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
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
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
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
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
,
Robbie
Date: Sat, 9 Jul 2011 16:59:29 +0800
From: caiq...@gmail.com
Subject: [ccp4bb] low resolution refinement
To: CCP4BB@JISCMAIL.AC.UK
Dear all,
Recently, I refine two low resolution structures in refmac 5.5. Their
resolutions
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 structure?
I
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@jiscmail.ac.uk
Hi,
Thank you for your suggestion.
Could you tell me what is riding hydrogens
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 refinement
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 refinementrestraint
refinement by refmac5.5, I got R factor 25% and R free 35%. And then
each time, after my model
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
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 resolution refinement
To: CCP4BB
Hi,
Thank you for your papers. I will read them carefully.
2011/7/9 Elizabeth McSweeney elizabeth.mcswee...@duke.edu
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
and lower values).
HTH,
Robbie
Date: Sat, 9 Jul 2011 16:59:29 +0800
From: caiq...@gmail.com
Subject: [ccp4bb] low resolution refinement
To: CCP4BB@JISCMAIL.AC.UK
Dear all,
Recently, I refine two low resolution structures in refmac 5.5
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 reference model function in refmac5.6?
2011/7/9 Robbie Joosten
: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 reference model function in refmac5.6?
2011/7/9
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.commailto:caiq...@gmail.com
Subject: [ccp4bb] low resolution refinement
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
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
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 schue...@anl.gov wrote:
Dear Joane,
Bert's recommendations are very good, but I'd like to add a little
caution. If just
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
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
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