Dear Eleanor,
Phenix reads and writes TLS records, both PDB and mmCIF format. It can also
read (but not write) TLS records in REFMAC and BUSTER format.
In ATOM records Phenix outputs complete B factors, which includes both
individual and TLS components (this is why they have ANISOU).
Phenix won'
Dear Gerard,
a possible programmatic approach may be a loop over all (model, map,
resolution) or (model, map, half_map1, half_map2, resolution) from PDB/EMDB
and calling
phenix.validation_cryoem model. emdb_.map resolution=value
> .log
or
phenix.validation_cryoem model. emdb_.map
half
Hi Matthias,
did you use correct model parameterization and optimal refinement strategy
for the resolution? Such as:
- Add H atoms;
- Refine all but H atoms with anisotropic ADPs;
- Model alternative conformations (that one'd expect many at this
resolution);
- Add solvent (water, crystallization c
Dear Colleagues,
please make a note of upcoming Phenix workshop focusing on crystallography
and Cryo-EM tools for structure solution, August 2nd 2020 in San Diego,
California. This is a day-long satellite workshop prior to ACA meeting. For
schedule and registration see ACA 2020 web site: www.acame
Interesting conversation! I see the 2017 paper is on bioRxiv. I wonder if
it ever made into a peer reviewed journal (couldn't find quickly)?
@Tim Gruene : have a look at d_model in
https://www.ncbi.nlm.nih.gov/pubmed/30198894 which is sort of along similar
lines of what you are hinting here.
Pavel
Clearly, it is a good idea to keep hydrogens:
http://phenix-online.org/presentations/hydrogens.pdf
Not sure why this keeps coming up as a topic given how much it was said
about it in the past, all the MolProbity arguments, etc..
Issue of missing side chains and loops is tricker indeed.
Pavel
O
Randy Read's paper in latest Acta D:
Measuring and using information gained by observing diffraction data
http://journals.iucr.org/d/issues/2020/03/00/ba5308/index.html
seems very relevant to this discussion!
Pavel
On Fri, Mar 6, 2020 at 8:44 AM James Holton wrote:
> Thank you Kay,
>
> Very
phenix.match_maps can overlay model B and map B onto model A and map A. A
and B can be any symmetry and box (unit cell) dimensions. Model A and map A
stay in its original frame of reference. Let me know should you have
questions.
Pavel
On Mon, May 11, 2020 at 3:19 PM Murpholino Peligro
wrote:
>
Hi Bernhard,
"Like comparing these map regions, excluding
intrusion of a solvent mask, etc.":
You didn't say much about the context.. So I'd say Polder map approach
comes to mind first based on these keywords. Next is "map comparison" (
https://doi.org/10.1107/S1399004714016289).
If none of the
Hi Vito,
many of us have probably experienced that, in the
> diffraction of protein ligands containing heavy atoms (cisPt, I3C, etc),
> the overwhelming electron density of the metal can totally flatten that of
> the light atoms around (or rather make it look insignificant).
>
I wo
Hi Cristina,
in Phenix it is:
Refinement settings -> Select Atoms -> Custom Geometry Restraints : you can
define bonds, angles, torsions, planes, etc...
Pavel
On Thu, Jul 2, 2020 at 8:11 AM Cristina Machon wrote:
> Dear all,
>
> I am writing regarding a problem we are facing with the refineme
Hi All,
there was a bug at some point that could potentially lead to this.
This all should be fixed in current Phenix nightly builds:
http://phenix-online.org/download/nightly_builds.cgi
If not, get back to us (phenixbb or Phenix help lists or reply directly to
me).
Pavel
On Mon, Oct 19, 2020
Hi Sam,
> Hi, the question may be a bit weird, but how do you define 'over-fitting'
> in the context of structure refinement? From users' perspective the
> practical aspect is to 'fit' the model into the density. So there comes
> this question from our juniors: fit is fit, how is a model over-fit
Hi Folmer,
I would choose to not do the real space refinement in phenix.refine during
> the last rounds of refinement of a model, when sidechain positions are
> essentially correct.
>
by design it is supposed to place and fit side chains as good as possible,
satisfying both map fit and geometry c
Hi Christian,
you can do it in Phenix PDBTools: GUI->Model Tools-> load files then
Options->Other modifications look for Rename chain ID.
