Hi Robert,
your completeness is only about 90 % on average in shells of reasonably
intensity.
I presume Eleanor would love to see the FObs Fcalc plots from Refmac to get
a better idea in which resolution region there are pronounced differences.
Cheers
Christian
On Thu, Nov 7, 2019 at 2:52 PM Ro
Hello, have you tried refining anisotropic B-factors? It should lower R-free a few percent at that resolution.On 7 Nov 2019 13:42, Robert S Phillips wrote:
I have several data sets of Salmonella tryptophan synthase with different ligands bound in the beta-site. The data look good, with high re
I have several data sets of Salmonella tryptophan synthase with different
ligands bound in the beta-site. The data look good, with high resolution, and
reasonable Rmeas. The ligand density is very clear. However, refinement seems
to be stuck at Rfree = 22%. For this resolution (~1.4 A) it sh
bro de 2019 11:29
Para: CCP4BB@JISCMAIL.AC.UK
Assunto: Re: [ccp4bb] Rfree from another mtz file
If you use either GUI2 or GUI you simply name the old file you want to take the
FreeR flags from..
The pipeline then initiates the steps catalogued by Robbie..
Eleanor
As Tim, and others say, you can
On 09/16/2019 06:29 PM, Mariana Ajalla wrote:
Dear all,
We tried to use the Rfree set from a lower resolution data with a higher
resolution from the same Crystal. To do so We used aimless at ccp4i with the
option use free flag from another mtz file and extend the data.
I think it worked, but
If you use either GUI2 or GUI you simply name the old file you want to take
the FreeR flags from..
The pipeline then initiates the steps catalogued by Robbie..
Eleanor
As Tim, and others say, you can assign new FreeR flags, but dont get upset
when starting refinement with the prevuis model you se
I totally agree. And because the new dataset is of higher resolution, there
will be new reflections in the test set anyway.
Now if you want to use the same testset always for series of isomorphous
datasets (even though you do not need to), you can do this:
- Use unique to make a full set of refl
Dear Mariana,
you can simply create a new set for Rfree, independently of the previous one.
It will be as good as the copied one, and there is no reason why you would
need to maintain the same flags. As Ian Tickle explained only briefly ago,
your new data set will have new, independent errors.
You should be able to get an idea of whether it has worked or not with viewHKL
in the old GUI e.g. find a few reflections with R-free flag zero in your old
dataset and note the indices. Then you can search the new dataset for these
reflections and see if they are still flagged zero. You may nee
Dear all,
We tried to use the Rfree set from a lower resolution data with a higher
resolution from the same Crystal. To do so We used aimless at ccp4i with the
option use free flag from another mtz file and extend the data.
I think it worked, but now we don't know how to be sure we have the s
) 645-6353 (fax)
From: CCP4 bulletin board on behalf of Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Saturday, April 21, 2018 1:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfree going up after refinement
I really need more i
I really need more information to comment properly.
However just check that you are using the same reflections for both Rfree
calculations.
An Rfree of 26% seems low to me from a Se met phased structure at 2.1A -
there are usually small corrections to be made, What is the Rwork?
Maybe attach the
Dear all
I have got my se-phase structure with ccp4-CRANK2-SAD, and its Rfree is 0.26
when CRANK2 output, but the Rfree is higher to 0.36 when I refine it with
refmac or phenix-refinement. does it mean I got a wrong phase, or I didn't got
the right parameters when refinement.BTW, the resolution
CMAIL.AC.UK] On Behalf Of Mohamed
Noor
Sent: 27 June 2016 10:42
To: ccp4bb
Subject: Re: [ccp4bb] AW: [ccp4bb] Rfree stuck at around 39 %
Dear Herman and others
I did run my data through Xtriage - it indicated no twinning but there's a
moderate anisotropy. There are also ice rings but not stron
bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Mohamed
Noor
Gesendet: Montag, 27. Juni 2016 02:08
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Rfree stuck at around 39 %
Dear all
I am working on a structure that extends to about 2.5 A (CC* of 0.5) in the SG
C 2221 (a=134.48, b=424.9, c
Dear Smith,
when you expand to P1, pointless should suggest the space group you
expanded from, unless you fiddled with the data after expansion.
