Hi Seema,
Small addition to the already abundant suggestions, if you have high solvent
content or significant portion of non-observable density, you normally get
higher R-free.
Clement
Clement Angkawidjaja, PhD.
G30 Assistant Professor
-
This is not my experience. Provided the solvent is featureless, I find
that a high solvent contents leads to a lower Rfree due to a kind of
solvent flattening effect. Of course, if a significant part of the
molecule(s) is/are disordered, this will lead to a degradation of the
Rfree.
My 2 cents,
H
The default output for REFMAC
Missing Data: For those reflections where the FP are missing, mFo is set
equal to dFc. Hence the terms become FWT=dFC and DELFWT=0.0.
the Rfree reflections are counted as "missing" hence there shouldnt be
any bias intoroduced towards those Fobs assigned as free
Recently I've installed CCP4 6.1.13 (RHL4) to use refmac 5.5 twinning
refinement (as stated in the current version) but the program list shows
refmac5 instead of the current one. So I followed the thread-
>Re: [ccp4bb] refmac 5.6 and the ccp4i task interface
>Garib N Murshudov
>Wed, 29 Sep 2010
But you have to do solvent flattening (density modification), which people
often (unintentionally?) skip for structures solved with molecular replacement.
Please correct me if I am wrong.
Clement
On May 24, 2011, at 6:01 PM, herman.schreu...@sanofi-aventis.com wrote:
> This is not my experienc
Dear Clement,
In case of a noisy experimental map, you have to do explicit solvent
flattening. However, in case of molecular replacement, if the model
occupies only say 30% of the asymmetric unit, the solvent where there is
no model, will be flattened automatically. You can also view it like
this:
I think you are just confused. The solvent flattening is just a step to make
your map clearer. You do not carry the modified phases from solvent flattening
to refinement (and I sincerely hope you don't refine against the solvent
flattened amplitudes but against the original data!)
Herman's obse
It's also possible that a lower Rfree is the result of reduced overfitting,
because increased solvent content pushes up the obs/param ratio, i.e. the
unit-cell volume is greater so you get more reflections for a given
resolution cutoff, while the no of parameters stays about the same (i.e.
there's
Dear Seema Nath,
Following that thread, Refmac5 is the name you gave to CCP4i to refer to the
program. The important thing is which binary is linked to that name. Run a
Refmac job and check the log. The version number is at the top.
Cheers
-- David
On 24 May 2011 10:14, Seema Nath wrote:
> R
If you run coot with the FWT/PHWT columns from refmac, you are fine
because refmac omits the observed F and substitutes a calculated F, giving
a map which is rather less biased by omission of the free set while not
contaminating the free set.
The buccaneer/refmac pipeline does the same.
On Tue, 2
Dear Herman,
You are right. Thank you for the explanation.
Clement
> Dear Clement,
>
> In case of a noisy experimental map, you have to do explicit solvent
> flattening. However, in case of molecular replacement, if the model
> occupies only say 30% of the asymmetric unit, the solvent where ther
Hi all,
I am working on a newly identified E3 ubiquitin ligase (RING type). I am
interested to co-crystallize it with E2 enzyme. Among the papers reported
so far, which are just a few, people have used a mixture of E2s including
UbcH1, UbcH5 and UbcH6 for the ubiquitination assays. However, there
Hi Manjeet,
You are describing a rather complicated situation but you can try to sort it
out in the following ways:
1. If you can make all the reagents i.e. your E3 ligase, all the putative
E2s and E1, then you can do biochemical assays to figure out which E2's
work. Boston Biochem sells E1 and a
Dear everyone,
I sent this email to lu...@mrc-lmb.cam.ac.uk but it appears that the
email is no longer active, so I'm hoping to get an input from you guys
to troubleshoot this problem.
I tried adding (.CBF) images onto Mosflm, which I recently acquired
from Diamond. And this message immed
Hi Allan
Luke left us nearly two years ago, so if you got that message you must be
running a very old copy of iMosflm!
The cure to your problem is to install the latest versions of iMosflm (1.0.5)
and Mosflm (7.0.7).
On 24 May 2011, at 16:51, Allan Pang wrote:
> Dear everyone,
>
> I sent thi
On 5/24/2011 2:35 AM, herman.schreu...@sanofi-aventis.com wrote:
Dear Clement,
In case of a noisy experimental map, you have to do explicit solvent
flattening. However, in case of molecular replacement, if the model
occupies only say 30% of the asymmetric unit, the solvent where there is
no mode
Hi Folks,
We have some membrane protein crystals that are grown in 30%PEG400,
0.1M Na Citrate pH 4.5, 0.1M LiCl. The protein is purified in DDM. The
crystals are long rods and grown under room temperature in a hanging
drop set up. But once we open the cover slip, we see the rods start to
bre
You probably use hanging drops. It's the surface tension effect. Check
if sitting drops are better.
Maia
Sitting drops
weikai wrote:
Hi Folks,
We have some membrane protein crystals that are grown in 30%PEG400,
0.1M Na Citrate pH 4.5, 0.1M LiCl. The protein is purified in DDM. The
crystals
you could try sitting drops. Perhaps you can fish a crystal quicker, before it
degrades. In sitting drops the crystals may also be further away from the drop
surface and take longer to degrade.
Or quickly add mineral oil to cover the sitting drop and fish the crystals
through the oil.
If this
Weikai,
What you might be experiencing is a detergent effect, i.e., you are
near a detergent-dependent crystallization boundary. We have been hit
with this many times. Under vapor diffusion conditions, sitting or
hanging drop, the protein-detergent complex crystallizes and the free/
bound
It's not a protein, but here's another example: the PreQ1 Riboswitch. In this
case the two methods revealed different structures, but the NMR group was able
to determine that the differences were due to calcium in the crystallization
condition.
Crystal Structure:
Nat Struct Mol Biol. 2009 Mar;
Dear CCP4 users,
I apologize for the non-crystallography question. Our French Press valve
have just been broken and we are looking for a replacement (see link for
valve's image):
http://www.cgp.co.il/Documentary/Zarivach-Lab/Misc/i-rcxfFhp/0/M/French-Press-Valve-M.jpg
Please email me or zarivach[a
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