Pavel
On Mon, Dec 7, 2020 at 9:49 AM Christian GALICIA <
christian.galicia.diaz.sant...@vub.be> wrote:
> Hello,
> I'm trying to swap the chain IDs of a struc
> Point #2 would hold if we routinely let our refinements run to
> convergence; seems common though to run "10 cycles" or "50 cycles" instead
> and draw conclusions from the behaviour of the metrics. Are the conclusions
> really much different from the comparison-at-convergence you advocate?
> Wh
Hi Yuri,
a possible option:
phenix.model_vs_data model.pdb data.mtz will do it. Look for lines like this
in the output:
ADP (min,max,mean):
all (136 atoms): 4.497.6 25.3
side chains (48 atoms): 4.996.8 21.0
main chains (64 atoms): 4.497
> You have those tools at hand, but you need to script them or type whatever
> you like.
> The RSR fit e.g. can be found in MAPMAN with the command RS_fit-real-space
> blabla
> All plots generated on the EDS server site should have a USF tool which
> produces some numbers which you then convert via
Hi,
did you use refinement strategy suitable for low (3.5A) resolution
(secondary structure restraints, Ramachandran plot restraints, proper ADP
parameterization, SA, etc etc...)?
If you send me the data and model files off-list I will have a look.
Pavel
On Wed, Sep 14, 2011 at 7:34 AM, Md
Hi Pete,
the rationale is: at that low resolution the density map and traditional set
of restraints are not enough to preserve secondary structure elements during
refinement. For example, if you start with a model having good secondary
structure elements, they will be distorted after refinement ag
Hi Zhiyi,
I am trying to refine a structure with two domains. The electron
> density of one domain is reasonable, but that of the other domain is
> poor. So, I am wondering whether the refinement by Phenix or Refmac
> can be done locally with two parts, the first domain is refined with
> normal r
Yuri,
note, the R-factors in case of twinning are not directly comparable.
Pavel
On Thu, Sep 29, 2011 at 7:25 PM, Yuri Pompeu wrote:
> after 1 round of refmac rigid body and restrained refinement with twin law
> (estimated alpha 0.47)
> I am looking at 0.25 -0.29 Rwork Rfree and overall FOM 0.
Hi,
On Tue, Oct 4, 2011 at 1:55 PM, Brigitte Ziervogel wrote:
> (...)
> Any suggestions or ideas of better ways to score ligand fits are
> appreciated, thanks.
>
another alternative:
phenix.model_vs_data model.pdb data.mtz comprehensive=true
will list triplet of numbers: {map CC, 2mFo-DFc val
On Tue, Oct 11, 2011 at 10:34 AM, Ed Pozharski wrote:
>
> "expected value of unknown structure factors for missing reflections are
> better approximated using DFc than with 0 values."
>
better, but not always. What about say 80% or so complete dataset? Filling
in 20% of Fcalc (or DFcalc or bin-av
Hi Ed,
On Tue, Oct 11, 2011 at 11:47 AM, Ed Pozharski wrote:
> On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
> > better, but not always. What about say 80% or so complete dataset?
> > Filling in 20% of Fcalc (or DFcalc or bin-averaged or else - it
> > doesn'
Do you have a real life example of Fobs=0 being better?
Hopefully, there will be a paper some time soon discussing all this - we
work on this right now.
> You make it
> sound as if it's 50/50 situation.
>
No (sorry if what I wrote sounded that misleading).
Pavel
Hello,
2011/10/12 Xiaopeng Hu
> I made a simple script for this, perhaps you can edit it for your case.
> Just save it as baverage.sh, then run it as ./baverage.sh your.pdb.
>
Here is another option:
phenix.pdbtools model_statistics=true model.pdb
or
phenix.model_vs_data model.pdb data.hkl
w
This may answer some of your questions or at least give pointers:
Grosse-Kunstleve RW, Adams PD:
On the handling of atomic anisotropic displacement parameters.
Journal of Applied Crystallography 2002, 35, 477-480.
http://cci.lbl.gov/~rwgk/my_papers/iucr/ks0128_reprint.pdf
Pavel
On Wed, Oct 12,
Hi,
yes, shifts depend on resolution indeed. See pages 75-77 here:
http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf
Pavel
On Fri, Oct 14, 2011 at 7:34 PM, Ed Pozharski wrote:
> On Fri, 2011-10-14 at 23:41 +0100, Phil Evans wrote:
> > I just tried refining a "finis
Hi,
On Sun, Oct 16, 2011 at 7:48 PM, Ed Pozharski wrote:
> On Sat, 2011-10-15 at 11:48 +0300, Nicholas M Glykos wrote:
> > > > For structures with a small number of reflections, the
> > statistical
> > > > noise in the 5% sets can be very significant indeed. We have seen
> > > > differences betwe
Yes, Rsleep seems to be just the right thing to use for this:
Separating model optimization and model validation in statistical
cross-validation as applied to crystallography
G. J. Kleywegt
Acta Cryst. (2007). D63, 939-940
Practically, it would mean that we split 10% of test reflections into 5%
u
Hi,
This is why the right way to distribute *nix software is to distribute
> software itself and ask the end-user to get all the dependencies (not
> that hard these days).
