Hi all -
I must say that I do agree with Tim. Either Refmac/Coot or Refmac/
ARP_waters do a good job (so does other software) but I always check
things manually.
The most obvious problems with software are:
-Putting waters in place of ions - when you think of chemistry you
will realize that many 'automated' waters are not waters. Keep the
buffer composition in mind.
-ARP (but also coot) will happily introduce waters at places of loops
you have not modeled, as well as in place of e.g. glycerol from your
cryo, or other ligands that come from your buffer.
These are for me the two main mistakes that you need to correct for
and is not easy to do automatically, so by all means look at these in
e.g. Coot, having the 'show environment' on to look at hydrogen
bonding distances. btw, the 'suspicious' waters option at coot is very
useful for a quick check.
A.
On Apr 17, 2010, at 22:53, Tim Gruene wrote:
Dear Ivan,
maybe I am too old-fashioned, but since I recommend to check each
water manually
after it has been placed, it does not really matter which program
you use.
Tim
On Fri, Apr 16, 2010 at 06:02:40PM -0700, xaravich ivan wrote:
Hi everyone,
I am in the process of refining my structure. I have built almost
the whole
protein. Now its time to add waters. Should I do refinement in
refmac5 with
(adding waters running coot) or should I use Arp/wArp waters or
both?. I
have 2.15 Angs near data and about 1200 residues.
Does it matter which program I use to add water? Is there something
specific
I should look for? I apologise in advance if this question has
already been
asked before.
Thanks,
Ivan
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Tim Gruene
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