> I am new to building into an EM map, and I wonder if I could get a
> recommendation for some standard routine for programs to use. I tried "find
> helixes and strands" tool in phenix, it found some secondary structure
> elements, however, it seems that there is more that could be done
> automatic
It's amusing how a seemingly innocent ad for a new tool can ignite a rather
prickly thread.. I see two keys to this.
Firstly, for those who are not familiar with the issue the add could be
better structured by providing a clearer statement of what the problem is
or why it is important (with approp
Perhaps this can be automated:
https://www.phenix-online.org/papers/wd5073_reprint.pdf
Software doesn't get tired or bored, and thus potentially can try more and
produce more plausible interretations. Then one can hire a number of people
of various expertise to choose "best" result according to t
Hi Radhika,
R-factor value is almost useless unless you know the resolution (which you
did not tell us): 26% is ok for 3A resolution and is nonsense for 1A, for
example. The Rfree-Rwork gap is obviously large, suggesting sub-optimal
refinement strategy. Try optimizing weights, let program update
(
See Table 1 and corresponding discussion here:
http://journals.iucr.org/d/issues/2013/04/00/dz5273/dz5273.pdf
Hope that hints you the answer. If not get back to me with questions.
All the best,
Pavel
On Mon, Nov 6, 2017 at 7:18 PM, Eze Chivi wrote:
> Hi, my PDB file lists only 4 resolution b
If by "it was truncated at 5A for clarity" you really mean you truncated
all low-resolution data from 5A and lower then I am not surprised you see
funny densities all over or don't see density where it is expected. Why?
Consult a textbook for the answer.
All the best,
Pavel
On Fri, Nov 3, 2017 at
Johan,
core functionality described in that paper is implemented in cctbx. Re the
stand-alone program -- I'm cc'ing to the author.
Pavel
On Thu, Oct 26, 2017 at 8:39 AM, Hattne, Johan
wrote:
> Dear all;
>
> Would anybody know where I can find efresol (as detailed in
> http://dx.doi.org/10.1107
A round of refinement with simulated annealing followed by minimization
should address your concern.
Pavel
On Wed, Oct 11, 2017 at 4:48 PM, Karsten Dreifus
wrote:
> Dear all,
> I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu.
> Molrep (template with 70 % seq identity) finds
And I should add this works just great! (given we are on the same page
defining 'great').
I used this for Cryo-EM model challenge; Nigel added this functionality at
that time to make this possible.
Pavel
On Wed, Oct 11, 2017 at 2:17 AM, Nigel Moriarty wrote:
> Since you are using phenix.real_s
Or using cctbx:
from scitbx.array_family import flex
import iotbx.pdb
def run():
xyz_1 = iotbx.pdb.input(file_name="file_1.pdb").atoms().extract_xyz()
xyz_2 = iotbx.pdb.input(file_name="file_2.pdb").atoms().extract_xyz()
print flex.mean(flex.sqrt((xyz_1 - xyz_2).dot()))
if (__name__ =
Hi,
also keep in mind that the total model structure factor used in refinement
and anywhere where model-to-data agreement needs to be evaluated (such as
maps or R factors) is:
Fmodel = ktotal * (Fcalc_atoms + F_bulk_solvent + F_something_else)
where ktotal ~ scale * exp(-h*Uoverall*h_transpose)
Hi Ed,
your suggestion makes perfect sense to me, and it's trivial to add an
option to do what you want. This will be available in next Phenix nightly
build (clearly not tomorrow given today's power outage).
Command line: use "write_map_coefficients_only=True" (by default is is
False).
Refinemen
>
> I know space is cheap these days, but is there a reason for Refmac to
> generate all those extra columns in the output mtz file? Refmac (as well
> as phenix.refine and buster-tnt) output mtz file is almost always used for
> only one purpose - look at the map in coot. You only need 4 columns f
Andrew,
phenix.refine may not use reflection-outliers (Read, R. J. (1999). Acta
Cryst. D55, 1759–1764.). Typically this is just a few reflections. If you
have a good reason to disable this, then use
xray_data.outliers_rejection=false.
