Hi Pete,
it's surely beneficial and good to know how software works especially if
it's part of your research, I entirely agree. Though, on the other hand, I
don't feel too bad about not knowing the CS behind the implementation of MS
Word when I use it for my documents editing. I guess it depends
Refinement against images is a nice old idea.
From refinement technical point of view it's going to be challenging.
Refining just two flat bulk solvent model ksolBsol simultaneously may be
tricky, or occupancy + individual B-factor + TLS, or ask multipolar
refinement folk about whole slew of magic
Hi Tim,
A side note: you are most likely not looking at 2Fo-Fc and Fo-Fc maps,
but a sigma-A weighted maps and sigma-A weighted difference maps. I
think it is worth differentiating between these terms.
Fully agree. I guess just typing them as 2mFo-DFc and mFo-DFc will solve
this particular
Hi James,
On Sat, Jul 6, 2013 at 6:31 PM, James Holton jmhol...@lbl.gov wrote:
I think it is also important to point out here that the resolution
cutoff of the data you provide to refmac or phenix.refine is not
necessarily the resolution of the structure. This latter quantity,
although
Hi,
I am wondering if I can fix a set of selected atoms during simulated
annealing in phenix.refine?
no.
Pavel
P.S.: There is Phenix mailing list for Phenix-specific questions
Hello Wei,
I have a refined structure with phenix.
FYI and as a reminder: there is Phenix mailing list for Phenix-specific
questions.
The resolution=3.2 Å. After refinement, the R-work=0.2186, R-free=0.2864,
Bonds=0.010, Angles=1.515.
Large Rfree-Rwork gap indicates overfitting, which in
Tim,
PDB file format is good because of its simplicity and that's perhaps it.
However, it cannot accommodate wealth of information that is available at
the end of refinement. Of course one can keep creating remarks for PDB file
etc but I guess mmCIF is just a better way of doing it rather than
Hi Paul,
I would have them both in PDB file with different non-blanc altLocs and
arbitrary starting occupancies and that will work in refinement (in
phenix.refine for sure, can't tell for other programs).
Pavel
On Fri, Aug 23, 2013 at 8:39 AM, Paul Paukstelis
shocksofmig...@gmail.comwrote:
Hi Emily,
I get 100% completeness above 1A and 41% completeness in the 0.9A-0.95A
shell.
However, my Rmerge in the highest shelll is not good, ~80%.
The Rfree is 0.17 and Rwork is 0.16 but the maps look very good. If I
cut the data to 1 Angstrom the R factors improve but I feel the maps
Excellent point about R-factors. Indeed, at this resolution they should be
quite lower than what you have. Did you:
- model solvent?
- use anisotropic ADPs?
- add H (this alone can drop R by 1-2%)?
- model alternative conformations?
- How R-factors (Rwork) look in resolution?
Pavel
On Mon, Aug
Hi,
a random thought: the data resolution, d_min_actual, can be thought of as
such that maximizes the correlation (*) between the synthesis calculated
using your data and an equivalent Fmodel synthesis calculated using
complete set of Miller indices in d_min_actual-inf resolution range, where
This may be worth to mention in this context:
http://cci.lbl.gov/hybrid_36/
Pavel
On Fri, Aug 30, 2013 at 9:14 AM, MARTYN SYMMONS
martainn_oshioma...@btinternet.com wrote:
Hold your horsemen!
Does not this option save us from 'formatagedon'?
We currently only have single letters or
Hi Alastair,
phenix.fake_f_obs might be of use depending on your goals. It's not a
fool-proof end-user tool (in terms of convenience of use, docs, etc etc
etc), and may require knowledgeable tweaking before you get a meaningful
outcome; if interested talk to me off list. I used it when some one
Hi Alastair,
since you mentioned it... In our article On the analysis of residual
density distribution on an absolute scale:
http://www.phenix-online.org/newsletter/CCN_2012_07.pdf
one of the conclusions was that we could not reproduce pronounced features
on the solvent/macromolecule border shown
Hi James,
I guess it depends on what you put in your simulated Fobs. With
phenix.fake_f_obs I can add lots of stuff including H, TLS, small random
rigid-body shifts averaged over ensemble of MD simulated models,
alternative conformations, libration motions of side chains around bonds,
etc..
