Hi all,
just be sure: does Low Resolution Refinement Pipeline in ccp4 always use
Free_R_flag=0?
Thanks,
s
--
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy
tel +39 02 943
3) Activating map sharpening results in mtz files that look just normal
and open in coot after the typical map calculation break, but no maps
are displayed. This is independent of the sharpening factor I choose
(between 5 and 60).
I haven't used coot for map sharpening, but using the range
Hi Andreas,
In your case, it sounds like a reasonable strategy would be to use external
restraints for a few rounds of refinement (as you have done), but then release
them and instead use jelly-body restraints. This two-stage process will help to
initially hold your model in a sensible conforma
Dear all,
I'm making first steps in the desolate world of low-resolution
refinement. With dodgy 3.8A data, the magic of Phaser was able to solve
the structure of a complex by MR with its components as MR models.
Jelly-body refinement does wonders for R free. There are three issues
that I wo
Roberto steiner has told you how to use these new REFMAC5.6 features,
Rob Nicholls has suggested how to generate secondary structure restraints,
and Martyn Winn given a page to install a new interface to make it easier
to use them..
But with such limited data it isnt surprising that the FreeR c
(start with 0.05 and
> compare refinements for higher and lower values).
>
>
>
> HTH,
>
> Robbie
>
>
>
>
> ------------
> > Date: Sat, 9 Jul 2011 16:59:29 +0800
> > From: caiq...@gmail.com
> > Subject: [ccp
Hi Quixu,
I also used phenix.refine with the "reference model" ( I have high
> resolution model for one domain of the low resolution protein) and
> "secondary structure restraints", but it seams the same. Any suggestion?
>
> BTW, is that simulator annealing not suitable for low resolution structur
When in doubt, try both. In my personal experience, adding hydrogens always
works. Especially at low resolution. But don't take my word for it, experiment
a little.
Cheers,
Robbie
Date: Sun, 10 Jul 2011 16:01:59 +0800
From: caiq...@gmail.com
Subject: Re: [ccp4bb] low resolution refineme
nk it is also explained
> in the talk and tutorials of the Refmac website.
>
>
>
> HTH,
>
> Robbie
>
>
> ____________
> > From: caiq...@gmail.com
> > Date: Sun, 10 Jul 2011 00:44:25 +0800
> > Subject: Re: [ccp4bb] low resolution re
imizing the matrix weight yourself (start with 0.05 and compare refinements
for higher and lower values).
HTH,
Robbie
> Date: Sat, 9 Jul 2011 16:59:29 +0800
> From: caiq...@gmail.com<mailto:caiq...@gmail.com>
> Subject: [ccp4b
>
>
>
> HTH,
>
> Robbie
>
>
> ____________
>> From: caiq...@gmail.com
>> Date: Sun, 10 Jul 2011 00:44:25 +0800
>> Subject: Re: [ccp4bb] low resolution refinement
>> To: robbie_joos...@hotmail.com
>> CC: CCP4BB@jiscma
ul 2011 00:44:25 +0800
> Subject: Re: [ccp4bb] low resolution refinement
> To: robbie_joos...@hotmail.com
> CC: CCP4BB@jiscmail.ac.uk
>
> Hi,
>
> Thank you for your suggestion.
> Could you tell me what is "riding hydrogens"?
> And it seems there is not &quo
t yourself (start with 0.05 and compare
> refinements for higher and lower values).
>
>
>
> HTH,
>
> Robbie
>
>
>
>
> ----------------
> > Date: Sat, 9 Jul 2011 16:59:29 +0800
> > From: caiq...@gmail.com
> > Subject: [
Hi,
Thank you for your papers. I will read them carefully.
2011/7/9 Elizabeth McSweeney
> Hi
>
> I highly recommend reading the two Brunger papers below: they will explain
> the important factors to take note of when refining low-resolution
> structures. I found them very useful when I was
hting in favour of
optimizing the matrix weight yourself (start with 0.05 and compare refinements
for higher and lower values).
HTH,
Robbie
> Date: Sat, 9 Jul 2011 16:59:29 +0800
> From: caiq...@gmail.com
> Subject: [ccp4bb] low re
Hi
I highly recommend reading the two Brunger papers below: they will
explain the important factors to take note of when refining low-resolution
structures.� I found them very useful when I was learning about
low-resolution refinement.
I would suggest using the deformable elastic network with
Dear all,
Recently, I refine two low resolution structures in refmac 5.5. Their
resolutions are 3A and 3.5A respectively.
For 3A structure, after MR by phaser and rigidbody refinement&restraint
refinement by refmac5.5, I got R factor 25% and R free 35%. And then
each time, after my model build
Dear Joane,
we had a case, where we had five molecules in the assymmetric unit where
the biological functional unit was a homotrimer. So we had one
non-crystallographic trimer and two monomers, which were located along the
3-fold symmetry axis of space group I213. One of the monomers also showed
e
Dear Joane,
We have had very good luck refining low resolution structures with dramatic
improvement using several newish options in refmac - particularly when NCS is
present! Those options are jelly body restraints, automatic NCS restraints,
and map sharpening. Here is a description cut-and-p
This reminds me of:
Pig heart short chain L-3-hydroxyacyl-CoA dehydrogenase revisited:
Sequence analysis and crystal structure determination
Barycki JJ, O'Brien LK, Birktoft JJ, Strauss AW, Banaszak LJ
Protein Science (Oct 1999) Vol 8, pp 2010-2018.
In which the protein in question also had on
Missing density could point to incomplete data, how is the completeness at high
and low resolution?
Sent from my iPhone
On May 19, 2011, at 11:54 AM, Jon Schuermann wrote:
> Dear Joane,
>
>Bert's recommendations are very good, but I'd like to add a little
> caution. If just part of the m
Dear Joane,
Bert's recommendations are very good, but I'd like to add a little
caution. If just part of the molecule has bad density then it is not
unusual, but if the whole chain does not look very good (missing
side-chains or backbone) you may have a couple of things going on.
First, I w
One more thing though: have you refined with the NCS restraints off or on?
Presumably on, seeing that you have a small gap between R and Rfree? It may be
worth turning the restraints off or modify the NCS selections: if your 3
molecules are substantially different, applying NCS may make things w
Hi Joane,
I'm not sure if I understand your description of the structure (chain A forms
the dimer? Does it form a dimer with a crystallographically related chain A?) .
But anyway, I don't think you need to worry. Your R/Rfree are excellent for
this resolution. There's not much you can do about t
Dear all
I am refining a structure at 3.4 A resolution that contains 3 molecules in the
a.u. The chain A sits on a 2-fold crystallographic axis forming the dimeric
functional structure expected for this class of proteins. The other two chains
B and C, which also form the functional dimer, seem t
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