P.S.: There is Phenix mailing list for Phenix-related question
Hi Lijun,
it's not a problem if you use mmCIF or PDB with two-letter chain ID (both
supported in Phenix).
Pavel
On Mon, Jul 24, 2017 at 5:09 PM, Lijun Liu wrote:
> Hi: this must be an old problem but I would like to know if there are
> other ideas to make things easier.
>
> I solved a structu
Hi Wei,
thanks for sharing the data (off-list). I did some detective work and yes,
Clemens is correct: what you see is the effect of bulk-solvent. After
adjusting the solvent contribution (mask) in regions occupied by altlocs A
and B the positive density mostly disappears.
Pavel
On Fri, Jul 21,
I agree with Dominika, I can't see major problems with this entry (I also
did some quick refinement and briefly looked at maps). Reported R factors
match re-calculated values using data from PDB, which is good.
Smaller issues I see are:
- no solvent (water) in the model, while density suggests som
Hi Mubinur,
try without "metal restraints" and see if that helps. As others suggested,
make sure 2+ is present in rightmost column of PDB file. The side may be
partially occupied, so refining occupancy of Mg2+ is not a bad idea.
Pavel
On Wed, Jun 14, 2017 at 2:44 PM, Mohammad Rahman
wrote:
> D
Yes, that is what I have been doing. Build one subunit and assemble into
> tetramer before realspace refinement (with "ncs" constraints). I used
> tetramer for refinement because I want the distances between the inter
> subunits interaction partners to be considered. The problem is, whenever I
> wa
Just use P1 and "ncs" constraints. What's the problem? Or just keep entire
map and have only symmetry independent copy to work with until finishes,
then make the whole molecule. For real-space refinement it's totally
irrelevant whether you have whole molecule or 1/Nth of it. So.. it isn't
clear wha
Hi,
2. How do I convert cryoEM map file to MTZ file?
>
While technically you can do it, normally there is absolutely no need to do
it. In cryo-EM the map is your data, not reflection data (structure
factors!). So no need to 'massage' your data (the map) by converting it
into "Fobs" and storing as
Hi,
I'm working on a crystal structure with resolution of 2.2A. At the final
> step, I use different strategies to refine the structure, they are:
> no4: strategy=individual_sites+individual_adp+tls / set_b_iso=20
> results: Rwork/free=0.2052/0.2658 b-factor=11.4/136.8/48(min/max/average)
>
> no
Dear Gerard,
I am sure others
> are certain to propose a cooler name for that very same type of map
> some day ;-) .
>
a free tip: how about DDM (Decarboxylation Detector Map)?
All the best,
Pavel
Also, see figure 4 here:
http://phenix-online.org/papers/dz5209_reprint.pdf
that illustrates the difference.
Pavel
On Fri, Apr 28, 2017 at 10:33 AM, Bernhard Rupp
wrote:
> Dear Fellows of the Bond,
>
>
>
> when validating a QM refined homology model with Molprobity, I noticed
> various 8 sigma d
Note, Molprobity has an option to use longer (neutron) X-H distances.
Pavel
On Fri, Apr 28, 2017 at 11:46 AM, Tristan Croll wrote:
> I believe the reason for the discrepancy here is that MolProbity by
> default places the hydrogens according to the centroid of the electron
> cloud (most relevant
I suspect most (if not all) refinement software now have a nice way to deal
with NCS in refinement locally. Technically, this means you can use NCS
restraints at any resolution and software should be able to be careful and
not wipe out local differences between NCS copies. In phenix.refine this is
Minimizing a red bar may be tricky.. Have you tried to make it less red
(blue or may be green)? Otherwise Rw/Rf~20/25 is just fine at 2.2A
resolution. What exactly your worry is about?
Pavel
On Mon, Apr 24, 2017 at 12:48 AM, Vipul Panchal
wrote:
> Hi all,
>
> I am solving structure of one of the
Except that Procheck is now ages behind the standard, with Molprobity being
the standard. I'm not sure even if Coot uses the latest libraries. Those I
quoted in example below come from latest Molprobity (Phenix that is) and
are the latest.
