Dear Dr Moriarty,
Thank you so much.
Looking forward for this meeting.
Kind regards,
Rini Chaturvedi
On Thu, Apr 8, 2021 at 12:11 AM Nigel Moriarty wrote:
> Rini
>
> It appears you are 30 minutes out but it is still early. Phenix Workshops
> will be recorded. As with the last two virtual
Dear Colleagues,
With this message I would like to announce the *“**First Regional
Structural Biology meeting** for** Balkans and the South-East Mediterranean*
* area”*, jointly organized by iNEXT-Discovery partners NHRF and NKI, to be
held online on *Friday afternoon, May 14th, 2021*.
The
Rini
It appears you are 30 minutes out but it is still early. Phenix Workshops
will be recorded. As with the last two virtual workshops, they will be
posted on YouTube. A simple search there will reveal all.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and
Hari
I'm happy to take a closer look if you send me the files directly.
Phenix has an omit map known as the Polder map that takes care of the
solvent masking.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National
> setting occupancies of omitted atoms to zero has the danger of leaving a hole
Not quite. We probably need Garib to confirm this, but I tried this many times,
and if in refmac the occupancy is really zero (0.00), then this does not
happen, and the ligand is treated as not present. An
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 :
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
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
Dear Dr Moriarty,
Thank you for sharing the Phenix workshop link.
Will it be possible for the recording of the sessions to be shared in the
CCP4BB mail?
The given time for the workshop i.e *3.45 pm PDT* which will be around *3.45
am* in India (*IST*) and it would be difficult for us to be
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,
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
Dear Fred,
the error message looks like ligplot was started through a script, that
uses an environment variable, which is not set, soemthing like
${MYLIGPLOTDIR}/components.cif
In case MYLIGPLOTDIR is not set, you would get this sort of error
messages.
Best,
Tim
On Tue, 6 Apr 2021 15:47:21
Dear All,
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 for this purpose but get this
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