Dear Jeorge
just as a curiosity:
1- do you see a continuous electron density for the ligand, before and after
performing the refinement?
2- do you have only one copy of the molecule(s), and if not, do you see the
same behaviour for all the ligands?
3- what are the B-factor values for the ligand?
Dear all,
I am working on my molecule, but after running
Refmac5 restrained refinement the bonding distances and angles are broken.
I used Phenix to create the ligand and used Coot to place the ligand
into the correct location in the molecule, merged the ligand and
molecule coordinates, and save
The most important thing is that you do it the same way every time.
But you might also put some thought into flexibility, in case you need
to explore cryoprotectants, etc.
On 11/21/14 11:48, amro selem wrote:
Dear All,
first i wish you nice weekend, then i wanna ask about formulation of
my ow
Generally one will make this up from stock solutions:
Make up
1 M Tris chloride pH 8
1 M magnesium chloride
50 % (weight/volume) PEG 6K
Then mix these together in the right ratios
(for 1 mL)
100 uL 1 M tris solution
200 uL 1 M MgCl2 solution
400 uL 50% PEG solution
300 uL water.
Janet Newma
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 11/21/2014 12:35 AM, "F.Xavier Gomis-Rüth" wrote:
>
>
> As to the convenience of carrying over a test set to another
> dataset, Eleanor made a suggestion to circumvent this necessity
> some time ago: pass your coordinates through pdbset and add
Yes, that's true. In such corner cases phenix.refine switches to LS, for
example. Alternatively you can generate many (say 100) different tests sets
and run 100 refinements. This will give you an ensemble of slightly
different structures with slightly different Rwork and Rfree. You can then
derive
POSTDOCTORAL FELLOW POSITION University of North Carolina DEPARTMENT OF
MICROBIOLOGY AND IMMUNOLOGY
We are seeking a motivated PhD crystallographer to drive two projects dealing
with host defense against pathogens. The first project involves peptide
binding to MHC and is a highly productive co
Dear All,first i wish you nice weekend, then i wanna ask about formulation of
my own mother liquor, i want to optimize a condition containing 0.2m MgCl2,
0.1m Tris , PH 8; and 20% PEG6K as pricipitant. (PACT)the question is , should
i make a stock solution from every ingredient by dissolving it
Hi Jacob,
If you have a sufficient number of unique reflections, use percentage
because it is more convenient. If not, at least make sure the below
criteria are met. If that's not possible, don't use maximum likelihood
for refinement ;-)
Cheers,
Tim
On 11/21/2014 05:09 PM, Keller, Jacob wrote:
>
Right about the 1000 in that case, but also Rfree with 5% would be
statistically poor. I guess one would be stuck in that case.
JPK
From: Pavel Afonine [mailto:pafon...@gmail.com]
Sent: Friday, November 21, 2014 11:16 AM
To: Keller, Jacob
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Free Refl
Oh I see, I though the answer follows from that. Fraction is better (or may
be fraction with a cap). Hardwiring a number may not always work. For small
crystals or small data sets or incomplete datasets say 1000 reflections may
mean 50% of the dataset.
All the best,
Pavel
On Fri, Nov 21, 2014 at
Agree with all of this—but how does it reflect on the original question of
whether to use a percent or an absolute number?
JPK
From: Pavel Afonine [mailto:pafon...@gmail.com]
Sent: Friday, November 21, 2014 11:02 AM
To: Keller, Jacob
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Free Reflectio
Hello,
choice of the size of free (or test, whatever you like to call them)
reflections is important for three different purposes:
- estimation of parameters for ML target for refinement;
- map calculation (coefficients m&D in 2mFo-DFc or mFo-DFc map are
calculated using test reflections);
- vali
Post-doctoral position
“Structural studies of post-transcriptional / translational modification
enzymes”.
Location: Palaiseau, Ecole Polytechnique, near Paris (30 minutes by regular
trains), France
A 2 years post-doctoral position, funded by the ANR (French National Research
Agency), is avai
The CCP4 Study Weekend (7 - 9 January 2015)
East Midlands Conference Centre, University of Nottingham
Wednesday 7 - MX User Meeting
Thursday 8 / Friday 9 - CCP4 Study Weekend
"Advances in Experimental Phasing"
We cordially invite you to participate in the 2015 CCP4 Study Weekend at the
the East
This PhD project is from the German-Israeli Helmholtz Research School in Cancer
Biology, a joint PhD training initiative of the German Cancer Research Center
and the Weizmann Institute of Science in Rehovot, Israel.
The successful candidate will be required to spend 6-12 months during their PhD
As pointed out by a reviewer recently, this has been object of study in
the past when Gerard K. and Axel B. found that actually 500-700
reflections should suffice to monitor Rfree with sufficient precision.
I guess everybody will agree on that we want to have the best refined
structure and this
17 matches
Mail list logo