it is a wonderful idea, apart from two tiny nuances: 1) many have no idea
about what the command line is, and 2) asking us
Ivan,
it might be helpful/instructive to have a look at this review on the
subject you seem to be actively interested:
Acta Cryst. (2004). A60, 19-32.
and some basic educational illustrations here:
http://phenix-online.org/newsletter/CCN_2011_01.pdf
(see "Electron density illustrations" articl
Continuing on the subject, as far as I know there are at least
three flavors of form-factors currently used in refinement programs:
"4 gaussian plus const":
International Tables for Crystallography (1992)
"5 gaussian plus const":
D. Waasmaier & A. Kirfel. Acta Cryst. (1995). A51, 416-431. "New an
Hi Kiran,
Yes! Indeed, Refmac (in Buccaneer) automatically calculates twin operators
> and fractions.
> But these values are slightly different from those calculated from Xtriage
> (Though twin operators are equivalent twin fractions is different).
>
phenix.xtriage estimates the twin frac
Hi Aaron,
here is what I would do:
- create 10-20 independent test sets containing 5% of reflections (make
sure lattice symmetry is taken into account - Phenix does it by default);
- solve and refine structure for each of the data set (make sure you use
such a refinement strategy so you don't get
Hi Yuri,
On Fri, Nov 25, 2011 at 9:05 PM, Yuri Pompeu wrote:
>
> Is there a utility for calculating anomalous maps, or is it simply an
> option in the refinement program?
>
phenix.refine, for example, always outputs Fourier map coefficients for
anomalous difference map if input input data contai
Christopher,
if you send me the input PDB and data files (off-list, of course) I will
have a close look and then explain what exactly happens and why. I also
promise to post the summary on this mailing list (without revealing the
identity of your structure, of course).
If you send me the command y
Hi Christopher,
just a remark: for phenix.refine it does not matter where the flags come
from and what is the "test"/"work" value since it automatically scores the
values in the flags array and guesses the right one. Still one can imagine
corner case, so it's good to be careful -:)
Pavel
On Fri,
does not
require changing habits.
Pavel
On Fri, Dec 9, 2011 at 6:34 AM, Ed Pozharski wrote:
> On Fri, 2011-12-09 at 05:45 -0800, Pavel Afonine wrote:
> > just a remark: for phenix.refine it does not matter where the flags
> > come from and what is the "test"/"work
Hi Stefan,
1)
just out of curiosity I wrote a tiny script using CCTBX that estimates
solvent content via bulk-solvent mask, and quickly run this script for all
PDB structures for which I could re-calculate the R-work within 5% from
published value. Also, this script extracted the solvent content v
Hi Debasish,
On Wed, Dec 14, 2011 at 9:23 AM, Debasish Chattopadhyay wrote:
> How about plotting the solvent content along with resolution limits of the
> structures?
>
here it is:
Resolution Number of Solvent % (mean/min/max) Solvent % (mean/min/max)
range structures from remarks
On Fri, Jan 6, 2012 at 10:00 AM, Pete Meyer wrote:
>
> Thanks for pointing this out to me - I'll have to check out the details of
> how phenix handles it, and give it a try.
>
Details can be found here:
http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf
(page 61 and a
Francis,
One common response is "try a number of different B-factor refinement
> protocols, use Rfree as a guide to determine which one is appropriate".
I recognize my advice along those lines above -:)
Although now I would say (assuming phenix.refine): "Try individual
ADP refinement first, and
>
> Or just print both Rfactors...?
This is what phenix.model_vs_data does, leaving for you to decide if the
difference is "significant":
http://phenix-online.org/documentation/model_vs_data.htm
Pavel
Yep, phenix.refine also always creates one reflection file that contains
map coefficients. In fact, it contains all together:
- original Iobs (or Fobs - whatever the user specified);
- Fobs used in refinement;
- Fmodel (the total model structure factor including all scales,
bulk-solvent etc), so on
One more to add to Ed's list:
highly accurate ultra-high resolution structures may allow calculation of
electrostatic potential around protein ligand binding site. There are
plenty of reference...
