Question about RMAX params

Submitted by Grigory on Thu, 2011-06-16 12:06

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Frealign

Hi,

I'm new to Frealign and trying to make a refinement for my RCT model. Among many other parameters I'm actually interested in RMAX1 & RMAX2. As far as I understood they determine the resolution range in Angstroms for search/refinement cycles. My question is do they correlate with RREC param? I mean, in README file RREC=10 looks good for initial search and RMAXs are 25-200A. What does this range mean?

How can I determine good values for rmax?

Thanks.

niko Thu, 2011-06-16 14:06

RMAX1 and RMAX2 are used during the refinement and describe the lower and upper resolution limit of the data to include for the particle alignment. It is often a good idea to limit the resolution range to the part of the data that contains significant signal. However, the extent of the signal is often not known and one has to go set the high-resolution limit to the resolution of the current reference (or a bit below that). The low resolution limit should be set to include important low-resolution information about the particle. For example, for a particle with 200 A diameter you should keep the information down to at least 200 A, better 300 A. The data below that resolution can be excluded to avoid interference of density gradients across images during alignment. RREC is the high-resolution limit used during reconstruction. It can be set to the Nyquist limit. However, if one does not expect signal beyond a certain resolution, it can be set to a lower value to speed up reconstruction a bit.