Re: [ccp4bb] Unmerged output from Scala

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Unmerged output from Scala
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-11-20

Next message:
Subject: Re: Unmerged output from Scala
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-11-20

Subject: Re: Unmerged output from Scala
From: "Winter, G (Graeme)" g {- dot -} winter {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-11-20

It is worth adding a note that if you are remerging data it is also a
great idea to have "sdcorrection noadjust 1.0 0.0" somewhere in your
script so that the errors are not inflated a second time by the default
values (sdadd of 0.02) - I am pretty sure that this is necessary,
certainly seemed to be.

Yes, people appear to do this.

I hadn't been bitten by this one quite yet as I have been using
"ONLYMERGE RESTORE" with the SCALES file and rescaling / remerging the
data but without recalculating the scales. Seems like this wasn't as bad
an idea as I thought it was ;o)

Perhaps naming the SCALE columns differently when they have been applied
so that they are not reapplied would be a good idea, something like
SCALEUSED. This takes us back to the beginning of this thread, always
fun.

Having output of both merged and unmerged reflection files by default
could be a cause for some confusion if someone tries to take one of the
unmerged files and put it into truncate... Bang!

Cheers,

Graeme

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Phil Evans
Sent: 20 November 2007 15:51
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unmerged output from Scala

If you don't put INSCALE OFF, the scales will be applied a second time &
you will get (much) worse data

I didn't know anyone was doing this

You should get the same statistics (Rmerge etc) if you reinput an OUTPUT
UNMERGED file with ONLYMERGE; INSCALE OFF

I'll look into how complicated it would be to write both files (but if
you have eg multi-wavelength you might get a lot of files out :-( )

Phil

On 20 Nov 2007, at 15:44, Frank von Delft wrote:

> Does it make a big difference if you *don't* have "INSCALE OFF"? I
> just notice I've been doing it for years.
>
> I use OUTPUT UNMERGED as well in my standard scaling script, in which
> I run two scalas in sequence: the first writes out the unmerged data
> and scales, the second only merges. The purpose is to have both
> unmerged and merged data after I've scaled, the former
> for xprep, pointless etc, the latter for sharp, refinement, etc.
> If scala could dump out both versions I wouldn't bother either.
>
> phx.
>
>
>
>
>
> Clemens Vonrhein wrote:
>> Hi Graeme,
>>
>> even with these options (ONLYMERGE and SCALES CONSTANT) you will have

>> the SCALE column applied again to the intensities (not good) - at
>> least that's how I understood Phil. You need to use
>>
>> ONLYMERGE
>> INSCALE OFF
>>
>> to use the already scaled intensities and avoid applying the SCALE
>> column again - Phil was the one telling me that. I was scratching my
>> head for a long time trying to understand those various
>> INTIAL/ONLYMERGE/INSCALE/NOSCALE options and how they relate to each
>> other ...
>>
>> Cheers
>>
>> Clemens
>>
>> On Mon, Nov 19, 2007 at 08:07:02PM -0000, Winter, G (Graeme) wrote:
>>
>>> Hi Phil,
>>> I use this option but not these columns. The only time I feed the
>>> file back I use "ONLYMERGE" and "SCALES CONSTANT", to remerge the
>>> reflections.
>>> Cheers,
>>> Graeme
>>>
>>> ________________________________
>>>
>>> From: CCP4 bulletin board on behalf of Phil Evans
>>> Sent: Mon 19/11/2007 5:07 PM
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: [ccp4bb] Unmerged output from Scala
>>>
>>>
>>>
>>> Is anyone using the OUTPUT UNMERGED option in Scala?
>>>
>>> This file contains columns called SCALE & SIGSCALE which are the
>>> applied scale and its SD
>>>
>>> I propose to change the names of these columns so that if you put
>>> the file back into Scala the scales do not get re-applied by default

>>> (which is wrong since they have been applied already)
>>>
>>> Will this cause anyone problems? I suspect that very few people or
>>> programs are using this file
>>>
>>> Phil Evans
>>>
>>>
>>
>>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Unmerged output from Scala
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-11-20

Next message:
Subject: Re: Unmerged output from Scala
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-11-20