Hi Almudena,
I am refining my structure with Phenix refine and I get the following error
> message just before starting:
>
> "no atom selected, "name CA ad chain A and resname CA and resseq 1".
>
this is due to atom selection syntax error that you provided:
after CA must be and not ad .
> I
ob
wrote:
> Right about the 1000 in that case, but also Rfree with 5% would be
> statistically poor. I guess one would be stuck in that case.
>
>
>
> JPK
>
>
>
> *From:* Pavel Afonine [mailto:pafon...@gmail.com]
> *Sent:* Friday, November 21, 2014 11:16 AM
>
> *
8:09 AM, Keller, Jacob
wrote:
> Agree with all of this—but how does it reflect on the original question
> of whether to use a percent or an absolute number?
>
>
>
> JPK
>
>
>
> *From:* Pavel Afonine [mailto:pafon...@gmail.com]
> *Sent:* Friday, November 21, 20
Hello,
choice of the size of free (or test, whatever you like to call them)
reflections is important for three different purposes:
- estimation of parameters for ML target for refinement;
- map calculation (coefficients m&D in 2mFo-DFc or mFo-DFc map are
calculated using test reflections);
- vali
Mike,
you can have a look here (from page 52 and on):
http://phenix-online.org/presentations/fem_06MAY2014.pdf
There it is shown that map kurtosis can be used as an optimization
criterion for choosing the best sharpening B.
Pavel
On Mon, Nov 17, 2014 at 5:01 PM, Mike Lawrence wrote:
> Dear
This conversation makes me more and more certain that water update
(add/remove/refine water) done as part of (a default) refinement run is a
good idea -:)
Pavel
On Wed, Oct 29, 2014 at 5:08 AM, luzuok wrote:
> Dear all,
> I found that there are some water molecules in my pdb that share the
Sudipta,
keep in mind that programs that detect twinning (like Xtriage) estimate
twin fraction, while refinement programs (like Refmac, phenix.refine and
others) actually refine twin fraction. This is why a discrepancy between
estimated twin fraction and refined one should not terribly surprise yo
Hi Gajanan,
I am using Qhelix, for the calculation of the orientation angles between
> helices. when am running the demo its working,but when am uploading my pdb
> file it is not working, can someone help me to resolve the problem.
can't help with Qhelix, but...
> suggest me the other softwar
See also:
page 141 in "The Bijvoet-Difference Fourier Synthesis",
Jeffrey Roach, METHODS IN ENZYMOLOGY, VOL. 374
Pavel
On Fri, Aug 29, 2014 at 12:17 PM, Ronald E Stenkamp <
stenk...@u.washington.edu> wrote:
> I think the answer is in this paper: LOW-RESOLUTION ELECTRON-DENSITY AND
> ANOMALOUS-
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 wrote:
> Dear CCP4BB members,
>
> I wonder if there is a CNS library file for electron scattering factors.
> Many thanks!
>
> Minglei
>
>
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 corre
> 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 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 exampl
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 whether
mage and Stability Centre
> Science Park Road
> University of Sussex
> Falmer, Brighton, BN1 9RQ
> - - - - - - - - - - - - - - - - - -
> email: antony.oli...@sussex.ac.uk
>
> tel (office): +44 (0)1273 678349
> tel (lab): +44 (0)1273 677512
>
> http://www.sussex.ac.
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
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 R-fact
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 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
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 from
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 G
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".
Bul
> 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 an
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 odditi
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. Shoul
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 th
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
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 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 Rfr
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
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 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
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 wrote:
> On Fri, Apr 4, 2014 at 1:57 AM, Tim Gruene wrote:
>
>> A more up-to-date reas
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, b
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 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, Mar
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
Chris,
On Sun, Feb 23, 2014 at 2:52 PM, Chris Fage 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 phenix.refin
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
0.
