Dear all,
Thank you very much for all the great suggestions on my case.
Yes, I run the latest version of Phaser in Phenix. The analysis showed that
there is one non-origin distinct peak more than 15 angstroms from the origin.
44.1% origin:FRAC 0.000 0.042 0.500 (ORTH -15.72.8 103.5)
We are seeking to appoint a Research Associate in the group of Dr Marko
Hyvonen to develop chemical tools against signalling proteins using
fragment-based drug discovery methods. The post is part of a Wellcome
Trust funded, multi-disciplinary programme between Departments of
Biochemistry (Prof
Dear Users,
The deadline for May/June 2012 Collaborative
Crystallography proposals will be *Mar 15, 2012. *
Through the Collaborative Crystallography Program (CC) at the
Advanced Light Source (ALS), scientists can send
Hi all,
This is just to draw the attention, of anyone who might find it
interesting, to the availability of the first public version of
CrystFEL: a new software suite for analysis of "serial femtosecond
crystallography" data acquired using free-electron laser sources such
as the Linac Coherent Lig
Dipankar,
An MR R-factor of 53% is close to what you get with a random, incorrect
solution. Even for challenging MR cases, your MR R-factor should
normally be under 50% before rigid-body refinement of the MR solution.
As others have mentioned, you should not proceed directly to refinement
unl
On Wed, 2012-03-14 at 09:26 +, Dipankar Manna wrote:
> After running molrep R-factor is around 53% (100% identity), after
> rigid body refinement its showing around 49% and after restrained
> refinement its showing around 47%.
Sounds like you didn't get a solution. With 100% identity MR in m
This sentence in my previous posting may or may not be correct technically-
May be make sure about this as it says reindex because only you need to rescale
it like in HKL2000. It its wrong I am Sorry in advance.
Date: Wed, 14 Mar 2012 07:43:15 -0500
From: ccp4...@hotmail.com
Subject: Re: [ccp4
Mahesh,
You should always use output_1.mtz for refinement.
Dont use output_2. mtz for further refinement instead use some ccp4 utilities
to change output_1.mtz (C222) to say output1_mod.mtz (C2221). This will become
your master file for all further refinement. What ever remaining 2.mtz, 3.mt
Sorry my answers were confusing..
There are two problems. 1) When you finish data processing you should have
the correct point group, but you may not have the correct spacegroup (SG).
You will get an mtz file after processing, but may have to correct the SG
later.
Eg an orthorhombic point gr
Dear crystallographers,
According *UMA RATU*'s mtz labellings,
*Vellieux Frederic *sir answered, output of the scalepack2mtz is
used as master mtz for all refining (refmac5) input(if i am wrong, sorry ).
am confused when Eleanor sir answered...
here my labellings !!!
scalepack2mtz o
Dear Dipankar,
It just occurred to me that your high Rfactors may also be due to a
large conformational change of your protein. In that case you have to
split your search model in separate pdb files for the separate domains
and rund Molrep with these separate domains.
Best,
Herman
_
Dear Dipankar,
Molrep Rfactors around 50% with a model with 100% identity means that
something went wrong and you did not find the solution. To find the
problem, I would proceed as follows:
1) check the processing of the data and the space group: Are the
statistics of the processing ok? Did you l
Hi Dipankar
If you've been reading the ccp4bb for more than a couple of weeks,
you should have realised that reducing your R-factor is *not* the
goal of refinement - having a low R-factor is one of the consequences
of having built your model well and of having performed a good
refinement.
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Dipankar,
if you refine your model straight after molecular replacement you risk
to further strengthen model bias which could result in hovering out
features in your data which otherwise help you improve your model.
Look at the model and the map
Hi Jerry,
You may find that pcDNA3.1 won't give you the protein yields needed for
crystallization. Have a look at PMID: 17001101 for an alternative. Your Kozak
sequence looks good,
radu
--
A. Radu Aricescu, PhD
University Research Lecturer
MRC Career Dev
Dear Crystallographers,
Can anybody guide me how to reduce R-factor, means which are the basic
parameters I have to look for to reduce the R-factor during refinement. I am
newly learning the refinement. After running molrep R-factor is around 53%
(100% identity), after rigid body refinement its
16 matches
Mail list logo