Pavel
On Tue, Jan 10, 2012 at 11:04 AM, Ed Pozharski wrote:
> On Tue, 2012-01-10 at 18:30 +, T
Tony,
Who needs hydrogens?
>
may be you need to read this (for example):
http://www.phenix-online.org/papers/dz5209_reprint.pdf
?
Pavel
Hi Yuri,
for example, you can use cctbx for this. Using cctbx you can do somethings
as simple as b-factor statistics (see example below) or as complex as write
your own refinement program (phenix.refine can serve as an example).
Example: compute min/max/mean B-factor for all atoms and for CA atom
Hi Bernhard,
I just calculated k_sol and B_sol for all PDB entries that
- have reflection data available,
- I could re-compute the R-factor within 5%, and
- R-work<30%
using a simple cctbx script. Here is what I get:
Distribution of k_sol:
0.000 - 0.060 : 27
0.060 -
Dialing,
After we refine the structure of the protein to satisfactory with
> satisfactory Rwork and Rfree, we pick water by phenix refine, and I find Rfree
> always increases slightly after the water picking refinment.
>
> Do you have nay idea to solve this problem or any comment?
>
Just a remin
Hi Bashir,
the R-factors seem to be hight given the resolution. I don't know what you
have tried so far and what you haven't, and the list of things to try is
too long. It might be more efficient If you send me the data and model
(off-list), so I have a quick look and may be suggest something.
Pa
Hi Dialing,
Will you please tell me a server of software which can draw a curve for the
> B factor of the atoms in a protein PDB file from the first residue to the
> residue?Or a server or software by which we can easily order the B factors
> of the atoms in the PDB file according to the B factor
Hi Pete,
yes, I wrote one a while ago:
phenix.reciprocal_space_arrays
https://www.phenix-online.org/documentation/reciprocal_space_arrays.htm
it does exactly what you asked for and much much more.
Let me know if you have questions.
Pavel
On Fri, Feb 24, 2012 at 9:28 AM, Pete Meyer wrote:
>
Hi Wolfram,
a few points:
- R-factors in twin refinement vs non-twin refinement are not directly
comparable:
G.N. Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261
http://www.science.az/acm/V10,%20N2,%202011,%20pdf/250-261.pdf
- did you make sure free-R flags assigned "having twinnin
Hi,
At 3.3A I would recommend trying a TLS model _instead_ of refining
> individual B factors.
may be it is implementation/software/mindset dependent, but in
phenix.refine refining TLS+individual ADP or simply individual ADP(*) is a
better option most of the time at low resolution.
For details
Thanks Ian,
I'm aware of this document. Personally I prefer "ADP = Atomic Displacement
Parameters" over anything ele, because, given that Atomic Displacement
Parameters can be parameterized in many different ways, it makes it easier
to operate with such terms like:
- isotropic Atomic Displacement
Hi,
On Mon, Mar 5, 2012 at 11:52 AM, Matthew Franklin wrote:
> Adding the riding hydrogens generally gives you some improvement in R
> factors even with a good quality (i.e. stereochemically correct) model.
>
and here are the results of more or less systematic test that prove this:
see "On cont
t;
> [1] "On contribution of hydrogen atoms to X-ray scattering"
> http://www.phenix-online.org/newsletter/
> [2] http://shelx.uni-ac.gwdg.de/SHELX/shelx.pdf
>
> On 03/05/2012 09:14 PM, Pavel Afonine wrote:
> > Hi,
> >
> > On Mon, Mar 5, 2012 at 11:52 AM, Ma
Hi Jürgen,
in phenix.refine I would do:
phenix.refine [PDB] [mtz] twin_law="h,-k,-l" main.ncs=true ncs.type=torsion
(or equivalent using the GUI).
Note, "ncs.type=torsion" will use the new NCS handling machinery that takes
care of NCS automatically with no need the user to provide definitions f
Given a data set (Fobs or Iobs) and atomic model it is not trivial at all
to tell whether they are real or fabricated.
I looked into this problem for quite some time at some point, and developed
my set of criteria that thoroughly attempt to distinguish between fake and
real, but they can only be i
Yep,
phenix.fake_f_obs
is available for use since April 22, 2011, but I made it such that it will
only do "the right thing" in experienced hands -;) and I wouldn't teach it
unless you sign a disclaimer -:)
It's good for developers though who want to do fully controllable numeric
experiments to t
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
stand 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,
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 wrote:
> Dear all,
> Is ligands and metals could also be NCS restrained du
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
g
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 wrote:
> On Sat, May 5, 2012 at 2:23 PM, Pavel Afonine wrote:
> > may be I'm missing s
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 contri
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 wrote:
> Hi all,
> I am having trouble generating a pdb and
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... embar
Hi Ethan,
So far as I know, there is still no provision in phenix for reading in
existing TLS parameters. It always wants to regenerate them for itself.
