRYSTAL PARAMETERS
=
 SPACE_GROUP_NUMBER=0  !0 for unknown crystals; cell constants are
ignored.
 UNIT_CELL_CONSTANTS= 139.53   249.90   119.83  90.000 112.511 90.000

! You may specify here the x,y,z components for the unit cell vectors if
! known from a previous run using the same crystal in the same orientation
!UNIT_CELL_A-AXIS=
!UNIT_CELL_B-AXIS=
!UNIT_CELL_C-AXIS=

!Optional reindexing transformation to apply on reflection indices
!REIDX=   0  0 -1  0  0 -1  0  0 -1  0  0  0

!FRIEDEL'S_LAW=FALSE !Default is TRUE.




However indexed cell parameter for a b and c is small and error
information indicates that cell solution is not accurate.  I suspect that
I need to change some input parameters besides selection
of ORGX=3072.0  ORGY=3072 when using XDS as the template is for ADSC Q105.

Here I want to know if anyone has experience to use XDS to process data
collected at Q315r and what error I made for using this script. 

Thank you very much for any suggestion.

Best regards,

Donghui




--
Konstantin Korotkov, Ph.D.

Research Scientist
University of Washington
Department of Biochemistry
Box 357742
Seattle, WA 98195-7742

(206)616-4512
k...@u.washington.edu
--

[ccp4bb] superposing (hkl) indexes on diffraction image

[Keitaro Yamashita]

Dear all,

I would like to make a picture of diffraction photograph with (hkl) indexes.

I found it in Fig. 1 in the paper: Acta Cryst. (2009). D65, 553-559
http://dx.doi.org/10.1107/S0907444909010725
Direct link to the figure:
http://journals.iucr.org/d/issues/2009/06/00/dz5158/dz5158fig1.html

Can LABELIT, Mosflm or other program make image file (jpg or
something) such like that?

Thank you very much in advance,

K. Yamashita