Hi Yafang,
perhaps you should calculate the actual resolution first (as described
here: *Acta Cryst.* (2013). D*69*, 1921-1934) and then go from that?
Pavel
On Thu, Oct 10, 2013 at 1:57 PM, Yafang Chen yafangche...@gmail.com wrote:
Hi All,
I have a structure at 2.45A which has been well
Hello,
just for the sake of completeness: this paper lists a bunch of known
pathologies (I would not be surprised if they've been remediated by now):
http://www.phenix-online.org/papers/he5476_reprint.pdf
Pavel
On Thu, Oct 17, 2013 at 6:51 AM, Lucas lucasbleic...@gmail.com wrote:
Dear all,
Hi Deng,
Recently, I received the comments from referees, they asked for the
SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated
annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven
thymidine nucleotide. Our data diffracted to 2.65A，but the
Hi Wenhua,
concerning phenix.refine: just run it again with weights optimization and
it should fix the problem (assuming everything else done right: such as you
are using correct refinement strategy). If using weights optimization does
not help then let me know off list or on Phenix mailing list
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
Hi Ursula,
you will find answers here:
http://www.phenix-online.org/papers/he5476_reprint.pdf
Pavel
On Wed, Jan 15, 2014 at 1:38 PM, Ursula Schulze-Gahmen
uschulze-gah...@lbl.gov wrote:
I am submitting a structure to the PDB database. The SfCHECK summary
report provided by the PDB
Hi Tim,
a non-ccp4 solution (since you haven't gotten any suggestion yet)..
1) Get atom selection of atoms involved into ion coordination:
phenix.metal_coordination model.pdb
2) Using atom selection from above extract portion of PDB that contains
atoms in question:
phenix.pdb_atom_selection
Chris,
what you get is not unheard of but clearly you are not in majority: at
around 1.95A resolution distribution of R-factors in PDB is:
Histogram of Rwork for models in PDB at resolution 1.85-2.05 A:
0.093 - 0.118 : 3
0.118 - 0.143 : 75
0.143 - 0.168 : 821
Chris,
On Sun, Feb 23, 2014 at 2:52 PM, Chris Fage cdf...@gmail.com wrote:
As suggested, I tried NCS and TLS in phenix.refine, although my R-factors
did not budge.
(...)
Forgive my ignorance, but I am not sure how to check whether the bulk
solvent model is reasonable.
I figure you used
Hi,
once upon a time I found myself interested in this topic, which prompted my
to read these papers:
1993 Gregory
2004 Harding
1996 Nayal
2005 Babor
1998 Rulisek
2005 Sommerhalter
1999 Harding
2006 Dudev
2000 Harding
2006 Harding
2000 Harding_2
2006 Stefan
2001 Pidcock
2007 Tamames
2002 Harding
Hi Amlan,
given that it should not depend on which school of thought you follow:
2*(Fo-Fc) + Fc vs Fo + (Fo-Fc), you should be able to see the same thing at
appropriately chosen contouring levels in both maps, I think... (I could be
wrong at this time of the night, of course!)
Pavel
On Mon,
Hi Almudena,
also, does anyone know how to within Phenix?
that's the tool that should do it:
http://www.phenix-online.org/documentation/reciprocal_space_arrays.htm
Note there is a corresponding utility in the GUI (if I recall correctly
under Reflection tools).
Pavel
Hi Eric,
I've been trying to run Phenix.model_vs_data on the whole PDB. That program
requires MTZ format,
not true, you can give it reflection date in CIF format as you get it from
PDB.