Regards,
Tim
On 07/01/2015 04:43 AM, Smith Liu wrote:
> If both the PDB and mtz for the pdb have been assigned to P1 space group for
> some reason, ca
rsday, July 02, 2015 10:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Rfree below Rwork
Hi Herman and Boaz,
in the trigonal setting R32 (not in the hexagonal setting "H32"), the unit cell
in R32 contains 6 copies. If you take the whole R32 unit cell as a P1 cell, yo
on:*Oganesyan, Vaheh [mailto:oganesy...@medimmune.com]
*Gesendet:* Donnerstag, 2. Juli 2015 15:48
*An:* Schreuder, Herman R&D/DE; CCP4BB@JISCMAIL.AC.UK
*Betreff:* RE: [ccp4bb] Rfree below Rwork
Hi Herman,
While you’re correct regarding increase in number of entities in the
asu upon lowering
]
Gesendet: Donnerstag, 2. Juli 2015 15:48
An: Schreuder, Herman R&D/DE; CCP4BB@JISCMAIL.AC.UK
Betreff: RE: [ccp4bb] Rfree below Rwork
Hi Herman,
While you're correct regarding increase in number of entities in the asu upon
lowering the symmetry, you're not correct for specific ca
etin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
herman.schreu...@sanofi.com
Sent: Wednesday, July 01, 2015 7:34 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] Rfree below Rwork
Dear Boaz,
One can equally well describe a R32 crystal with one molecule in the asymmetric
unit a
gt; Cheers,
>
> Robbie
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *
> wtempel
> *Sent:* Tuesday, June 30, 2015 18:59
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Rfree below Rwork
>
>
>
> Hello,
>
> my question
it. In this case,
> the NCS in P1 is identical to the crystallographic symmetry in R32.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Boaz Shaanan
> *Gesendet:* Mittwoch, 1. Juli 2015 12:10
>
] Im Auftrag von Boaz
Shaanan
Gesendet: Mittwoch, 1. Juli 2015 12:10
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Rfree below Rwork
Just wondering about Eleanor's interesting remark: would the Rf & Rw go as low
as reported by Wolfram (0.22) in case of a wrong space group?
Boaz
Boa
z.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson [eleanor.dod...@york.ac.uk]
Sent: Tuesday, June 30, 2015 8:55 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfree below Rw
will also reindex
your mtz.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Liu
Gesendet: Mittwoch, 1. Juli 2015 04:43
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Rfree below Rwork
If both the PDB and mtz for the pdb have been assigned to P1 space
If both the PDB and mtz for the pdb have been assigned to P1 space group for
some reason, can this lead to Rwork higher than Rfree during refinement?
If after converting my PDB and mtz to P1 space group, and I have forgotten what
is the original space group for my PDB and mtz before conversion
bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor
Dodson
Sent: Tuesday, June 30, 2015 1:55 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfree below Rwork
I suppose if I was the referee for this structure and your FreeR is so close to
the Rfactor I would ask you to ensure you
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of wtempel
Sent: Tuesday, June 30, 2015 18:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rfree below Rwork
Hello,
my question concerns refinement of a structure with 6-fold NCS (local automatic
restraints in REFMAC) against
I suppose if I was the referee for this structure and your FreeR is so
close to the Rfactor I would ask you to ensure you had the right space
group - is the 6 fold NCS actually 2 fold NCS with a crystallographic 3
fold..
Cases occur where R32 is indexed as C2..
Certainly if the Rfree set is assign
Dear Wolfram,
I have a perhaps optimistic view of the effect of high-order NCS
on Rfree, in the sense that I don't view it as a "problem". People
have agonised to extreme degrees over the "difficulty" of choosing a
free set of reflections that would produce the expected gap between
Rwork and
Hello,
my question concerns refinement of a structure with 6-fold NCS (local
automatic restraints in REFMAC) against 2.8 A data. The size of my free set
is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to
4.3 % of reflections.
