[sharp-discuss] once more: combining MR phases with HA phases

[Guenter Fritz]

Hi Francis,

thanks a lot for the prompt reply. I am a bit puzzled.
> Guenter
>
>
> There are two ways to do this.
>
> [1] Simply cad the HL coefficients (and only the HL coefficients) from phaser to the combined and scaled Se peak/infl dataset.  (if you have not already, get autosharp to generate the combined and scaled Se peak/infl dataset). 
>  
> When you select this combined dataset (with HL coefficients) in the main sharp window, you'll see the external phase information check buttons below the chemical composition of the asymmetric unit. 
>   

This does not work. I don't get the extra button. (Something wrong in my 
installation? ) My other SHARP  jobs run fine.
> [2] The second option is to take the phaser PDB and copy it as model_*.pdb  to sharpfiles/datafiles directory. Make a dummy sharp job (simply select your combined Se/peak/infl dataset turn off the ML refinement but keep the outlier detection and calculation of the experimental density map on... specify one G-site). 
>
>
> In the results window you'll have this dummy sharp job, but more importantly you'll have access to the Phase Improvement Control Panel.. Click this. 
> Under the Utilities section, go to the 'Extract ABCDs for use as external phases in SHARP from <pick your model_*.pdb here). 
>   

Also here: I just get in the 'Phase Improvement and Interpretation 
Control Panel'  under Utilities the button ' [Calculate]    difference 
fourier map(s) using phases from: [SHARP]


I had also a try using the tutorial dataset KrEl since there a file 
model_KrEl.pdb is given already in the datafiles folder. From your 
description in [2] this should work   - however no success. I don't get 
the 'Extract  ABCDs for use as external phases in SHARP' option. Hm?

Best,
Guenter

> This will use sharp to generate the 'external phases' .. note the .mtz that is written as a result of this procedure and use it as a sharp job. Upon selecting this file,  in the main SHARP window, you'll see the checkboxes for the External Phase information for use in refinement, LLG map calculation, and finally calculation of the experimental density map. 
>
>
>
> [2b] I've found that if your MR model is bad, SIGMAZ will give 'problems' , be highly suspect if this occurs when you submit your SHARP job.
>
>
> I personally like [2], it has worked very well for me .
>
>
> Cheers
> F
>
>
> On Nov 6, 2011, at 10:28 AM, Guenter Fritz wrote:
>
>   
>> Hi,
>> I am working on low resolution phases (5A, native 3.8 A). I have 
>> meanwhile a partial model and would like to include this in phase 
>> calculation.
>>
>> I used phaser rigid body to place the partial model in the SeMet cell 
>> writing out HL to the mtz.
>> So I have now a mtz with Se peak, Se infl and HL from the model. 
>>
>> As pointed out recently on the board including HL coefficients should 
>> open in SHARP an additional panel for to include external phase 
>> information. However, the additional panel does not show up. Any 
>> suggestions are welcome.
>> Best,
>> Guenter
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>>     
>
>