Hi Pavel,

 

Higher resolution structure will have more accurate phases than the one determined at 10A resolution and therefore the 10A maps generated from that structure will not be quite the same as maps from the data that extended to only 10A. Am I missing something?

Cheers,

N.

 

Ruslan Sanishvili (Nukri), Ph.D.

GM/CA-CAT
Biosciences Division, ANL
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From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Pavel Afonine
Sent: Wednesday, June 01, 2011 7:15 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Very low resolution map.

 

Hi Nat,

 

playing with fake data you know the answer. Real data are good too, although you have to keep in mind how its completeness will affect what you look at. I can't see how B-factors are relevant if you take a model from PDB: in this case the B-factors are what comes from PDB - real ones.

 

Pavel. 

On Wed, Jun 1, 2011 at 5:01 PM, Nat Echols <[log in to unmask]> wrote:

On Wed, Jun 1, 2011 at 4:45 PM, Pavel Afonine <[log in to unmask]> wrote:

to get feeling about how maps may look like at different resolutions do the following learning exercise: download a structure from PDB and compute Fcalc maps at different resolutions:

 

phenix.fmodel model.pdb high_res=1

phenix.fmodel model.pdb high_res=2

phenix.fmodel model.pdb high_res=3

phenix.fmodel model.pdb high_res=4

phenix.fmodel model.pdb high_res=5

...

phenix.fmodel model.pdb high_res=10

phenix.fmodel model.pdb high_res=20

 

then load them in Coot and you will get your answer.

 

But fake data will always look much better than real data - to start with, the B-factors will be all wrong.

 

There are actually a handful of PDB entries that are between 8.0 and 12.0 and have experimental data deposited:

1H1K, 1PNS, 1PNX, 1VCR,1ZBB, 2QIJ, 2QZV, 3LVH, 3PCQ

and 1VOQ, 1VOR, 1VOS, 1VOU, 1VOV, 1VOW, 1VOX, 1VOY, 1VOZ, 1VP0, which are all the same structure split over multiple files.

I'd suggest downloading a few of these and looking at the maps.
-Nat