[phenixbb] Phaser RMS - What happens when it is too high

Randy Read rjr27 at cam.ac.uk
Wed Jul 29 07:26:39 PDT 2009


I'm afraid there isn't an obvious sign that the RMS is set too high.   
Whether the model is good or poor, if you give a high value for RMS,  
then data at a resolution much higher than 2*RMS will essentially be  
ignored, the likelihood functions will be relatively insensitive  
(which makes sense because by giving a high RMS you're saying that not  
much of the data can be explained), and the LLG values and Z-scores  
will be relatively low.

All you can do in this situation is try a lower value of RMS and see  
whether that makes the Z-score increase for a potential solution  
(which might indicate that it is correct), or whether all the LLG  
values are negative (which means you were right to have a high RMS to  
begin with).

For EM maps, my guess (based on intuition and not yet on data) is that  
dividing the nominal resolution by two would give you a sensible  
starting value for RMS.


Randy Read

On 29 Jul 2009, at 14:56, Peter Grey wrote:

> Hi all,
> In Phaser RMS is a crucial parameter. I had several cases where  
> underestimation of  RMS  resulted in negative LLG.
> The cure was simply increasing the RMS. But I wonder, are there  
> negative effects to a too high RMS.
> What are the dangers of  giving Phaser a too high RMS ? Are there  
> any indications in the output for that.
> This is also important with EM maps as models since in that case  
> estimation of RMS is difficult.
> Many thanks in advance for your advice and insight,
> Peter.
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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