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 mode
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 valid
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 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 a
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 th
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 wrote:
> Dear all,
>
> I've been lecturing
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 wrote:
> Hi All,
>
> I have a structure at 2.45A which has been well refined. However, sinc
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.. etc...
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 show
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
ch
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 nu
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
d_mi
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 26
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
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
wrote:
> Greetings,
>
> We have bee
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 ugl
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
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
Hi James,
On Sat, Jul 6, 2013 at 6:31 PM, James Holton 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 emotionall
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
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 ksol&Bsol simultaneously may be
tricky, or occupancy + individual B-factor + TLS, or ask multipolar
refinement folk about whole slew of magi
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 h
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 depos
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 wrote:
> In my opinion pdb must perform more strict chec
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.
Pavel
P.S.: you are not alone having such R-factors
On Fri, Apr 12, 2013 at 9:50 AM, Jan van Agthoven wrote:
>
>> Could this be due to an excessive low R
>> factor that phenix.refine has generated: R=17.9 and Rfree=23.3 at a
>> resolution of 2.85 A?
>
>
Histogram of Rwork for models in PDB at resolutio
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
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
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
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
> alrea
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 1.
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 PM
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 <
muhammad.bashir.k...@univie.ac.a
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
wrote:
> Hi Bhat,
>
> You can
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 wo
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 occupie
Just to add one more vote: can't agree more, Ed. I remember those days
working on implementing ultra-high resolution refinement in phenix.refine
and repeatedly heard remarks like "hey, I can figure out if ligand's there
at 2A a few refinement cycles away from my MR solution, so why bother with
0.75
le will be surrounded
> by a huge number of other features when you contour at 0.18 e/A^3
> and by very few in the last map, but isn't that as it should be?
> The map is supposed to be flatter at the end.
>
> Dale Tronrud
>
> On 11/28/12 12:30, Pavel Afonine wrote:
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 wrote:
> You stated that the map is set to 3 sigma, bu
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:
http://cci.lbl.gov/public
Dear Bernhard, dear John,
On 11/20/12 6:10 AM, Bernhard Rupp wrote:
As already mentioned by jrh, I again want to impress that B-factor and
occupancy are in principle two entirely different parameters.
They may appear as achieving the same thing upon refinement at the
resolution we deal with in
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 (smear
+1-410-955-3655
> http://lupo.jhsph.edu
>
> On Nov 17, 2012, at 14:26, "Pavel Afonine" 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
>
>
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 1
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 l
47.9421
> > 10 3.54414 3.54415 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 numbe
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 forma-factor
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) Central
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
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 so
Hi,
I'm not sure I understand why you can't calculate the maps using a tool of
your preference if model and data files are available in PDB? Am I missing
something?
I, for example, just typed
phenix.fetch_pdb 3tvn --maps
and got mFo-DFc and 2mFo-DFc maps in about 20 seconds. In fact it took me
m
Hi,
there is Phenix mailing list for questions like this (
http://phenix-online.org/).
This should answer your question:
http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf
Pavel
On Mon, Aug 6, 2012 at 9:07 AM, Scott Foy wrote:
> Hello everyone,
>
> I am having a difficult time
(which are
> redundant anyway), and uses the correct xHM symbols (such as R32:r).
> It also accepts the PDB-only symbols H3 & H32.
>
> Well done Pavel - Like + :).
>
> Cheers
>
> -- Ian
>
> On 2 August 2012 18:06, Pavel Afonine wrote:
> > Hi,
> >
> >
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 wrote:
> Dear ccp4
>
> I ask a very fundamental question because I have not had formal training
> in this and I would like to understand.
>
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 1:
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 ind
What happens if you do a round of refinement in phenix.refine after you
have done the mutations? Note: Phenix Autobuild is a tool to build your
model, not refine it (though it does some refinement internally but may not
be as fine tuned as your data/model may require).
Pavel
On Wed, Jul 18, 2012
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 arr
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
Hendricks
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 th
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>
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