This manual contains information to assist you during the processing of the data with the HKL program suite. From starting guide and installation process. The information provided in this site is specific for running HKL at SSRL. The HKL on-line manual is available at the HKL Research. HKL Online Manual. Your diffraction data. In this exercise you will be working with an X-ray diffraction data set collected for a single crystal of trypsin at .
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Under the Global Refinement section of the scale tab there’s a variety of options that fall under manua, general heading of postrefinement so named because it occurs after the data integration step, but “global” is perhaps a more informative name.
As k,B are expected to be smoothly varying they are often restrained during scaling. The goniostat has no vertical hkkl2000 on the phi axis, but there is a certain amount of vertical travel on the goniometer head.
If you selected 2 or 3 data sets e. How do I start? Sets of data from these windows for further processing can be selected or deselected by clicking on the Select hkl200. The gkl2000 limits on goniostat angles are: Hkll2000 do I stop and start over? I nearly always do the former. Note the percentage of reflections marked for rejection and the total linear R-factor – they will be very importanf during space group determination.
Can I index on peaks collected from several contiguous frames? I’ve not yet tested to see if autoProc can process this data smoothly – you may need to pull. Do I have to have a. Can I click more than one set of data? If some of the parameters are incorrect, it can be corrected by typing their values in the above “Main HKL window” by clicking on the “Edit Set S ” button.
The Distance that came up in the Experiment Geometry window is wrong. On the lines above primitive triclinic, Denzo permutes and potentially distorts that unit cell to obey the symmetry-mandated requirements for each subsequent Bravais lattice, with highest symmetry toward the top.
Where do they go? However with the module boundaries being horizontal – perpendicular to the rotation axis – this might give rise to systematic discs of missing data – and this is likely to be more pronounced in low symmetry space groups at lower resolutions. The Special Integration and Cryst. The completeness is plotted versus intensity of the reflections.
How can I flip through my frames at this stage to see if they all look ok? Appendix – Installation note. Profile Fitting Radius sometimes needs to be increased for particularly weak or anisotropic data or Denzo will refuse to integrate weak data with insufficent nearby strong spots to estimate the profile from.
What are the files that make up the HKL suite, and what do they do? What do the Collect, Denzo, and Scale buttons in each window do? Now, back to the Collect sub-tab within Collect. Is the number of selected peaks sufficient for indexing?
Scaling Scaling your data is where you start to find out what your intrinsic data quality is, so we need to define this: Clicking “OK” at this point will write peaks from both images to the ukl2000 file. These work well with strong diffractors. Can I rename them? What are all those the Refinement Information values for, and what do they mean?
Table of Contents
The default files for each of these detectors are available in these areas and they can manua accessed by selecting the corresponding detector and clicking on Ok. Wow, my crystal diffracts great! Repeat for a few more frames. No part of this document shall be reproduced, stored in a retrieval system, or transmitted by any means, electronic, mechanical, photocopying, recording, or otherwise, without written permission from HKL Research, Inc.
Why would I want to click Scale Sets Only? After the initial round of scaling we can adjust the error model, edit rejection file, check log file, etc.
The HKL-2000 Manual
Once the integration is complete, should I update the site? Select the Scale tab. A general view of the “Scaling window” before running scaling program is shown below. Therefore, an indexing attempt without saving the newly selected beam position into the “Site Configuration” window will use the old beam position values.
I think the direct Beam Position is wrong. How do I set the Mosaicity?
How can I flip through my frames at this stage to see if they all look ok? Setting up Data Hk2000. The final steps are: Once the integration is complete, should I update the site?