I've tried (with multiple versions of Phenix) to use Phenix.cif_as_mtz to
perform the conversions, but
Here you can find a list of reasons for R-factor discrepancy and how much
each of them affects the R-factor:
http://phenix-online.org/papers/he5476_reprint.pdf
Pavel
On Fri, Apr 4, 2014 at 8:18 AM, Nat Echols nathaniel.ech...@gmail.comwrote:
On Fri, Apr 4, 2014 at 1:57 AM, Tim Gruene
Hello Yarrow,
in some refinement software (phenix.refine), if you run TLS refinement and
you don't specify the TLS groups, the entire structure is considered one
TLS group
if you use TLS parameterization and do not specify TLS groups, two
scenarios are possible: a) each chain will be treated
Hello,
I read your paper and it seems very relevant to the present discussion (and
future referee comments). Have the criteria that you propose for
determining the effective resolution been implemented in any program or
crystallographic suite in way that we can read in a data set and get out
Hello Peter,
1、THE RESOLUTION OF THE DATA IS 2.5 angstrom. After first refinement of
refmac5 I got R factor which is 0.26 and R FREE which is 0.31. My question
is what the final R factor and R FREE should be after several rounds of
refinement by refmac5 and coot.
answer can be found here:
Hi Robbie,
I agree with Ed that you probably should not leave out your free
reflections in real-space under normal circumstances.
Phoebe is right: you should not use free-r reflections in calculation of
map that you are going to use for real-space refinement. Otherwise you will
be biasing
Hi Robbie,
I agree that you bias R-free after the real-space refinement
well, ok, isn't it enough to realize that this is bad and should be avoided
? (I guess we all know we should never bias Rfree!)
My point was that we normally do not calculate R-free after real-space
refinement,
It's
Hi Robbie,
I agree that you bias R-free after the real-space refinement
well, ok, isn't it enough to realize that this is bad and should be
avoided ? (I
guess we all know we should never bias Rfree!)
My point was that we normally do not calculate R-free after real-
Hello Robert,
since you are going to use Phenix tools for refinement (phenix.refine, to
be precise), then
1) why don't you use Phenix utilities
http://phenix-online.org/version_docs/1.9-1688/
to obtain a suitable ligand dictionary (CIF file) assuming that it is going
to be more compatible with
Hi Chris,
In my 2.5-angstrom structure, there is negative Fo-Fc density
surrounding a metal ion after refining in Phenix. From anomalous
diffraction I am certain of the metal's identity and position in each
monomer. Also, the ion is appropriately coordinated by nearby side
chains. Should I
TWILIGHT database, PDBREDO database, ... what else I forgot to name? I
wonder why it should be under different brands and names, and not just be
where it belongs to - the PDB?!
Back in 2005 when I (and colleagues) started re-refining the entire PDB (to
test phenix.refine, mostly) and seeing
What about structures that are obviously wrong based on inspection of the
density, but no one has bothered to challenge yet? The TWILIGHT database
helps some, if that counts, but it doesn't catch everything.
How about this utopia.. Imagine PDB has two versions: one is the original
data and
the R-factor is a complicated thing that depends on things like
weighting factors and solvent model - several things that are not part
of your model and that need to be adjusted by the refinement program
during refinement.
I think a more accurate is are not part of your ATOMIC model.
Ezequiel,
since you mentioned you tried Phenix too:
in Phenix you can remove a particular disulfide bond by using a parameter,
for example:
disulfide_bond_exclusions_selection_string=(chain A and resseq 1 and name
SG) or (chain B and resseq 10 and name SG)
This works in the command line and
Carles,
a few points to consider:
- you might be comparing B-factors coming from local atomic vibrations
alone (residual B, or whatever it's called), and the total atomic B-factor,
that includes all components: Btotal = Btls + Bresidual +... . (for
comprehensive review on this topic see: TLS
Hi Nick,
Is this conformation refineable in refmac5 or phenix if the occupancy is
set to zero?
Should I allow clashes to push both copies either side of the density as
is currently happening?
