Hi, 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. Regards, 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 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www- structmed.cimr.cam.ac.uk