Hi Pavel,
Thanks a lot as usual. I learnt that one can also make Refmac output like
that, but it is not the default. So, that confusion is clear.
At your leasure, if you could explain a bit about the water picking
parameters, that would be great. In my case, for 132 residues and 55%
solvent content, the default setting was picking 330 waters, which is bit
too much I felt. Did change the b_iso_min = 10 and b_iso_max = 40, just to
see what happens.. (because I thought for ordered water the later should not
be too high..) but I was not sure what the other parameters mean. Like pick
water above 3 sigma, remove below 0.9 sigma as we are used to from Arp..
No comparison between the different programs and what their keywords are..
just a feeling that if some of these key words are explained at the last
section instead of True/False in Red / Blue, it could help the users, just
as b_iso_min/max is explained..
Best, Partha
On 10/9/07, Pavel Afonine
Hi Partha,
I am bit confused with two things. First I did specify individual isotopic, as following, still see ANAISOU in PDB. Is it from TLS strategy? I have used TLS in refmac, don't see it there.
Any atom participating in a TLS group will have ANISOU record. This is explained in the Manual: http://phenix-online.org/documentation/refinement.htm paragraph "Refinement of atomic displacement parameters (commonly named as ADP or B-factors)".
You don't see this in Refmac because Refmac does not output this right (= as efficient as it should be).
Second thing is, I want to tighten the water picking. How can I do that?
1) http://phenix-online.org/documentation/refinement.htm paragraph "Water picking".
2) Below is the extract with default water picking parameters related to your question:
refinement { ordered_solvent { b_iso_min = 1 b_iso_max = 50 primary_map_cutoff = 3 secondary_map_cutoff = 1 min_solv_macromol_dist = 1.8 max_solv_macromol_dist = 6 min_solv_solv_dist = 1.8 } }
To tighten the water picking I would change it like this (for example; depending on model quality, resolution):
refinement { ordered_solvent { b_iso_min = 10 b_iso_max = 50 primary_map_cutoff = 3.5 secondary_map_cutoff = 1.5 min_solv_macromol_dist = 1.8 max_solv_macromol_dist = 4 min_solv_solv_dist = 1.8 } }
Try several values and see the effect -- you will get less waters and more confidence that they are all real waters. I can explain some more about each parameter, if necessary.
As usual, let us know if you have any questions.
Pavel.
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