Any tips on dealing with this?
if occupancy is to 0 then it is not refined in phenix.refine. You
Hi James,
a remark: different programs may treat occ=0 differently. In phenix.refine
(phenix.maps, etc) atoms with zero occupancy will be ignored for
bulk-solvent mask calculation, unless you ask to do otherwise. For example,
this means that if you want to calculate a ligand OMIT map both options
Hi Tim,
just to spice your words up with some numbers
You may also want to note that constrained hydrogen positions are a
crude approximation and only work with X-ray data where hydrogen atoms
have little impact on the data.
This contribution can be as large as 1.5% difference in
Hi Antony,
Apologies for the cross-posting, but I *do* routinely use programs from all
three software packages.
I find myself refining a relatively low resolution structure (3.5
Angstrom) - with 8 molecules in the asymmetric unit.
Is there a *simple* automated way to place “optimal-fit to
9RQ
- - - - - - - - - - - - - - - - - -
email: antony.oli...@sussex.ac.uk
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512
http://www.sussex.ac.uk/lifesci/oliverlab
http://tinyurl.com/aw-oliver
- - - - - - - - - - - - - - - - - -
On 18 Jun 2014, at 17:13, Pavel Afonine pafon
Hi Bernhard,
phenix.refine makes use of charge if specified in PDB file (rightmost
column after the chemical element type) to use appropriate form-factors.
However, occupancies and B-factors are very efficient mops to accommodate a
broad range of discrepancies between model and reality. So
Hi Bing,
I think residual density you see is a result of inaccuracy in parameters of
Fe, such as coordinates, occupancy or B-factor (or any mixture). This
applies to all atoms, but since Fe has more electrons these errors become
more readily visible in residual map. Here are a few simulated
How we can define NCS in phenix.refine.
phenix.refine uses torsion ncs and top-out restraints target, which all in
all means no need to do anything special apart from enabling using ncs in
refinement.
Details:
http://journals.iucr.org/d/issues/2014/05/00/rr5054/index.html
Acta Cryst. (2014).
Hi Armando,
can be many reasons, a few for instance:
- are you sure the ligand you modeled in is the one that is actually there?
- is the positive density around or overlaps with ligand atoms you places?
Then that would means ligand parameters are underrefined (need more
refinement) or not
Hi Minglei,
I can't remember if CNS has this, but I it is available in Phenix.
Pavel
On Fri, Jul 18, 2014 at 2:22 PM, Minglei Zhao mlz...@mbi.ucla.edu wrote:
Dear CCP4BB members,
I wonder if there is a CNS library file for electron scattering factors.
Many thanks!
Minglei
Hi Alex,
It is not clear to me how to report the resolution of data when it is 3A
in one direction, 3.5A in another and 5A in the third.
can't be easier I guess: just switch from characterizing data sets with one
single number (which is suboptimal, at least, as Phil pointed out earlier)
and
to understand the resolution of
my data. We need more studies into this issue (correlation between the
resolution of anisotropic data and model quality). And there should be a
common rule how to report and interpret such data (IMHO).
Regards,
Alex
On Apr 9, 2012, at 11:02 AM, Pavel Afonine
Hi Rajesh,
I guess they could (in most programs), but the question is whether they
should? Can't you try both options to see which one works best in your
specific case?
Pavel
On Sat, May 5, 2012 at 6:02 AM, Rajesh Kumar ccp4...@hotmail.com wrote:
Dear all,
Is ligands and metals could also be
Hi Peter,
may be I'm missing something but I think all you need to do is to place
(add to PDB file) a Zn2+ into a blob of density that you believe that Zn
belongs to, and then most of refinement tools will take care of it
automatically. So I'm not seeing why you need files for a Zn atom I
Oh, I was thinking more primitively: I would just open a PDB file with my
favorite text editor and type in an ATOM record -:) As simple as this!
