Thanks. So it seems that I need to rerun XDS if I change the DATA_RANGE -process a subset of the data. Is this correct?
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
________________________________________
From: Francis Reyes <[log in to unmask]> on behalf of Francis Reyes <[log in to unmask]>
Sent: Friday, July 1, 2016 10:18 AM
To: Reza Khayat
Cc: [log in to unmask]
Subject: Re: [ccp4bb] Scaling a range of images in XDS
XSCALE should be used for scaling multiple crystals/datasets together.
I believe running XSCALE with a single dataset is the same as running CORRECT.
If, for a single dataset/crystal, you want to to scale a subset, CORRECT respects DATA_RANGE.
Therefore, if XDS.INP originally has DATA_RANGE = 1 180 ..
and is changed to DATA_RANGE= 1 90
rerunning XDS will produce an XDS_ASCII.HKL containing images 1 to 90.
Then you could use the resulting XDS_ASCII.HKL for subsequent XSCALE runs where you would like to scale multiple datasets.
F
On Jul 1, 2016, at 9:34 AM, Reza Khayat <[log in to unmask]> wrote:
> Hi,
>
> Is it possible to scale a range of images with XSCALE if I have already processed the entire data set with XDS? Thanks.
>
> Best wishes,
> Reza
>
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
>
> ________________________________________
> From: CCP4 bulletin board <[log in to unmask]> on behalf of Kay Diederichs <[log in to unmask]>
> Sent: Thursday, June 16, 2016 2:38 AM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] visualise xds predicted spots - SUMMARY
>
> Andy Arvans wrote to me:
> "
> I compiled a couple new binaries you can try:
>
> http://www.scripps.edu/~arvai/adxv/adxv_1.9.11beta/adxv.x86_64FC18
> http://www.scripps.edu/~arvai/adxv/adxv_1.9.11beta/adxv.x86_64Centos6
>
> Andy
> "
>
> These work well for me.
>
> Kay
>
> On Wed, 15 Jun 2016 11:06:25 +0100, Kay Diederichs <[log in to unmask]> wrote:
>
>> On Wed, 15 Jun 2016 10:17:21 +0200, Tim Gruene <[log in to unmask]> wrote:
>> ...
>>> 1) Fred Dyda (and Kay Diederichs in a personal email) pointed at generate_ADX
>>> on the xds-wiki (http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_adx)
>>> The program is available as source code and compiles out of the box.
>>> This program does exactly what I asked for: when the program is run in the XDS
>>> processing directory, it creates, for every image file, a file with the suffix
>>> .adx. When given to adxv as second input, it highlights the reflections (with
>>> their centroids) on the frame. When clicked, the hkl values are provided.
>>
>> unfortunately this seems to work (for me) with adxv 1.9.8 x86_64 for RHEL4, but not with 1.9.9 x86_64 for RHEL5 nor with current 1.9.10 for RHEL6. In the latter two versions, the HKL values in the "Adxv Predictions" window are somehow scrambled. Which version works for you?
>>
>>> @Kay: maybe this feature could be implemented in xdsgui, as all information is
>>> already there in INTEGRATE.HKL?
>>
>> well, INTEGRATE.HKL (or better XDS_ASCII.HKL) can be multi-megabyte files, and they are sorted on unique indices, not on frame numbers. That means that XDSGUI would need to read the file and (at least) re-sort it, to enable a reasonably fast lookup of HKL values when displaying a frame. Possible to do, but currently low in priority.
>>
>> BTW the compression algorithm of PCK files was AFAIK invented by JP Abrahams, and used e.g. as a format of MAR image plate data. It is in no way specific to XDS.
>>
>> Thanks for the summary!
>>
>> Kay
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