Pavel
On Fri, Mar 24, 2017 at 2:55 PM, Edward A. Berry
le :
> A 2 ASN:56.93:-60.58:141.19:Favored:General alpha helix
> A 3 ASN:48.44:-119.25:125.15:Favored:General alpha helix
>
> On Fri, Mar 24, 2017 at 1:09 PM, Pavel Afonine wrote:
>
>> Trivial using command line. Example:
>>
>> - get a file from PDB:
>&
Trivial using command line. Example:
- get a file from PDB:
phenix.fetch_pdb 1yjp
- get all phi/psi for all residues:
phenix.ramalyze 1yjp.pdb
residue:score%:phi:psi:evaluation:type
A 2 ASN:56.93:-60.58:141.19:Favored:General
A 3 ASN:48.44:-119.25:125.15:Favored:General
A 4 GLN:16.2
Hi Evette,
(1) best practices in refining against lower resolution data (~4 angstrom)
> to achieve the best model,
>
obtain a model that fits data best under requirement that it has zero
geometry violations (Ramachandran, Cbeta deviations, rotamers, CABLAM,
etc..).
Note, a geometry outlier (R
Normally, these days at least, a model that is result of TLS refinement
contains total B factor in ANISOU records and its TLS component in TLS
records (REMARK3), with Btotal = Btls+Bresidual.
If TLS matrices are available, it's trivial to calculate Btls from TLS
matrices in REMARK3 and subtract it
Hi,
Is there a straight-forward way to estimate the amount of missing electron
> density that a particular protein structure is missing based on the
> difference between Fo and Fc?
>
Any refinement or map calculation software that uses likelihood-based
approach does this routinely. In phenix.refi
gment of "prior art" - a notion that surely
> has to be recognised as existing outside the confines of standard,
> neatly packaged, immediately quotable Acta D publications :-) .
>
>
> With best wishes,
>
> Gerard.
>
> --
> On Thu, Feb 09, 2017 at
Hi Tommi,
Polder map allows you exclude selected region from bulk-solvent filling
Acta Cryst. (2017). D73, 148-157
This explains how to calculate it:
https://www.youtube.com/watch?v=TcTuMJayh5c
Pavel
On Fri, Feb 10, 2017 at 1:37 AM, Kajander, Tommi A <
tommi.kajan...@helsinki.fi> wrote:
> Hi
In addition to excellent Kay's reply..
Also make sure to check refined B factors. Note, if the ligand is not there
then that volume is likely filled with bulk-solvent. Now low occupancy in
combination with very large B factors may approximate bulk-solvent quite
well. The Polder map along with thre
Hi Tim, hi Natesh,
one expression is mathematically, the other one is technically 'more
> correct'.
> I favour the terms poor and good resolution to avoid confusion, or
> explicitly
> list the values.
just out of curiosity.. what's your definition of 'poor' and 'good'
resolutions? I suspect ther
Tools like DSSP and such rely on model geometry to annotate SS elements, so
GIGO applies. For example, something that by eye looks like an obvious
helix but has enough distortions is unlikely to be annotated correctly.
Pavel
On Sun, Jan 29, 2017 at 3:50 AM, Antonio Ariza
wrote:
> I always use DS
Hi,
assuming you've exhausted modeling choices and applied proper refinement
strategies, after all Rree=32% is not unheard of at 2.6A resolution (which
actually may be even worse than 2.6A if data set is not 100% complete).
Have a look at R-factors of models in PDB with data resolution around 2.6A
Hi,
can't you infer this from refined atomic displacement parameters (ADPs;
also knowns as B-factors)?
Or run a 100 or so SA refinement jobs, each starting with a different
random seed. This will generate an ensemble of models with some atoms
occupying more conserved positions than the others.