Pavel
On Sat, May 5, 2012 at 2:29 PM, Nat Echols nathaniel.ech...@gmail.comwrote:
On Sat, May 5, 2012 at 2:23 PM, Pavel Afonine pafon...@gmail.com
Hi Chris,
- there is Phenix mailing list for Phenix-related questions. Please check
http://www.phenix-online.org/
- the data resolution of 2.5A does not mean hydrogen atoms are not present
in the crystal. There are methods to account for them. For details see (and
references therein):
On
Shya,
Elbow command:
phenix.elbow --smiles=O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45
will give you CIF and PDB files. I just tried, it took 5 minutes to
calculate them on my mac.
Pavel
On Wed, May 9, 2012 at 9:08 AM, Shya Biswas shyabis...@gmail.com wrote:
Hi all,
I am having trouble
Hi LISA,
if you send me more details I might be able to address your questions (as
Phenix developer). Though a better place to post your Phenix related
questions is a Phenix mailing list, not CCP4bb.
P.S. Ugh, I find Ed's reply totally.. how to say it softer using my
non-native-English...
Hi Mike,
Is it reasonable to refine occupancy in phenix at 2.2 A resolution?
yes, but only for those atoms that need it.
FYI: there is a Phenix mailing list for Phenix-specific questions.
Pavel
reflections.
So all in all my suggestion is to not make too much sense of absolute
values of the Fourier map you are looking at.
Best,
Pavel Afonine
On Wed, Jun 6, 2012 at 12:47 PM, Ursula Schulze-Gahmen
uschulze-gah...@lbl.gov wrote:
I calculated threefold averaged omit maps in coot. These maps
Hi Qixu Cai,
first off -- as a reminder, there is Phenix mailing list to post
Phenix-related questions:
http://www.phenix-online.org/
Your first question: yes, give it one sequence file containing all.
Your second question: see here
http://phenix-online.org/documentation/autobuild_gui.htm
Pavel
Hi Herb,
yes, I know one:
phenix.pdb_interpretation model.pdb write_geo_files=true
Optionally you can give it ligand's cif files too:
phenix.pdb_interpretation model.pdb ligands.cif write_geo_files=true
Pavel
On Tue, Jun 19, 2012 at 11:11 AM, Axelrod, Herbert L.
haxel...@slac.stanford.edu
Hi Tim,
a possible way of thinking about this is:
say you have N (=nx*ny*nz) nodes of the grid on which you sampled the map,
and the unit cell volume is Vcell, and you are looking at a blob identified
at some level. Then the volume of this blob can be defined as Vblob =
np*Vcell/N, where np is
Hi Wojtek,
you need to convert your EM map into a reflection file (for example, cns or
mtz formatted, format doesn't matter). This reflection file should contain
Fobs - the amplitudes of Fourier map coefficients and phases
corresponding to your EM map. The phases should be presented as
Hi Wojtek,
attached is a simple Python script that will read in your EM map (in ccp4
format; I can trivially change the script so it reads x-plor map too) and
it will write out MTZ file containing:
- complex array of Fobs (Fobs_cmpl), which is just a Fourier transform of
the input map;
- real
Norman,
the value of free-R alone doesn't tell a whole lot, though the numbers you
quote seem good given the resolution. What's Rwork?
The behavior of free-R you tell is also totally expected: in rigid-body
refinement there are way less refinable parameters!
Most likely you should proceed with
Hi,
you can't expect to see something with occupancy ~0.3 at the same cutoff
level as you use to see fully occupied sites. So most likely the solution
is to use a lower cutoff levels, as many suggested already. Two maps you
attached look totally expectable to me.
Pavel
On Fri, Jul 27, 2012 at
Hi,
cctbx Explore symmetry will do this and lot more:
http://cci.lbl.gov/cctbx/explore_symmetry.html
Pavel
On Thu, Aug 2, 2012 at 1:37 AM, Careina Edgooms careinaedgo...@yahoo.comwrote:
Dear ccp4
I ask a very fundamental question because I have not had formal training
in this and I would
Hi Deepthi,
1) refine anisotropic ADPs for Zn,
2) make sure charge is accounted for,
3) refine f' and f'' for Zn (that means you need to use anomalous data in
refinement).
