Re: [ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?

2012-07-04 Thread Graeme Winter
Hi Phil,

Usually with something like this I use:

 Data line--- bins 20
 Data line--- resolution 2.80
 Data line--- run 1 batch 1 to 900
 Data line--- resolution run 1 high 2.80
 Data line--- name run 1 project AUTOMATIC crystal DEFAULT dataset SAD
 Data line--- scales constant
 Data line--- exclude sdmin 2.0
 Data line--- sdcorrection fixsdb noadjust norefine both 1.0 0.0
 Data line--- anomalous on

This was from xia2 merging data from XDS / XSCALE, but it should work. The
sdcorrection card is to stop Scala adjusting the errors further.

Best wishes,

Graeme


On 3 July 2012 16:43, Phil Jeffrey pjeff...@princeton.edu wrote:

 I'm not exactly a Scala veteran so am looking for advice as to what would
 be the best way to run Scala in the following scenario:

 * data integrated with Denzo
 * data scaled with Scalepack and output with NO MERGE ORIGINAL INDEX
 * .sca data imported into MTZ via Pointless

 Do I just use the SCALA keywords:

 run 1 all
 onlymerge
 anomalous off

 or would there be a better set of commands ?  I've toyed with:

 sdcorrection norefine
 scales constant  bfactor off
 reject merge 4
 anomalous off

 which produces similar results.  no merge original index data is already
 scaled and Lp-corrected so I want to avoid applying things twice.

 Thanks
 Phil Jeffrey
 Princeton



Re: [ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?

2012-07-04 Thread Tim Gruene
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Hash: SHA1

Hi Phil,

why do you want to use scala to merge the data? I think the default
output from scalepack is already merged, so by avoiding scala
altogether you would also avoid making extra mistakes.
Unless you want certain statistics or graphs from scala output.

scalepack2mtz from ccp4i is usually my program of choice to convert
sca-format to mtz and works really well.

Cheers,
Tim

On 07/03/12 17:43, Phil Jeffrey wrote:
 I'm not exactly a Scala veteran so am looking for advice as to what
 would be the best way to run Scala in the following scenario:
 
 * data integrated with Denzo * data scaled with Scalepack and 
 output with NO MERGE ORIGINAL INDEX * .sca data imported into MTZ 
 via Pointless
 
 Do I just use the SCALA keywords:
 
 run 1 all onlymerge anomalous off
 
 or would there be a better set of commands ?  I've toyed with:
 
 sdcorrection norefine scales constant  bfactor off reject merge 4 
 anomalous off
 
 which produces similar results.  no merge original index data is
  already scaled and Lp-corrected so I want to avoid applying
 things twice.
 
 Thanks Phil Jeffrey Princeton
 

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

GPG Key ID = A46BEE1A

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Re: [ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?

2012-07-04 Thread Jeffrey, Philip D.
Hi Tim,

While I use Scalepack2mtz (not from the gui) all the time, Scalepack has the 
unfortunate feature that once Rsym  1.0 it gets reported as 0.0.  Now that I'm 
exploring higher resolution limits along the lines of the recent Karplus and 
Diederichs paper (Science Vol. 336, pp. 1030-33 (2012)) I actually want a real 
number for this.

Additionally:
Scala reports Rmeas and Rpim but Scalepack does not 
Scala reports CC_IMEAN which I see from Materials and Methods in the Karplus  
Diederichs paper is the same as CC1/2.

Since I do intend on exploiting data for which Rsym  1, at least for this 
quite redundant F432 dataset I'm working with, I think these extra statistics 
are very useful.

Thanks
Phil


From: Tim Gruene [t...@shelx.uni-ac.gwdg.de]

Hi Phil,

why do you want to use scala to merge the data? 




Re: [ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?

2012-07-04 Thread Eleanor Dodson
I use the GUI with most of the defaults , and just ask for SCALES constant 
And anomalous on of course but that is by default in SCALA ..
  Eleanor

On 3 Jul 2012, at 16:43, Phil Jeffrey wrote:

 I'm not exactly a Scala veteran so am looking for advice as to what would be 
 the best way to run Scala in the following scenario:
 
 * data integrated with Denzo
 * data scaled with Scalepack and output with NO MERGE ORIGINAL INDEX
 * .sca data imported into MTZ via Pointless
 
 Do I just use the SCALA keywords:
 
 run 1 all
 onlymerge
 anomalous off
 
 or would there be a better set of commands ?  I've toyed with:
 
 sdcorrection norefine
 scales constant  bfactor off
 reject merge 4
 anomalous off
 
 which produces similar results.  no merge original index data is already 
 scaled and Lp-corrected so I want to avoid applying things twice.
 
 Thanks
 Phil Jeffrey
 Princeton


[ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?

2012-07-03 Thread Phil Jeffrey
I'm not exactly a Scala veteran so am looking for advice as to what 
would be the best way to run Scala in the following scenario:


* data integrated with Denzo
* data scaled with Scalepack and output with NO MERGE ORIGINAL INDEX
* .sca data imported into MTZ via Pointless

Do I just use the SCALA keywords:

run 1 all
onlymerge
anomalous off

or would there be a better set of commands ?  I've toyed with:

sdcorrection norefine
scales constant  bfactor off
reject merge 4
anomalous off

which produces similar results.  no merge original index data is 
already scaled and Lp-corrected so I want to avoid applying things twice.


Thanks
Phil Jeffrey
Princeton