P
Apply BIOMT:
phenix.pdb.biomt_reconstruction model.pdb
Apply MTRIX:
phenix.pdb.mtrix_reconstruction
GUI: Model Tools -> Model Reconstruction
Pavel
On Wed, Jan 18, 2017 at 2:13 AM, Armando Albert
wrote:
> Dear all,
> Does any one know how to generate a complete biomolecule out of the
> BIOMO
See notice on Phenix mailing list that answers your question.
On Sat, Jan 14, 2017 at 12:58 PM, D Bonsor
wrote:
> Is the phenix website down? Anyone know when it will be back up?
>
Hi Claire,
I afraid you did not provide enough information to answer your question
clearly.
What reflection file you submitted to PDB?
Note, Phenix refinement outputs MTZ file with four blocks of arrays:
- copy of input data (Fobs or Iobs, free-R flags);
- data actually used in refinement. Thi
Hi,
The structure solved with MR; high sequence identity. Disorder occurs
> only when ligand is bound. Model is almost 90 % complete except the
> disordered region. Please let me know if I can deposit structure as it
> is. I took example 1fcc (also low resolution). Seems many residues are
> outsi
Explore this:
http://cci.lbl.gov/cctbx/
Pavel
On Wed, Jan 4, 2017 at 8:20 AM, Aaron Finke wrote:
> Dear CCP4-keteers,
>
> Is there a program that can visualize symmetry operation positions (e.g.
> twofold screws, fourfolds) in protein structures, like CCDC Mercury does
> for small molecules?
>
Hi Peng,
first off, there is Phenix mailing list for Phenix-related questions.
phenix.real_space_refine is Phenix program, not CCP4 so any issues related
to it are best addressed at appropriate mailing list (Phenix mailing list,
that is).
To answer your you question: please send me all inputs (1.
Your PDB file contains atoms that are less than 0.001 A apart. This doesn't
look like a good model. Please consider fixing it first.
Pavel
P.S.: There is Phenix mailing list for Phenix related questions.
On Tue, Jan 3, 2017 at 6:10 AM, Vikram Dalal
wrote:
> Hi all,
>
>
> I have added the water
phenix.elbow --chemical_component GOL
will give you legitimate PDB and CIF files that you can use to model the
map (PDB) and run refinements (CIF).
Alternatively, compare files you get using above command with what you are
using.
Pavel
P.S.: There is Phenix mailing list for Phenix-specific ques
Needless to say, validation is important. This applies to all model
parameters, not just coordinates!
3) Someone better off investing some effort into redoing TLS refinement
protocols... just to stop adding nonsense to the database!
Happy holidays and all the best,
Pavel
On Tue, Dec 20
Hi Dirk,
I want to check the validity of the refinement of anisotropic B-factors vs.
> TLS + isototropic B-factors using the Hamilton R-value ratio test as
> described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol
> 68, pp 468. This test uses the generalised R-factors (assuming
upancies are 1 does phenix still refine them? Anyway, they can
> be explicitly fixed if necessary.
>
> Pedro
>
> Às 03:00 de 20/12/2016, Pavel Afonine escreveu:
>
> Hi Perdo,
>
> technically this should work too with the caveat that non-blanc altid will
> trigger occupancy re
shall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
> On Tue, Dec 20, 2016 at 1:28 PM, Pavel Afonine wrote:
>
>> Hi Andrew,
>>
>> you can define
Hi Perdo,
technically this should work too with the caveat that non-blanc altid will
trigger occupancy refinement for corresponding atoms which may not be
desired.
Pavel
On Mon, Dec 19, 2016 at 12:54 AM, Pedro Matias wrote:
> Hi Andrew,
>
> The simplest way would be to place the "offending" a
Hi Andrew,
you can define a weak bond between clashing atoms which will disable
repulsion. A weak bond should not introduce any bias.
Pavel
On Sun, Dec 18, 2016 at 9:39 PM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.au> wrote:
> Hi all,
>
> I have a structure of a condensing enzyme with s
I find Lothar's comments regarding H and RSRZ excellent! I would think of
it as a pretty much bug report. I hope developers at that end listen. This
goes very well in line with Phoebe's comment earlier today.