You are right, given suggested optimal selection for TLS groups
phenix.refine is capcabale to do the rest as good as it can. There is
sim
Hi Tim,
following this discussion, I was wondering how much sense it makes to use
TLS domains and experimental phases at the same time.
I guess both things are completely irrelevant. With using experimental
phases you bring in more data. And with using TLS you simply use a more
adequate mo
Hi Ethan,
yes, I must be missing something indeed...
You are missing the point.
What if you want to calculate Fcalc based on an existing model?
What if you want to explore application of the _same_ TLS model
to different sets of starting coordinates?
Yes, if I do need to calculate Fcalc bas
Hi Ed,
may be "not always" (in a sense that mask-based one sometimes may leave a
negative footprint in areas where there is no solvent), but I still want to
remind this paper where there is some discussion about exponential vs
mask-based bulk solvent model:
http://journals.iucr.org/d/issues/2002/
Hi Ethan,
Do you know of any published or unpublished results that compare
> the R factors achieved by Babinet treatment with those obtained from the
> state-of-the-art mask models?
>
I afraid I don't know about published ones, and I see Sacha replied for
unpublished one.
I could spend a few h
Hi Tim,
...but I hope this answers the question:
Babinet's vs. the flat model? Use them together! ;)
thanks a lot for your reply.
Could you please explain the *physical* meaning of using both models
together? Flat (mask-based) bulk solvent model has clear physical meaning
and its adv
Hi Dirk,
may be too late... but (may be) better later than never -:)
Here is the working example of how you can do it. Note, the procedure just
builds the dummy atoms in spheres with user-defined centers and radia. You
can specify as many spheres as you wish. Dummy atoms clashing with model
atoms
Hi Dirk,
yes, the apparently larger radius of convergence in real space refinement
> impresses me, too. Therefore, I usually do local real space refinement after
> manually correcting errors, either with Moloc at lower resolution or with
> Coot at higher resolution, prior to reciprocal space refi
Hi Maiclo,
> After I make Molecular replacement with Phaser and combine the resulting
> mtz and the anomalous .mtz using CAD, I obtain an anomalous map which shows
> me good anomalous signal. I'm displaying this map in coot by choosing in the
> expert mode the labels DANO and PHWT (or PHIC toget
Hi Kenneth,
...1.2A resolution... refinement of individual parameters for a hydrogen
atom... Hm.. Are you refining against neutron diffraction data?
Anyways, to answer your question: technically yes, you can refine individual
parameters of any selected atom(s) against X-ray or neutron data (or bo
Hi Mischa,
We have a similar case. There is difference density, but only for some of
> the hydrogens (mostly methyl groups on Leu, Ile, Val, Ala). How does one
> decide which hydrogens to include in explicit refinement? The case in
> question has 0.99Å data (diffraction is significantly better, b
Hi,
for each PDB file run:
phenix.pdb_interpretation model_1.pdb ligand.cif
phenix.pdb_interpretation model_2.pdb ligand.cif
...
phenix.pdb_interpretation model_N.pdb ligand.cif
and it will result in a buch of output files
model_1.pdb.geo
model_2.pdb.geo
...
model_N.pdb.geo
where each *.geo fil
Hi Chen,
first off, I suggest posting PHENIX related question on PHENIX mailing list:
http://www.phenix-online.org/
The command:
phenix.refine mode.pdb data.mtz main.ncs=true
will determine and use NCS automatically. Note, that if you use
"strategy=rigid_body+individual_adp" the NCS restraints
> > No disorder is involved.
> >
> > The occupancy of an (fully occupied) atom on an n-fold rotation axis is
> 1/n
> > If a two-fold, 1/2
> > If a three-fold, 1/3
> >
> > When you sum over all the atoms in the unit cell, application of the
> symmetry operations to atoms lying on the rotation axis g
Hi Charlie,
hope there are simpler solutions. Meanwhile, here is the universal one -:) :
step 1:
save the lines below (between *) in a file called split_pdb.py:
*
import os
import iotbx.pdb
import sys
def run(args):
pdb_inp = iotbx.pdb.input(file_name = args[0])
hierarchy = pdb_inp
Hi Afshan,
you didn't mention the resolution, which is essential.