A refmac run of 10 cycles of TLS and 10 cycles of
rod Mousa
> Sent: Saturday, January 24, 2015 19:05
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Rfree
> Hi all,
>
> I am wondering what the conditions are when Rfree is less than Rwork. I
> have seen this when trying certain models to solve my structure, but I am not
> su
Hi all,
I am wondering what the conditions are when Rfree is less than Rwork. I
have seen this when trying certain models to solve my structure, but I am
not sure why this occurs, or if this is valid or not.
Thanks,
Jarrod Mousa
U. of Florida
Hi,
Reflections related by twin operator(s) should have
same FreeR flag. FREERFLAG program in CCP4 takes care of
it by default.
http://www.ccp4.ac.uk/html/freerflag.html
> if the keyword NOTWIN is not set, all reflections that are equivalent
> by the symmetry of the point group of the twin latt
Hi all,
Is there anything that needed to pay attention to while choosing Rfree set for
twinned data set? Or we can choose Rfree set randomly as untwined data set?
Thanks!
Best wishes!
Yamei Yu
Hi Nazia,
you did not say what Rwork and Rfree values are... If, for instance,
Rwork=20% and Rfree=21% then a situation when Rfree stays the same or even
increases and Rwork goes down is totally valid as long as a reasonable
Rfree-Rwork gap is maintained.
The point is that you need to look at thre
Hi,
The current rwork is 0.31 and Rfree is 0.4, after 10 sets of
refinement. I build quite a large portion before sending it for
refinement.
Thanks a lot for all the answers. I have started working as per suggestions.
--
Nazia Nasir
PhD Scholar
Protein Crystallography Lab
National Institute of I
Dear Nazia Nasir,
it is important to know what you do BETWEEN the refinement cycles. Rfree
not moving and R1 dropping is often a sign of overfitting, i.e. you
might be adding water molecules into the noise or refine the occupancy
of single atoms, e.g. in a ligand or of the water molecules.
As a g
: Dienstag, 10. Dezember 2013 07:52
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Rfree problem
Hi,
I am facing a problem in refining one of my structures. With every refinement
the Rwork is going down. However, the Rfree is stuck and is not going down with
refinement. I have already solved the structure
Hi,
I am facing a problem in refining one of my structures. With every
refinement the Rwork is going down. However, the Rfree is stuck and is
not going down with refinement. I have already solved the structure
without the co-factor bound. This structure is with the co-factor
bound. Can anyone sugg
Just a word of warning -
1) you cant really compare R factors between twinned and untwinned
refinements - they are calculated differently.
2) If the data is twinned the Free R set needs to be selected in the
higher symmetry Laue group and expanded so that twinned pairs are
either both in the Free
Dear experts,
Yes, you were right the data is twined and shows 1 merohedral twin
operator. Now I am performing twin refinement, hope the refinement
statistics will improve. Thank you very much for your valuable suggestions.
Regards
DCB
On Sun, Oct 13, 2013 at 3:01 PM, Kay Diederichs <
kay.die
Dear Dilip,
yes, your data probably are ok, at least based on the value of I/sigma=3.2 in
the highest shell (and based on that, the data could even be used to 1.6 or
maybe 1.5A). The overall and the highest shell Rmerge actually do not carry
much information. It would be rather interesting to k
Dear experts,
Thank you very much for your valuable the suggestions. Dear Tim, the
electron density map is good and fitted well. Krishnaswamy sir, there are
some unmodelled blobs with positive density, I have added respective ions
and refined the model using phenix.refine (Rf- 20.56 and Rfree- 25
Are you certain that the data are not twinned?
HTH
Kay
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear DCB,
do not look at the R-values too much, look at your structure and your
maps. If they look as though you cannot improve the model any further,
accept that the R1/Rfree are 21% and 25% - at 1.7A resolution these
values are acceptable. Go publis
Hello Experts,
I am trying to solve structure of a protein (213 a.a) complexed with a
peptide (14mer) using molecular replacement method. The complex crystals
are diffracted around 1.7 A and data is processed in p3(2)21 space group.
The structure was solved using apo protein with good LLG -3148
---
*Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im
Auftrag von *??
*Gesendet:* Mittwoch, 26. Juni 2013 06:05
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [ccp4bb] Rfree is 20%,why still green and red density?