If 1-3 do not help, add
4) refine occupancy of Zn,
5) make sure you visualize your map using correct levels.
This should
Hi,
Python, of course (if you know some basic math). Otherwise, Python and a
good math text book -:)
Pavel
On Wed, Sep 12, 2012 at 7:32 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
Dear List,
since this probably comes up a lot in manipulation of pdb/reflection files
and so on, I
Hi,
pointers listed here may be of help:
1) CCP4 Newsletterhttp://www.ccp4.ac.uk/newsletters/newsletter42/content.html
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev
2) https://www.phenix-online.org/presentations/latest/pavel_maps.pdf
3)
Hi James,
using dynamic N-Gaussian approximation to form-factor tables as described
here (pages 27-29):
http://cci.lbl.gov/publications/download/iucrcompcomm_jan2004.pdf
and used in Phenix since 2004, avoids both: singularity at B=0 and
inaccurate density values (compared to the raw
3.5439
1000.217171 0.21717 0.21714
weird numbers. A proper description would have 6e/A^3 for a C at
x=(0,0,0) with B=0. How are these numbers 'not inaccurate'?
Cheers,
Tim
On 09/19/2012 06:47 PM, Pavel Afonine wrote:
Hi James,
using
Joao,
I am using the latest version of phenix 1.8.1-1168
1.8.1-1168 should not have that problem.
If you suspect there is still a problem, you can send me the data and model
files off list, explain what exactly the problem is, and I will have a look
right away.
FYI: there is Phenix mailing
Hi Rex,
as easy as:
phenix.pdb_atom_selection model.pdb within(3, chain L and resseq 9 and
name CA) --write-pdb-file=cut.pdb
which in the above example selects all atoms within 3 A from CA atom in
chain A of residue number 9, and writes them into cut.pdb file.
Pavel
On Sat, Nov 17, 2012 at
, 2012, at 14:26, Pavel Afonine pafon...@gmail.com wrote:
Hi Rex,
as easy as:
phenix.pdb_atom_selection model.pdb within(3, chain L and resseq 9 and
name CA) --write-pdb-file=cut.pdb
which in the above example selects all atoms within 3 A from CA atom in
chain A of residue number 9, and writes
Hi Grant,
sounds like you did the right thing (as far as I can guess given the amount
of information you provided).
In a nutshell, both, B-factors and occupancies, model disorder. The
difference is that occupancies model larger scale disorder (such as
distinct conformations) than B-factors
Hi Dirk,
cctbx has tools to obtain N-gaussian approximation of scattering tables,
for any element, where the number of gaussians N is determined dynamically
to obtain desired accuracy of fit. That's what is used by phenix.refine and
other related tools.
See page 27 here:
For map in e-/A^3 units to make sense one needs to obtain F000, which may
be more tricky than one may think. Interesting, how Coot does this given
just a set of Fourier map coefficients?
Pavel
On Wed, Nov 28, 2012 at 12:21 PM, Greg Costakes gcost...@purdue.edu wrote:
You stated that the map is
Hi,
or here, page 25:
http://www.phenix-online.org/presentations/latest/pavel_validation.pdf
Nat's plot is better though as it shows the spread.
B-factor needs to be weighted by occupancy, I think.
- or show two plots: one for fully occupied atoms only, and the other one
for partially
Hi,
It would be nice if default setting was the same in different suites.
it's a nice idea of course, but I feel it is impractical as it would
require changing a lot of software, both modern and legacy.
However, given array of flags it is algorithmically trivial to figure out
what is test and
One more option:
phenix.fetch_pdb 1akg --maps
will fetch structure and reflection data files from PDB and generate
2mFo-DFc and mFo-DFc maps (as well as anomalous difference map if
reflection data is anomalous).
Pavel
On Mon, Feb 4, 2013 at 5:52 AM, Robbie Joosten
Hi Bashir,
if you send me the data and model (directly to my email address, not the
whole list), then I will have a look.
