edu]
Sent: Tuesday, March 27, 2012 5:14 PM
To: b...@hofkristallamt.org
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] REFMAC5 residues with bad geometry
On Tuesday, March 27, 2012 04:35:40 pm Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> >phenix.refine allows any number of alternate c
On Tuesday, March 27, 2012 04:35:40 pm Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> >phenix.refine allows any number of alternate conformers.
>
> Hmm. quoting our old friends from the validation circuit: Where freedom
> is given, liberties will be taken
True, but...
[warning: back of t
>phenix.refine allows any number of alternate conformers.
Hmm. quoting our old friends from the validation circuit: Where freedom
is given, liberties will be taken
BR
Hi James,
my understanding is that phenix.refine allows any number of alternate
conformers. There may have been a limit of 4 some time in the past, but no
longer. So your idea could be tested.
Cheers,
Paul
On Mar 27, 2012, at 12:33 PM, James Holton wrote:
> Try this:
>
> 1) tak
Try this:
1) take your favorite PDB file and set all the B factors to ~80 (reduces
series-termination errors)
2) use sfall/fft in CCP4 to calculate structure factors to 4A resolution
3) use sftools to add a "SIGF" column (0.1 will do) to make refmac5 happy
4) refine the "perfect" model against
here the missing
> residues are. They may even have been removed by a protease.
>
> Cheers,
> Herman
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed
> Pozharski
> Sent: Monday, March 26, 2012 4:50 PM
> To: CCP4B
: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] REFMAC5 residues with bad geometry
On Mon, 2012-03-26 at 16:30 +0200, herman.schreu...@sanofi.com wrote:
> It is like with Heisenbergs uncertainty principle. Either one has a
> complete model with a number of atoms having a coordinate uncertainty
On Mon, 2012-03-26 at 16:30 +0200, herman.schreu...@sanofi.com wrote:
> It is like with Heisenbergs uncertainty principle. Either one has a
> complete model with a number of atoms having a coordinate uncertainty
> of 4-6 Å, or one has a model where the uncertainty of all atoms is
> below say 0.5 Å,
On Mon, 2012-03-26 at 10:17 -0400, Gregory Bowman wrote:
> But what about the issue of resolution? As was previously pointed out,
> at say 3.2 Å resolution, many side chains will fail to fit, but it
> doesn't seem appropriate to trim them all down.
Why is it inappropriate to trim them down? Some
: Monday, March 26, 2012 4:17 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] REFMAC5 residues with bad geometry
But what about the issue of resolution? As was previously pointed out,
at say 3.2 Å resolution, many side chains will fail to fit, but it doesn&#
This is a personal preference. I do model at low sigma levels if there IS
some indication of where to put atoms, always try to keep the correct
sequence even if some atoms are missing, and just for coot convenience keep
atoms with occ = 0, rather than delete them altogether. (COOT will refine a
But what about the issue of resolution? As was previously pointed out, at say
3.2 Å resolution, many side chains will fail to fit, but it doesn't seem
appropriate to trim them all down. The users need to also be aware of the
quality/resolution of the structures that they are looking at.
Greg
I agree with Eleanor 100%...
In my biased opinion, only the atoms supported by electron density
should be included in deposited models. To satisfy the "but this will
mess up the electrostatic potential coloring" argument (a valid one, of
course), the "projected model" can be deposited alongside w
As Garib says - an atom with occupancy 0.00 is treated as a marker - useful
for coot - but is not included in any X-ray refinement at all.. Maybe it
would be more aesthetic to maintain geometry but as crystallographers I
think we should be interested in the fit of model to experiment - right? -
Hi David
Occupancis of input file are very suspicious and not all atoms of resides are
present, some occupancies are zero. In refmac zero occupancy means it does not
exist. It may explain the problem
In refinement we could add an option to make occuancies one if there are no
alts but it would b
On 03/24/12 15:15, Kendall Nettles wrote:
David, how can you justify reducing occupancy of some parts of amino acids?
I don't have to, since I didn't do it. Read again the bit about this
being a carryover from the MR model.
Cheers,
I don't understand this. I can understand deleting stuff
CCP4 6.2.0
Refmac_5.6.0117
Scientific Linux 6.1
In my current model, I notice that several sidechains are falling apart,
despite having gone through a few rounds of refinement with REFMAC5 and
model building with COOT. The worst examples were all Glu and Arg residues.
I tried switch to the RE
17 matches
Mail list logo