Pavel
On Mon, Nov 28, 2016 at 2:51 PM, Dale Tronrud wrote:
> On 11/28/2016 12:52 PM, e
On Mon, Nov 28, 2016 at 10:17 AM, Phoebe A. Rice wrote:
> RSRZ, in my most humble of opinions, seems like one of those statistics
> that is far more useful in theory than reality.
>
Can't agree more!
Pavel
I guess I've just seen two extreme-opposite versions of something
(etiquette, politeness?). Regardless, RM part of Damian's message is a fine
idea -;) Everything else can be filtered out!
On Thu, Nov 24, 2016 at 7:50 PM, Yoder, Marilyn wrote:
> Hi Ting,
>
> What D. Ekiert was so ungraciously s
Hi Ian,
I'm aware that this can be done with Buster (and probably also
> phenix.refine): I'm asking specifically about Refmac.
>
since you mentioned phenix.refine:I confirm it is possible to freeze any
refinable parameters (coordinates, occupancy, xyz and iso/anisotropic B
factors for any selecte
Of course not claiming it the best, but two options I'm aware of are:
phenix.cif_as_mtz file_name.cif
phenix.fetch_pdb 1f8t --mtz
Pavel
On Fri, Nov 4, 2016 at 6:34 PM, Keller, Jacob
wrote:
> Dear crystallographers,
>
>
>
> What program is best used to convert pdb-downloaded sf’s to mtz format
Hi Amit,
you will find the answer on page 47 here:
https://www.phenix-online.org/presentations/latest/pavel_validation.pdf
Pavel
On Sat, Oct 15, 2016 at 7:38 AM, amit sharma <
0d1d6aa5c57b-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi,
>
> What is the average Wilson B-factor for all single crys
> I do not know what the current state is of developing the ML target for
> refining
> against twinned (I, F) data is.
>
Formulas are there, see "Maximum likelihood refinement for twinned
structures" here:
https://www.phenix-online.org/newsletter/CCN_2011_01.pdf
someone just need to code it.
> If you are still worry about your Bfactor, you could try TLS,
>
Or NCS, but SA with MLHL might be better.
(A joke).
I fully agree with Dale in not understanding what the problem is. Perhaps I
have a better chance if you clearly explain what exactly you mean by "is
there any way to better the B factors".
Pavel
On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud
wrote:
>I'm sorry but I don't understand what your
Hi,
since several people mentioned R factors in this conversation I thought I
remind that R-factors are not comparable between refinements using twinning
and not. For example, R-factor decrease after switching to twin refinement
doesn't mean much; you can't use R factor drop as an argument for
con
phenix.simple_ncs_from_pdb will detect NCS from input PDB file, write out
NCS operators (matrices) and atom selections for NCS related groups.
On Fri, Jun 19, 2015 at 6:07 AM, Tobias Beck wrote:
> Dear all,
>
> I have a PDB file that contains NCS in the asymmetric unit, probably point
> group D3
Why not just use CIF files directly? Note, most Phenix tools accept input
model and data in cif format (and can write them back in cif too).
Pavel
On Mon, Jun 15, 2015 at 10:52 AM, StrBio wrote:
> Hi All,
>
> How one can convert pdb-sf.cif file downloaded from PDB to a workable
> format for furt
Hi Kerstin,
"Should I refine a low-resolution dataset 6 A": usually we refine a model
of the crystal structure against measured data set.
Besides, technically you can do this, and I hope other replies will help
you set correct expectations about the realities of the process.
At this resolution y
Hi Xiao,
just calculate it yourself. All you need to do this are model and
reflection data files (and, desirably, free-r flags). For example, in
Phenix this is
phenix.maps model.pdb data.xxx
where xxx can be .sca, .cif, .cns, .hkl or .mtz or any mixture.