Also, please note there is Phenix mailing list for Phenix specific
questions.
Pavel
On Fri, Feb 15, 2013 at 12:35 PM, Muhammed bashir Khan
Hi Mike,
if you send me the inputs (data, model and any parameter files) I will tell
you what's wrong. If you choose to send the files, please do so to my email
address (not the whole mailing list).
FYI: there is Phenix mailing list for questions like this.
Pavel
On Tue, Mar 5, 2013 at 10:11
Hi Sonali,
regarding isotropic vs anisotropic parameterization of your individual
ADPs: apart from common sense and theoretical considerations, this is also
in great part software dependent.
I can't speak for other programs, but for phenix.refine I would say the
rule of thumb is:
- higher than
Hi Ethan,
I would place the expected resolution break-even point at more like
1.2 - 1.3 A. But that's only an expectation, not a rule to rely on.
You should justify anisotropic refinement of a structure on the basis
of its own particular model and measured data. Robbie Joosten has
already
Hi Chen,
I also tried the Superpose maps utility in PHENIX, however, since they
are nucleic acid structures, it seems that the sequences cannot be
recognized.
I'm not aware of such problem. If it does exist and you want me to fix it
please send me the files and I'll have a look.
Pavel
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
Hi,
not knowing other details, the most naive guess is that this may be a
footprint of mask-based bulk-solvent model. Next one is that you are
contouring at too low/high level (note, sometimes, if, for instance,
solvent content is high, you need to look above/below 3sigma). Of course,
there could
This explains why I cannot reproduce published R-factors (with files from
PDB I get ~40%). If I force my favorite refinement program to use P21212
then I get R close to reported in PDB file header.
This makes it worth reminding that it's rarely a good idea to edit PDB file
out of refinement.
In this particular case attempting to calculate R-factor using data and
model files and making sure that the R you get is not twice as large as
published one would entirely suffice -:)
Pavel
On Fri, Apr 12, 2013 at 12:42 PM, Eugene Osipov e.m.osi...@gmail.comwrote:
In my opinion pdb must
Hi Robbie,
Which seems a sort of reasonable attitude to me.
Not quite, the depositor has to give, i.e. type, the space group
what I don't get is why one needs to type in this information if it is
already present in both, model and data files? Any human typing is typo
prone. Ideally
Hi Emmanuel,
try MZ protocol (MZ = multi-zone) in phenix.refine. It does the smart
rigid body refinement starting from a few low resolution reflections and
ending up with using all data. In-between it does the maximum-likelihood
bulk-solvent modeling and scaling. All together it results in a
Hi,
phenix.refine allows unlimited number of TLS groups of any size.
More :
general info: http://www.phenix-online.org/
refinement info: http://www.phenix-online.org/download/cci_apps/ (click
Documentation or QuickFacts right next to phenix.refine link).
or write me back with your
Hi Mike,
the best is to do both in a loop:
for cycle in cycles:
- do real space refinement;
- do reciprocal space refinement
Have a look at this very nice paper:
Acta Cryst. (1999). D55, 835-845
Critical initial real-space refinement in the structure determination of
arginine kinase
G.
Anastassis Perrakis wrote:
On 10 Aug 2007, at 18:59, Pavel Afonine wrote:
Hi Mike,
the best is to do both in a loop:
for cycle in cycles:
- do real space refinement;
- do reciprocal space refinement
Well - thats what we all do - right ?
The real space refinement can be done either
Hi all,
here is very incomplete list of why the statistics is different:
- different bulk solvent models (flat mask based, Babinet, etc.);
- different parameters for mask calculation (shrink and solvent radii,
grid step) if flat bulk solvent model is used;
- different scattering factor tables
Hi,
Just to explaine: it is assumed that if you came from using phenix
AutoSol and AutoBuild then for refinement you use phenix.refine
(refinement program in PHENIX). phenix.refine uses 1 for TEST and 0 for
WORK (similar to CNS). It is not clear to me at all why you need to do
the swap.
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