Skip to Content

Bfactor program help

3 replies [Last post]
taha
Offline
Joined: 5 Mar 2014

Hello

I wished to try b-factor sharpening of my reconstructions using the bfactor program, but do not know how to judge parameters such as resolution range, filter radius etc for the software’s inputs.

Could I please be advised as to what would be appropriate values, in light of things such as particle size, resolution as per the various criteria, the Nyquist etc.?

Please also let me know as to whether the models ought to be binary masked, and if the technique works with negative-stain models as well.

I could provide values for the aforementioned measurements if that'd be helpful.

Thanks

Taha

niko
Offline
Joined: 5 May 2009
Yes, or use something else.

Yes, or use something else. The measurement will not work in any case and you should simply try different B-factors.

niko
Offline
Joined: 5 May 2009
You should use the bfactor

You should use the bfactor program on unmasked volumes. For the resolution filter, you should use a cosine-edged filter with a width of something like 5 pixels. The resolution limit should be set to whatever resolution you determined for your map. For the resolution range that is sued to estimate the B-factor, use something like 15 and 10 Angstrom. I suspect that in your case the measurement will not work correctly because you have a low-resolution map. So just provide the range I indicated and then enter a B-factor for sharpening, such as -500 or -2000. You will have to judge from the output map what kind of B-factor is reasonable (too noisy/too smooth).

taha
Offline
Joined: 5 Mar 2014
Thank you. The 0.143

Thank you.

The 0.143 resolution from my unmasked model (not binary masked nor circularly masked), is 16.7 Å. Would it still be appropriate to use the 15 - 10 Å resolution range?

Taha