Pavel
On Tue, Jun 9, 2015 at 11:11 PM, X
> It seems to me that the "how many is too many" aspect of this
> question, and the various culinary procedures that have been proposed
> as answers, may have obscured another, much more fundamental issue,
> namely: is it really the business of the data processing package to
> assign FreeR fla
> in a data set with just below 800,000 independent reflections I use 1 %
> for freeR which
> is still impressive 8,000. xia2 would have assigned 40,000 for freeR
> at 5 %. I think this is way too much.
>
I think it is relative, isn't it? That is 100 out of 1,000 is the same as
1,000 out of 10,00
Hi Graeme,
free reflections are used for two purposes, at least: cross-validation
(calculation of Rfree) and ML parameters estimation (sigmaa or alpha/beta).
For the latter it is important that each relatively thin resolution bin
(sufficiently thin so that alpha/beta can be considered constants in
Hi,
a few things to keep in mind:
Secondary structure (SS) restraints in refinement programs (at least in
Phenix) depend on correct SS annotation that the program either takes from
the user input or attempts to do automatically.
Quality of automated SS annotation strongly depends on geometrical
that is not to be
> automatically interpreted as a lower level of significance. Omit maps
> are a good idea of course, but do bear in mind the (B/B0)^(-3/2)
> effect, where B0 is the mean B in the well-ordered region, and B is
> the same quantity in a less well ordered one. Above all, don'
Sagar,
what you see may be model bias unless you calculated these maps without
that region of molecule.
Pavel
On Wed, May 27, 2015 at 12:03 PM, Sagar De'Biomimic <
sagarbiophys...@gmail.com> wrote:
> Dear all,
>
> We have solved a structure of Protein-DNA complex. In an ASU we have two
> protei
In the PDB file, the b-factors were only determined by the quality of the
> map, is this view right or not?
>
I would say it is a function of data quality (measured reflections in case
of crystallography or cryo-EM map).
Pavel
This is what we call N/Q/H flips done as part of phenix.refine refinement
based on Molprobity evaluation.
Pavel
On Wed, May 20, 2015 at 2:10 PM, Smith Liu wrote:
> Dear All,
>
> Suppose the protein crystal resolution is about 2-3A, then in the map it
> should be rather difficult to distinguish t
Hi Faisal,
if you are particularly interested in refinement of atomic models into
cryo-EM maps then you may check this too:
http://phenix-online.org/presentations/real_space_refine.pdf
(Of course by no means I claim this being a good reading!)
Good luck,
Pavel
On Tue, May 19, 2015 at 12:01 AM
Hi All,
what happened to Randy happened to me several times in the past, with one
most remarkable example being editing the 47 page long text that were
mostly formulas. While most responses so far suggest using latex or flavors
thereof, I for one would still be using MS Word mostly because I find
Posted on behalf of Prof. Ren Wei and Jeffrey Reimers.
*Post-Doctoral Fellowships in Quantum Refinement of Protein X-ray
Crystallographic Structures and related work in Biophysics, Biochemistry,
Biomaterials, Chemistry, and Soft Condensed Matter*
Shanghai Universit
"phenix.reduce -HIS model.pdb" should do it. Use "phenix.reduce -h" to see
more options.
Pavel
On Fri, May 15, 2015 at 5:54 AM, Smith Liu wrote:
> Dear All,
>
> After CCP4 or phenix refinement, I find the H position of N in specific
> His residues needs to be regularized based on the function o
Hi,
On Sun, May 3, 2015 at 4:15 AM, Smith Liu wrote:
> If for both a mtz density and mrc map I set the contour level as 0.15,
> does the 015 has the comparable significance for the mtz density and mrc
> map?
>
may be. Depends how your map (3D grid function in "mrc" file) and Fourier
map coeffic
Ramachandran outliers aside, amount of other outliers seem a bit worrying
to me, especially given that it may not be all that trivial to justify them
against 3.5A resolution map:
all-atom clashscore : 29.19
ramachandran plot:
outliers : 0.51 %
allowed : 5.44 %
favored : 94.05 %
rot
Hi,
I entirely agree with Phoebe. This is 2008 structure (publish date, so
refinement was probably done in 2007) - that is before all the new methods
and tools for low-res refinement became available.
