I wonder if the "rejects" file had a large number of reflections in it in one case, but not in the other case.  One can be playing with various options and create or add to such a large list.  That's why there is the "Delete Reject file" option.

Jim

________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Tim Gruene [[log in to unmask]]
Sent: Sunday, July 07, 2013 11:43 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] HKL2000 sigma cutoff

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Dear Ursula,

in your first email you wrote that you were confused by [...] HKL2000
for scaling, and in this email you wrote that your fix is to scale the
data with scalepack. In my understanding scalepack is part of HKL2000
- - would you mind explaining what the difference is to you? Just to
understand what caused a problem and how you fixed it.

Regards,
Tim

On 07/05/2013 11:18 PM, Ursula Schulze-Gahmen wrote:
> I found a fix, but not an explanation. I scaled the same data with
> scalepack and had no problem with loosing reflections. I am not
> sure what happened in HKL2000.
>
> Ursula
>
> On Fri, Jul 5, 2013 at 12:38 PM, Phil Jeffrey
> <[log in to unmask]>wrote:
>
>> Ursula,
>>
>> I/sigI of -3 as I recall.
>>
>> Are you sure that the downstream programs you are using aren't
>> the ones applying the cutoff ?  Scalepack is, in general,
>> perfectly happy to write negative intensities to output.sca and
>> certainly is doing so as of HKL3000. Perhaps you need to use the
>> TRUNCATE YES option in Truncate ?  Does the output MTZ from
>> Scalepack2mtz show the number of reflections you expect ?
>>
>>
>> Phil Jeffrey Princeton
>>
>>
>> On 7/5/13 3:24 PM, Ursula Schulze-Gahmen wrote:
>>
>>> Sorry for the non-CCP4 question.
>>>
>>> I am confused about the sigma cutoff used by HKL2000 for
>>> scaling. I scaled a data set to 3.0 A resolution. I collected a
>>> complete dataset to 2.8A, but the I/sigma is about 1.0 at 3.0
>>> A. The scaling logfile in HKL2000 shows 100% completeness in
>>> the highest resolution shell, but about 50% of the reflections
>>> are below I/sigma =0 in the highest resolution shell. I am
>>> guessing that these negative reflections are not being written
>>> out, because the output file from HKL200 does not have 100%
>>> completeness anymore. I would like to include these negative
>>> reflections. Is there a setting in HKL2000 that I can change or
>>> do I need to switch to a different program.
>>>
>>> Ursula
>>>
>>>
>>
>
>

- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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