For ultra-high resolution structures the average B may be well less than 10,
and less than ~4-5 is the condition to see the bonding density (see
aldose reductase, 1uso, for instance). While a structure at 3.5A resolution
may have B
Hi Bill,
if you put a water oxygen in place where a heavier atom is, then water
oxygen's B-factor will refine to a value close to zero. This is the feature
that we currently use as one of many criteria to develop automatic
identification and building of metals.
Overall Wilson B-factor of 0.6A**2
Here is another set of relavant papers and instructive pictures:
1) CCP4 Newsletter
http://www.ccp4.ac.uk/newsletters/newsletter42/content.html
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev
2) Some Facts About Maps (pages 30, 32, 33):
http://www.
Hi,
creative language, you say... ha-ha. Go through this:
A number of publications define ultrahigh or subatomic resolution in the
range of 1.0–0.5A (Lecomte et al., 2008; Petrova et al., 2006; Howard et
al., 2004; Guillot et al., 2008; Housset et al., 2000).
Right? When you see ultra-high resolu
HI James,
Obviously, this depends a bit on which refinement program you use, and I am
> not familiar with all of them. However, I have had some conversations with
> Garib "refmac" Murshudov and Pavel "phenix.refine" Afonine about this, and
> the shocking answer appears to be "no".
>
wow, I've g
Bulk-solvent mask calculation (if that's what you want) is available in
CCTBX library, and it can be easily used. Let me know if interested and we
can discuss it off-list. I can send you some ten-line Python script-example
that computes it given a PDB file.
Pavel.
On Wed, Jan 12, 2011 at 10:00 PM
Hi Jon,
a partial answer:
> 2) Under Refinement, Refinement Statistics section: Number unique
> reflections (all)
>
> I looked in my log files for HKL2000, PHASER, and PHENIX but am confused on
> where to find the required values above. I tried searching the logs for the
> mmCIF items but that
Another option:
phenix.maps can create any number and almost any kind of X-plor formatted
map around selected atoms (and within a certain distance, which is a
user-defined parameter). Then all you need is load this map and model into
Pymol and - voila - you have what you asked for. This can be don
Hi Hui,
(sorry for non-ccp4 recipe)
IF I understand correctly what you want to do, then I guess you can achieve
this using Map Superposition:
http://www.phenix-online.org/documentation/superpose_maps.htm
and/or Structure Comparison tools in PHENIX:
http://www.phenix-online.org/documentation/stru
Hi Todd,
in addition to all other suggestions, here is some basic sanity check that
you can do in no time:
- how the R-factor vs Resolution plot looks like?
- did the bulk-solvent correction was done right (what are k_sol and B_sol
values)?
- plot the scatterer graph Fobs vs Fmodel and see if t
Hi Leila,
it was 10 years ago when I looked at the maps this way, and at that time I
used the program called CAN to do this (see below). It worked really well.
If you are lucky it might still be available by request from the authors.
Pavel.
1. Vernoslova, E.A., Lunin, V.Yu. (1993) "The FROG PC s
Hi Jochen,
phenix.tls command is designed to do this and similar manipulations.
Specifically, the command:
phenix.tls model.pdb combine_tls=true
will do what you want.
Pavel.
On Thu, Feb 3, 2011 at 12:33 AM, Jochen Kuper <
jochen.ku...@virchow.uni-wuerzburg.de> wrote:
> Dear All,
>
>
> sorry
Hi Lisa,
> Can some one show me how to install phenix (...)?
>
how to install phenix:
http://www.phenix-online.org/
I afraid you will need to have a look at this page before you know how to
get and install it (hint#1: click on Full Documentation link; hint#2: the
link is located at the upper-
Hi,
make sure you have Coot installed. Coot is not part of Phenix. This may be
useful:
http://www.phenix-online.org/download/other.html
http://www.phenix-online.org/documentation/coot.htm
Pavel.
On Mon, Feb 7, 2011 at 4:52 PM, LISA wrote:
> Hi all,
> I installed phenix1.7 on my mac osx 10.6.
Hi Yury,
- make sure you correctly generated free-R flags, so there is no cross-talk
between test/work sets. Illustration: see page number 123 here:
http://cci.lbl.gov/~afonine/for_ccp4/PavelAfonine_PHENIX.pdf
- compare regular vs missing-fobs-filled maps. See pages188-190 here:
http://cci.lbl.go
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