Lawrence Berkeley National Laboratory

User Manual - Data Processing

 

Processing Computers

Each beamline has multiple linux machines for processing data

 

Beamline	Data Processing Computer	Type
5.0.1	bl501k1.als.lbl.gov bl501k2.als.lbl.gov bl501z.als.lbl.gov	linux linux linux
5.0.2	bl502k1.als.lbl.gov bl502k2.als.lbl.gov nl502k3.als.lbl.gov bl502z.als.lbl.gov	linux linux linux linux
5.0.3	bl503k1.als.lbl.gov bl503k2.als.lbl.gov bl503k3.als.lbl.gov bl503z.als.lbl.gov	linux linux linux linux
8.2.1	bl821k2.als.lbl.gov bl821k3.als.lbl.gov bl821k4.als.lbl.gov	linux linux linux
8.2.2	bl822k2.als.lbl.gov bl822k3.als.lbl.gov bl822k4.als.lbl.gov	linux linux linux

Software Documentation  

HKL2000: If you collected binned images you need to click the "binned" button on the main page under other options. Licence information and manual (pdf) can be found on the HKL-xray website.


Prep scripts    

The prep scripts copy files that can be modified in any text editor and then used as input files to the software of interest. You must edit items such as the directory path, name of the first filename you wish to analyze and various other parameters, such as wavelength, beam center, etc.

denzoprep creates the files:

auto.dat
batch.com
scale.com

mosflmprep creates the files:

index.inp
strategy.help

solveprep creates the files:

add_solve.txt (add on more sites)
analyze_solve.txt (input heavy atom sites that are known)
ccp4_mir.txt (for ccp4 .mtz files)
ccp4_mad.txt (for ccp4 .mtz files)

Prep scripts Beam Center: Currently, the beam center is written to the .img files in the adxv format. The beam center as written on the hutch page in dcs is in denzo/mosflm format, and these numbers should be correct in the prep scripts. If you do need to enter the numbers manually, you can convert the adxv format to the mosflm/denzo format as follows:

mosflm x = 210 - adxv y
mosflm y = adxv x

Note: Use1 210 for the Q210 detector. Use 315 for the Q315 detector.




Using HKL2000 At The Beamline  

1. Log on to one of the processing machines using your account
2. Open up a terminal window and type HKL2000
3. Choose the correct image type ( adsc 210 on 8.2.1, and adsc 315 on 8.2.2)
4. If you collected binned images you need to click the "binned" button on the main page
5. Licence information and manual (pdf) can be found at HKL-xray website.

 

Links To Def Site Files   

The current def.site files are here:   5.0.1    5.0.2    5.0.3    8.2.1    8.2.2



Using Mosflm At The Beamline   

1. Log on to one of the processing machines using your account
2. Open up a terminal window and type mosflmprep. This will create the file index.inp, which is specific to the beamline you are working on
3. Edit the file index.inp. Change the directory path to point to your data directory (for example: /data/dcsuser/corie/xtal1). Change the filename to the first file you wish to analyze (for example: Lyso_0_001.img). Change the other parameters if necessary: wavelength, beam center, resolution...etc, although leaving them commented out will force the program to use the values from the image headers.
4. Save the new index.inp file.
5. Type mosflm at the prompt.
6. Within mosflm, type @index.inp.

A note on beam center: Currently, the beam center is written to the .img files in the adxv format. The beam center as written on the hutch page in dcs is in denzo/mosflm format, and these numbers should be correct in the index.inp script. If you do need to enter the numbers manually, you can convert the adxv format to the mosflm/denzo format as follows:

mosflm x = 210 - adxv y

mosflm y = adxv x

(for the Q315 detector, use 315 instead of 210)


Processing When Using 2-Theta   

For HKL2000

First find the new direct beam position. You can do this one of two ways:

(the easy, less accurate way): Estimate the beam center by looking at the beamstop shadow on the image. Enter the values in the "Beam position" pop-up from the Index/Refinement page.

(the harder, more accurate way): Take a powder diffraction image and find the exact beam center using the program Fit2d. (Staff can help with this)

Put the 2-theta value in the "Rotation X" under the "Site Configuration" menu.

Calculate the number cos(2-theta). This is a correction to the detector distance. Add this to the detector distance used and input the value in the main page of HKL2000.

Proceed with processing as usual.

For Mosflm

First find the new direct beam position. You can do this one of two ways:

(the easy, less accurate way): Estimate the beam center by looking at the beamstop shadow on the image. Enter the values in the "Direct X beam" and "Direct Y beam" on the main window. Note: you can also enter these values using the keywords "beam swung_out x y".

(the harder, more accurate way): Take a powder diffraction image and find the exact beam center using the program Fit2d. (Staff can help with this). Enter the values in the "Direct X beam" and "Direct Y beam" on the main window.

Enter the value of -(2theta) on the main page. For example, if your 2theta is 5, you will enter -5 (a negative number)

Proceed with processing as usual.

 

Processing Software Available 

501

502

503

821

822

501k1

501k2

502k1

502k2

502k3

503k1

503k2

503k3

821k1

821k2

822k1

822k2

linux

linux

linux

linux

linux

linux

linux

linux

alpha

linux

alpha

linux

Software

Version

Call

HKL200

varies

HKL2000

x

x

x

x

x

x

x

x

x

x

x

x

Denzo

1.97.2/3

denzo

x

x

x

x

x

x

x

x

x

x

x

x

Mosflm

6.2.4

mosflm

x

x

x

x

x

x

x

x

x

x

x

x

CCP4

6.0

ccp4i

x

x

x

x

x

x

x

x

x

x

x

x

Solve/Resolve

2.10

solve/resolve

x

x

x

x

x

x

x

x

x

x

x

x

O

9.0.6

ono

x

x

x

x

x

x

x

x

na

x

na

x

Mapman

7.7

mapman

x

x

x

x

x

x

x

x

x

x

x

x

CNS_solve

1.1

cns/cns_web

x

x

x

x

x

x

x

x

x

x

x

x

ARP/wARP

6.1.1

(via ccp4i)

x

x

x

x

x

x

x

x

x

x

x

x

Epmr

2.5

epmr

x

x

x

x

x

x

x

x

x

x

x

x

ShelX (pro)

97

shelxpro

x

x

x

x

x

x

x

x

x

x

x

x

Elves

1.0

Elves

x

x

x

x

x

x

x

x

x

x

x

x

Pymol

pymol

x

x

x

x

x

x

x

x

na

x

na

x

XtalView

4.0

xtalmgr/xfit

x

x

x

x

x

x

x

x

na

x

na

x

Predict

1.0

predict

x

x

x

x

x

x

x

x

x

na

x

na

Chooch

autochooch

chooch

x

x

x

x

x

x

x

x

na

x

na

x

Moleman

7.3.5

moleman

x

x

BEST

best

x

x

x

x

x

x

x

x

x

x

x

x

FIT2D

V10.132

fit2d

x

x

x

x

x

x

x

x

x

x

x

x

phaser

1.2

phaser

x

x

x

x

x

x

x

x

x

x

x

x

phenix

1.21a

phenix

x

x

x

x

x

x

x

x

x

x

x

x

SnB

2.2p1

snb

x

x

x

x

x

x

x

x

x

x

x

x

XDS

xds

x

x

x

x

x

x

x

x

x

x

x

x

Uppsala<suite

Denzo Prep

denzoprep

All computers have all prep scripts. These scripts copy software input files into your home directory for you to edit.

Mosflm Prep

mosflmprep

Solve Prep

solveprep

**Problem reports and requests for other software can be made to: cbtrame@lbl.gov or cyralston@lbl.gov