HKL2000 indexing problem

From: Peter Hsu
Date: 21 February 2012 00:28
Hi all,

I recently collected a data set off a single crystal and have had problems with indexing it. Every time I go pick peaks for indexing it constantly picks peaks that are just slightly off the actual peak. After indexing, it would always be that 2 of the 3 cell dimensions would be fairly normal, while the 3rd would have some impossible value such as 1.

On some other occasions if it manages to pick peaks properly, and every time I go to index it, it gives back an error that I don't have enough peaks picked to index (picked nearly 500).

I've tried using a number of different images to index from and have run into the same problem.

Has anyone else run into these problems? Does anyone have any idea what might be wrong w/my dataset and/or crystal?

Thanks in advance for any insight,

Peter

----------
From: Jim Pflugrath
There could be many causes for this.  Perhaps you do not have the best def.site file for your detector / beamline / hardware.  What do your local HKL2000 experts tell you?

You could e-mail me an image and I can help you.

Jim

__

----------
From: Kelly Daughtry
Sounds exactly like something is off in your site.def file. I would look to the beam center.

Also, have you tried indexing with another program? Mosflm perhaps. I find that if one program cannot index the data, another usually can (as long as the data isn't too horrible!). Thus I always try to process my data in several programs in parallel.

Best,

Kelly Daughtry

*

----------
From: Green, Todd

Hello Peter-

Is it possible that you are shooting close to an axis? If you are shooting near parallel to one of the crystal axis, you will get values that are reasonable for 2 cell lengths but extremely low values for the third. Try indexing a frame that is say 30 degrees into the collection and see if you have the same problem. If the crystal is aligned with one axis along the direction of the x-ray beam, and the goniometer rotating around that direction then you may likely have to reorient the crystal and recollect the data. This may be why you it hasn't worked for several images. Outside of beam center, i think this is something for you to have a look at.

-Todd

----------
From: Jacob Keller
Is the direction of rotation correct? I got some data that were going
the wrong way once.

JPK

----------
From: Green, Todd

This is a possibility, but probably you should be able to get the initial index in this situation. The integration is a different story. To fix that problem, usually you can change the def.site fix with: {alig,1} {180}   as opposed to 0.

-Todd

This email was scanned with Mcafee's Anti-Virus appliance, but this
is no guarantee that no virus exists. You are asked to make sure you
have virus protection and that it is up to date.

----------
From: Appu kumar

Hi peter,
                 I agreed with Kelly, You should try indexing your data in different program. I recently collected a diffraction data which showed problem in indexing in HKL2000, but data indexed very fine in imosflm giving right cell parameter. So it is worthfull to index your data in different program.

----------
From: Joe Watts
If you have tried all of the other things suggested by others (especially beam-center and direction of rotation), you can try the keyword 'weak level' in indexing box (see page 29 on HKL manual http://hkl-xray.com/sites/default/files/manual_online.pdf  or http://www.hkl-xray.com/denzo-keywords-alphabetical-order).

This has solved that very problem for me more than once.  You will need to play with the value for your data try weak level 2, 5, 20, etc...

I assume you don't have the darkest spots in the world, right?

----------
From: Nic Steussy

Our most common problem is an incorrect beam center.  The crystal we collect most frequently has large cell dimensions, so if the beam center is off even a bit it will bollix up the indexing.  What we usually do at the synchrotron is look for a refined beam center from the group there before us.  That has been our secret to success on a number of occasions.

Nic out

--   ================================  C. Nicklaus Steussy, M.D., Ph.D.