Hi everyone,
I now me
4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Bernhard Rupp
> Sent: Wednesday, June 26, 2013 13:31
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree is 20%,why still green and red density?
>
> >you may have only a few hundred and thus not get a reliable R
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Sure, but in P6422 with 2.8A I'd say that 5% of reflections are more
likely near 40-50 than 'a few hundreds' if the cell too small. And
most people simply flag 5% of their reflections without checking how
many these really are. Splitting these up into
>you may have only a few hundred and thus not get a reliable Rfree value.
The estimate for the error in R free as a function of the number of
reflections is as follows:
Brunger initially estimated^35 that the uncertainty in R-free is
proportional to
(Nref )^-1/2, which is reasonable to assume
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Jiang Yan,
how many reflections to you have in the free-set. At P6422 with a
resolution of 2.8 you may have only a few hundred and thus not get a
reliable Rfree value. Its low value may be due to overfitting.
What does the cyrstal packing look l
>The Matthews function is based on an average protein crystal with 50%
solvent.
Not sure what that a 'Matthews function' exactly would be - and that an
assumption of 50 solvent
content is made anywhere in the Vm calculation is new to me. The only
defensible
prior that goes into the calculat
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Rfree is 20%,why still green and red density?
Hi everyone,
I now meet some problems when trying to solve structure.Space group is P6422,
and Mathews function shows there are 4 molecules in one asymmetry unit.
However, Phenix-autobuild shows only 2
Hi everyone,
I now meet some problems when trying to solve structure.Space group is P6422,
and Mathews function shows there are 4 molecules in one asymmetry unit.
However, Phenix-autobuild shows only 2 molecules in on one asymmetry unit,
after refinement, Rfree=20%,(resolution is 2.8A). Althou
Tim,
r-free flags are used to calculate maximum-likelihood parameters (sigmaa,
or alpha/beta - depending on parameterization), as well as m and D in
2mFo-DFc and mFo-DFc maps. For this they are supposed to be evenly
distributed across resolution range, and the number of flags per thin
enough resol
--- Original message
> From: Robbie Joosten
> Date:
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree reflections
>
>
> Hi Tim,
>
> The derivation of sigma(Rw-free) is in this paper: Acta Cryst. (2000). D56,
> 442-450. Tickle et al.
> Note
: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfree reflections
Hi Tim,
The derivation of sigma(Rw-free) is in this paper: Acta Cryst. (2000). D56,
442-450. Tickle et al.
Note the difference between the sigma of weighted/generalized/Hamilton
R-free and that of the 'regular' R-free (th
m: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Tim Gruene
> Sent: Tuesday, March 26, 2013 11:05
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree reflections
>
> Hi Robbie,
>
> thank you for the explanation. Heinz Gut and Michael Hadders po
ons.
>
> HTH,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> > Tim Gruene
> > Sent: Tuesday, March 26, 2013 09:33
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] Rfree
al Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Tim Gruene
> Sent: Tuesday, March 26, 2013 09:33
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Rfree reflections
>
> Dear all,
>
> I recall that the set of Rfree reflections should b
Dear all,
I recall that the set of Rfree reflections should be 500-1000, rather than
5-10%, but I cannot find the reference for it (maybe Ian Tickle?).
I would therefore like to be confirmed or corrected:
Is there an absolute number required for Rfree to be significant, i.e. 500-1000
irrespectiv
Thursday, February 28, 2013 10:33
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree flag
>
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Kavya,
>
> As far as I understand the PDBRedo project attempts to make the
reflections
> unbiased from th
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Kavya,
As far as I understand the PDBRedo project attempts to make the
reflections unbiased from the structure by a random shift of
coordinates (e.g. 'NOISE' keyword in pdbset, although I am not aware
of an investigation about whether this actual
Dear All,
Thank you Folmer and Fred for your suggestions. Mine is
an isomorphous crystal. I had refined without using the
same set of Rfree reflections, finally getting larger
difference between the R and Rfree. I hope considering
the same Rfree set would solve this problem.
Thank you
With regard
Although it is not "mandatory", I think it would be a very good idea,
especially if you have the exact same spacegroup and the native and
ligand-bound forms of your protein are essentially the same.
