Hi Pavel,<br><br>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.<br><br>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.. <br><br>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..
<br><br>Best, Partha<br><br><br><br><br><div><span class="gmail_quote">On 10/9/07, <b class="gmail_sendername">Pavel Afonine</b> <<a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Partha,<br><br>> I am bit confused with two things. First I did specify individual<br>> isotopic, as following, still see ANAISOU in PDB. Is it from TLS<br>> strategy? I have used TLS in refmac, don't see it there.
<br><br>Any atom participating in a TLS group will have ANISOU record. This is<br>explained in the Manual:<br><a href="http://phenix-online.org/documentation/refinement.htm">http://phenix-online.org/documentation/refinement.htm
</a><br>paragraph "Refinement of atomic displacement parameters (commonly named<br>as ADP or B-factors)".<br><br>You don't see this in Refmac because Refmac does not output this right<br>(= as efficient as it should be).
<br><br>> Second thing is, I want to tighten the water picking. How can I do that?<br><br>1) <a href="http://phenix-online.org/documentation/refinement.htm">http://phenix-online.org/documentation/refinement.htm</a><br>
paragraph "Water picking".<br><br>2) Below is the extract with default water picking parameters related to<br>your question:<br><br>refinement {<br> ordered_solvent {<br> b_iso_min = 1<br> b_iso_max = 50<br>
primary_map_cutoff = 3<br> secondary_map_cutoff = 1<br> min_solv_macromol_dist = 1.8<br> max_solv_macromol_dist = 6<br> min_solv_solv_dist = 1.8<br> }<br>}<br><br><br>To tighten the water picking I would change it like this (for example;
<br>depending on model quality, resolution):<br><br>refinement {<br> ordered_solvent {<br> b_iso_min = 10<br> b_iso_max = 50<br> primary_map_cutoff = 3.5<br> secondary_map_cutoff = 1.5<br> min_solv_macromol_dist =
1.8<br> max_solv_macromol_dist = 4<br> min_solv_solv_dist = 1.8<br> }<br>}<br><br>Try several values and see the effect -- you will get less waters and<br>more confidence that they are all real waters. I can explain some more
<br>about each parameter, if necessary.<br><br>As usual, let us know if you have any questions.<br><br>Pavel.<br><br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">
phenixbb@phenix-online.org</a><br><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote></div><br><br clear="all"><br>-- <br>MRC National Institute for Medical Research
<br>Division of Molecular Structure<br>The Ridgeway, NW7 1AA, UK<br>Email: <a href="mailto:pchakra@nimr.mrc.ac.uk">pchakra@nimr.mrc.ac.uk</a><br>Phone: + 44 208 816 2515