est, BR
>
> *From:* CCP4 bulletin board *On Behalf Of *Dirk
> Kostrewa
> *Sent:* Wednesday, April 7, 2021 03:59
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Omit maps in phenix and ccp4
>
>
>
> Dear Eleanor,
>
> setting occupancies of omitted atoms to
BR
From: CCP4 bulletin board On Behalf Of Dirk Kostrewa
Sent: Wednesday, April 7, 2021 03:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Omit maps in phenix and ccp4
Dear Eleanor,
setting occupancies of omitted atoms to zero has the danger of leaving a hole
with the shape of these atoms in
Hmm - yes.
For refmac the default scaling is:
2) Mask based bulk solvent correction. It is activated using the following
keywords to build a mask based bulk solvent correction:
scale type simple
solvent yes
The solvent mask is generated with default parameters to mask the whole
model : vdwprob
Dear Eleanor,
setting occupancies of omitted atoms to zero has the danger of leaving a
hole with the shape of these atoms in the bulk solvent mask, leading to
positive difference density just because of the missing bulk solvent
density. Since the days of X-PLOR, I always removed the omitted at
Well - I use COOT for this sort of task, and dont trust the automated tools.
my procedure is
load COOT - probably after a refinement cycle
set occupancy of ligand(s) to 0.00 ( Measures - residue information -
change occupancy)
Look at the environment critically . eg if an ARG or other bulky side ch
Dear Hari,
With regards to 1) Is 15 the number of atoms in your molecule? Or is it the
number of hydrogens? The CIF file may have the wrong residue name or lack the
hydrogens depending on how you built the ligand-protein complex.
There is also a phenixbb for phenix questions,
http://www.phenix-
On 07/04/2021 07:46, Hari shankar wrote:
I have a ligand-protein complex and I wish to calculate different kinds of omit maps (say, composite omit
maps, simulated annealing maps, other unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D
space around it. I have tried phenix fo
