14.1 User Manual: Quick Guide

      Quick GuideTo bleep Rob Kehoe dial: 
      73 1 383 3842 
      Useful contact numbers


This is a quick guide for EXPERIENCED users. If you need further instruction, 
please read the full manual and/or ask station personnel. 
Station Hardware
Station 14.1 operates in either PX or fibre mode. 
  Station SpecificationWavelengthMaximum Resolution@70mmMaximum 
      Resolution@500mm
      1.488Å1.65Å7.98Å
      1.244Å1.38Å6.67Å
      Intensity relative to station 9.5 = 10-20

The PX camera includes: 
  Collimator assembly with twin photo-diode beam position monitors (not 
  operational), a set of (pre shutter) collimating slits, twin ion chambers and 
  an x-ray shutter. 
  Single phi rotation axis with continuous phi angle readout and logditudinal 
  translation (approx. 5cm). It can also be rotated by hand for rapid crystal 
  centering. Standard goni. heads fit. 
  Crystal viewing camera, and monitor with movable cross-hairs. 
  Adjustable beam-stop. 
  Oxford Cryostream. 
    Use the pressurised dewar to top up the liquid nitrogen level of the 
    Cryostream dewar. 
    For liquid nitrogen bleep 392 or 393 out of hours. 
    Set dry air flowrate to about 8 L/min. 
  ADSC Quantum 4R CCD Detector 
The fibre camera includes: 
    An x-y stage allowing rastored data collection in air; a sample environment 
    chamber allowing sample tilt and tranlation; other ad-hoc facilities see 
    here 
    Fitting the Fibre Chamber 
      Station Computers(Computer Problems)Problems with the table motors 
      Problems opening beamline and station shutters 
      Detector Problems

  bl142alpha1 An ALPHA running LINUX runs the data collection software 
  bl141alpha1 An ALPHA running LINUX is provided for data processing 
  bl141vig4 A PC running Linux is used to optimise the station flux. 
  bl141vig5 A PC running Windows NT is used to let x-rays into the hutch 
  /data1 and /data2 Two data discs, 245MB capacity each 
Usernames and passwords for the station computers can be obtained from the front 
of the station log-book or from any member of the PX team 
Other equipment available at the station includes a cold light source, optical 
microscope, soldering ion, thermocouple based thermometer and an Oxford 
Cryostream for data collection down to 100K. 
Control Software
  Beamline 14.1 Synoptic for letting x-rays into the hutch. 
  PXGEN to drive motors 
  ADX for data collection 
Getting X-Rays
The camera must be aligned to maximise the signal on the ion chambers, but first 
the hutch has to be searched, personnel evacuated and the hutch interlocked. 
  If you aren't sure that the back stop is well aligned, place the lead shield 
  in front of the detector. 
  Search and interlock the hutch; the search switches are mounted on the search 
  control box, on the left of the hutch door. There is one search point inside 
  the hutch. 
  Let x-rays into the hutch. 
  Use the move motors option in PXGEN to maximise the signal on each ion chamber 
  in turn.
Starting Experiment
Once you have optimised the ion chamber readings you may want to: 
  create a directory, on the root directory, of the station data discs /data1 or 
  /data2 (capacity 245GB each). Give your directory the name of your home 
  institution 
  do a pink paper test 
  mount and align your crystal 
  check quality of diffraction 
  set the crystal to detector distance 
  start data collection 
  take a wax image 
IMPORTANT 
  There is a rough guide to the detector distance mounted on the detector runway 
  but the only way to accurately determine the crystal to detector distance is 
  to take a wax image. 
Data Handling
The diffraction pattern on the image plate is digitised, and stored on the 
stations hard disks as files with extensions . img. These image files can be 
viewed on the station computer with the adsc display program or ipdisp type 
ipdispq4. The image files can be processed on this computer with a selection of 
programs: denzo, mosflm or xds. Programs, from the CCP4 suite, are also 
available for scaling and data reduction e.t.c. 
Data Processing Packages
Use the station SGI O2 (pxsv3) for data processing. 
  DENZO. 
  Type: 
    denzo & (to get the denzo command line); 
    xdisp [format] [filename] & (to get the display window). 
  MOSFLM 
There should be manuals for both programs on the station, and example script 
files have been set up in the directory: 
  /usr/people/ipuser/examples/ 
Backing-Up Data
Two tape drives are available at the station: a DAT drive (dat1) and an Exabyte 
(ex1). A unix script has been written to automate the backing-up procedure. 
  Using bl14alpha1, type backup from the dir. your image files are in and follow 
  the instructions. 
    Type ? at the prompt for help choosing options. 
  Unix Stuff 
    mt -f /dev/device_name status 
    mt -f /dev/device_name unload 
    mt -f /dev/device_name rewind 
  Type man mt for help 
It is advisable to ftp your data to your home institution in addition to backing 
it up. We cannot guarantee, without prior arrangement, that your data will not 
be removed from /data1 or /data2 after you leave the station.