If you do not use the same reflections, you are actually not reporting an
independent (free) R-fact
Hello,
I think this depends on the type of problem you are facing:
if the 2 crystals are not isomorphous then you cannot have the same
R-free sets;
if the 2 crystals are isomorphous then either you do not worry about
keeping the same R-free set (but then the starting structure must be
"pertur
Dear Kavya,
It is not so. It is not
mandatory.
best,
Sekar
> Dear users,
>
> Is it mandatory to use the same reflections for
> Rfree calculations of a ligand bound data as that
> of its native?
>
> Thank you
> With Regards
> Kavya
>
>
> --
> This message has been scanned for viruses and
> dan
Dear users,
Is it mandatory to use the same reflections for
Rfree calculations of a ligand bound data as that
of its native?
Thank you
With Regards
Kavya
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
Dear Al,
Refmac by default divides reflexions in 20 shells ("bins") - this can
mean a few of them do not contain a thin Rfree shell.
When this happens I add "bins 10" to the refmac com-file, or, in
CCP4i, instead of "run", do "run and view com file" and add "bins 10"
to the file before conti
Greetings CCP4-ers,
The situation:
I have 10 fold NCS, and thought it would be fun to try the Rfree in thin
shells.
After using SFTOOLS (rfree 0.05 shell) to divvy up the Rfree flag,
everything went swimmingly until i looked at my REFMAC log in the section
"Things for loggraph, R factor and others
-- Ian
> -Original Message-
> From: Lijun Liu [mailto:li...@uoxray.uoregon.edu]
> Sent: 24 September 2009 19:00
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree in similar data set
>
> Sticking to the same test set is a great and practical i
sly.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Edward A. Berry
> Sent: 24 September 2009 20:53
> To: owner-ccp...@jiscmail.ac.uk
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree in similar
7;memory' of
fitting to the new data.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Tom Terwilliger
> Sent: 24 September 2009 16:58
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject
17:21
To: Ian Tickle
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfree in similar data set
While I agree with Ian on the theoretical level, in practice
people use free R's to make decisions before the ultimate model
is finished, and our refinement programs are still limited in
their ab
if the new data is of high enough resolution and the original
structure was solved by MR - it may be little extra (human) effort to
just redo the MR followed by automatic building.
This can have the advantage that, after building, comparing the two
structures, you may discover small mistakes in th
our
convergence time.
Lijun Liu
On Sep 24, 2009, at 10:24 AM, Ian Tickle wrote:
-Original Message-
From: Dale Tronrud [mailto:det...@uoxray.uoregon.edu]
Sent: 24 September 2009 17:21
To: Ian Tickle
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfree in similar data set
Whil
> -Original Message-
> From: Dale Tronrud [mailto:det...@uoxray.uoregon.edu]
> Sent: 24 September 2009 17:21
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree in similar data set
>While I agree with Ian on the theoretical level, in pract
ickle wrote:
>> -Original Message-
>> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
> On
>> Behalf Of Eric Bennett
>> Sent: 24 September 2009 13:31
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Rfree in similar data set
>
eptember 2009 13:31
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Rfree in similar data set
Ian Tickle wrote:
For that to
be true it would have to be possible to arrive at a different
unbiased
Rfree from another starting point. But provided your starting point
wasn't a local maximum LL and you ha
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Eric Bennett
> Sent: 24 September 2009 13:31
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Rfree in similar data set
>
> Ian Tickle wrote:
>
&
009 13:21
> To: CCP4BB
> Subject: Re: [ccp4bb] Rfree in similar data set
>
> Hi Ian,
>
> consider the case where two data sets have been collected from the
same
> crystal (or a crystal from the same drop), each processed separately,
and
> the structure refined against one of
Ian Tickle wrote:
For that to
be true it would have to be possible to arrive at a different unbiased
Rfree from another starting point. But provided your starting point
wasn't a local maximum LL and you haven't gotten into a local maximum
along the way, convergence will be to a unique global ma
Hi Ian,
consider the case where two data sets have been collected from the
same crystal (or a crystal from the same drop), each processed
separately, and the structure refined against one of the two data sets
until convergence. The two data sets will be somewhat different due to
measureme
Hi, I beg to disagree with the 'perceived wisdom', including just about
everyone on this BB, but my answer is NO, there should be no bias -
*provided* you do the subsequent refinement properly. First off, Rfree
is useless as any kind of statistical measure of overfitting etc
*unless* the refinemen
Hi Mike and other interested colleagues,
I agree - it is best to select the observed data with the same indices
for the new Rfree set as in the previous isomorphous crystal(s),
selecting new ones for higher resolution shells (which can be
conveniently done in XDS during conversion to other
Mike England wrote:
Hi all,
I will appreciate your comments on the following case:
I have two datasets from the same or identical crystals. Initially, I
refine a structure against the first data set and later on switch to
another dataset for further refinements.
