SFCHECK (method unknown)
please see CCP4 documentation
I wish I knew more about OMIT maps, but after testing Kevins procedure
(which omits overlapping sphers with perturbation) and SFCHECK (method
unknown) I got quite biased results. It is years since I have run the
full CNS/Phenix procedure which attempts to remove bias by simulated
annealing..
I hacked up a little program to do composite omit maps a couple of years
back. The purpose of the program was to try out an idea I had - an
ML-omit map based on real space restraints on the rest of the density,
using the same mathematics as is used for statistical density
modification. This
On Dec 10, 2008, at 17:02, Mischa Machius wrote:
On Dec 10, 2008, at 9:52 AM, Mark J. van Raaij wrote:
as a small variation on this, I would first finish the protein,
and then include ligands, working from larger to smaller (ATP =
citrate = glycerol = sulphates = waters). Sometimes several
Hi Tassos,
Am 11.12.2008 um 13:58 schrieb Anastassis Perrakis:
...
Having said these, I will shamelessly admit here (as I think I also
did in the latest Gordon conference?) that I have never found an
omit map to be *really* useful,
and it never told me something I could not see in the
Hi
What about the SFcheck omit map calculation in 'Map and Mask utilities' module
in CCP4?
R.Sreekanth
On Wed, 10 Dec 2008 Kathleen Frey wrote :
Hi Everyone,
Can anyone tell me a relatively easy way to generate an omit density map for
a ligand? I know that CNS can do this, but I was
There used to be a program called OMIT in CCP4. Seems to be still
supported.
I believe I used it years ago but I vaguely remember problems with
some space groups (might be wrong though...)
Regards,
Roberto
On 11 Dec 2008, at 16:20, rajan sreekanth wrote:
Hi
What about the SFcheck omit
Hi Everyone,
Can anyone tell me a relatively easy way to generate an omit density map for
a ligand? I know that CNS can do this, but I was wondering if there's a CCP4
related program to generate omit maps.
Thanks,
Kathleen
Subject: generating omit maps
From: Kathleen Frey [EMAIL PROTECTED]
Reply-To: Kathleen Frey [EMAIL PROTECTED]
Date: Wed, 10 Dec 2008 10:30:47 -0500
Hi Everyone,
Can anyone tell me a relatively easy way to generate an omit density
map for
a ligand? I know that CNS can do this, but I was
as a small variation on this, I would first finish the protein, and
then include ligands, working from larger to smaller (ATP = citrate
= glycerol = sulphates = waters). Sometimes several waters (from
automated solvent building) in place of a bona fide ligand (or a
glycerol for example)
On Dec 10, 2008, at 9:52 AM, Mark J. van Raaij wrote:
as a small variation on this, I would first finish the protein,
and then include ligands, working from larger to smaller (ATP =
citrate = glycerol = sulphates = waters). Sometimes several
waters (from automated solvent building) in
Let me also follow up on this point. I also agree that the ligand should be
added very late in the refinement/model-building procedure. I also encourage
people in my group to create a subdirectory BEFORE_LIGANDS into which
they put the current PDB and map (or mtz) files prior to adding the
Kathleen - The easiest way is to simply remove the ligand from the
coordinates and refine for a few cycles. Whether that is particularly
meaningful is another question. Better would be to remove the ligand
coordinates, shake the remaining coordinates (i.e., randomly
displace them by a
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