Do you think, my Rfree will be
nt. Acta Cryst. 1998; D54:547-557"
HTH,
Robbie Joosten
Netherlands Cancer Institute
Amsterdam, The Netherlands
> Date: Wed, 23 Sep 2009 22:37:17 -0700
> From: det...@uoxray.uoregon.edu
> Subject: Re: [ccp4bb] Rfree in similar data set
&
Yes
Dale Tronrud
Mike England wrote:
Hi all,
I will appreciate your comments on the following case:
I have two datasets from the same or identical crystals. Initially, I
refine a structure against the first data set and later on switch to
another dataset for further refinements.
Do you t
Hi all,
I will appreciate your comments on the following case:
I have two datasets from the same or identical crystals. Initially, I
refine a structure against the first data set and later on switch to
another dataset for further refinements.
Do you think, my Rfree will be biased as Rfree refle
maybe those loops are right - ish.
Eleanor
kumar wrote:
Dear members,
I am refining a structure and I notice that when I delete loops that have
none, or very little density, the Rfree (which is around 40% at 3.4A) goes
up instead of going down. Much of the remainder of the molecule is in good
d
Dear members,
I am refining a structure and I notice that when I delete loops that have
none, or very little density, the Rfree (which is around 40% at 3.4A) goes
up instead of going down. Much of the remainder of the molecule is in good
density. Wondering how it works?
Thank you.
Kumar
It is actually possible to calculate R(free) with SHELXL for the outer
most resolution shell. Gabor Bunkoczi indicated the solution and I
forward it here to the public:
- Rename the .res file of the last refinement run to .ins
- adjust the CGLS parameter in the .ins file to 0 -1 (Zero refinement
(F>4SIG(F)) :
> REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) :
> REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) :
> REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 35043
>
> Best wishes,
>
> Boaz
> - Original Mess
SHELX is much older than the free R so this was added as an afterthought,
and unfortunately I did not think of calculating R-free for just the outer
resolution shell. There isn't an easy way of doing this without some
programmeing effort. I also think that it is NOT a good idea, in the outer
re
Dear all,
I used SHELXL for anisotropic structure refinement of high-resolution
data (1.3 Angstroem) and a reviewer asked me to include refinement
statistics for the outer most resolution shell in the crystallographic
table. While R-factors for the outer most resolution shell belong to the
st
Dear Vineet
Following points shall be kept in mind.
1.If you have been able to model most of the protein
into the electron density, then its a bit strange.
your refinement parameters suggest that refinement is
still away from convergence.
2.You might be trapped in local minima, and in this
case
Hi all
i m solving a structure at 2.2 A using MIR. rt now my Rfree is 30.55% and
Rcryst is 28.51%. i have already carried out B factor refinement n water has
also been picked up to 2.3 sigma cut off. now i m not able to refine the
structure any further.
The protein has been purified directly from
Hi James,
F2mtz will do it.
On Thu, 31 May 2007, James Pauff wrote:
Good day all,
What is the best means of getting a freeR column into
an existing mtz file? I've noticed the "Edit MTZ"
command bar in CCP4, but there are other options (such
as conversion to XPLOR and then back to MTZ) that s
bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
James Pauff
Sent: 31 May 2007 13:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rfree into an existing mtz...
Good day all,
What is the best means of getting a freeR column into an existing mtz
file? I've noticed the "Edit MTZ"
1 - 100 of 104 matches
Mail list logo