Now, let's have a closer look... Given rather large amount of various
geometry outliers (in mode
My understanding is that NCS restraint can significantly enhance the speed
> of calculation, but considering the subunits even with the eactly same
> sequence may not be identical, to have NCS restraint may be not necessary
> or may be not good for the refinement, am I right?
>
Non-crystallograph
Hello,
John, the lower-resolution datasets in your paper were generated by
> truncating a high-res dataset, i.e. the "lo-res" datasets are of great
> quality. Would the conclusions still be valid if the data are "true
> low-res"? (i.e. I/sigI 1.5-2 in last shell)?
>
genuinely low-res data set is
This should do it (if not please get back to me off-list with sending data
and model files):
Refinement settings -> Ligand linking , then Options->Link metals .
phenix.refine does not trust anything in PDB file header except CRYST1
records.
Pavel
On Fri, Mar 6, 2015 at 10:17 AM, Kgosisejo, Oara
> I would like to ask if any of you know how to measure the angle between
> two nucleic acid helices? I am trying with pymol, but have not found a
> solution to it yet.
>
phenix.angle might help, with or without effort on your side.
Pavel
> What about the bogey of Fourier truncation ripples--I have heard many have
> been fooled by the into thinking they were seeing orbitals. How does one
> tell the difference?
Indeed, there are such dangers. Hints are here:
On the possibility of observation of valence electron density for
individ
Hi Almudena,
some graphic programs connect atoms based on distance only (draw a line
between two atoms that represents the covalent bond). I suspect this is
what PyMol does. Some may employ more information such as one encoded in
Monomer Library CIF files. Some try to do both. I suspect this is wh
Isn't it simply FSC? Then according to Wikipedia the citation goes back
even further, 1986 !
Pavel
On Tue, Jan 27, 2015 at 2:06 PM, Randy Read wrote:
> Hi,
>
> Bart Hazes' sftools program does map correlation in resolution shells in
> this way, and may even have been doing it before 1996 if I'm
Hi Patrick,
while I agree with Tim this task may be a bit less straightforward than it
appears, I think you can get ballpark numbers by looping over all PDB
entries and searching for a keyword in PROGRAM card. All you need is to
make an upfront definition of what you count as "phenix", "ccp4", "sh
>
> >If you do that then what chemical type you are going to put into that
> rightmost column of ATOM record of PDB file? Note, that must be a valid
> chemical element symbol so that you can use such PDB file to calculate
> R-factors, maps and whatnot (Obviously, "X" would not work!).
>
>
>
> Why,
>For those who insist on annotating every density blob, UNX atoms are the
> PDB's officially supported method for doing so (unless this has changed
> recently), or UNK/UNL for unknown amino acids and ligands. These are not
> without their own problems but they at least make both the presence of an
Dear Armando,
Is there any reason for using Babinet scaling for bulk solvent correction
> instead of mask based scaling?
>
in addition to Dirk's excellent comment:
Babinet bulk-solvent model is fine at resolutions lower than 15-20Å while
not so much at higher resolutions as demonstrated by Podja
Hi Ed,
I didn't see any way to refine with no free set in phenix, even with
> least-squares target function,
xray_data.r_free_flags.ignore_r_free_flags=true
will make phenix.refine use all reflections. Obviously, reported
Rwork=Rfree in this case. This works for any available refinement target.
Hi Ursula,
I also tried to just superimpose the complete model onto the partial
> solution. This results in quite nice packing, but doesn't refine. Is there
> a rigid program refinement program with very large convergence?
>
depending on what you call "very large", this may be helpful:
Automat
Hi Venu,
please send me PDB file and I will try to help.
FYI: There is Phenix mailing list for Phenix related questions.
Pavel
On Thu, Dec 11, 2014 at 1:07 PM, Venu V wrote:
>
> Hello everybody,
> I need some help with handling modified DNA bases in phenix refinement.
> I am refining a duplex
Hi Randy,
I can see all good reasons for using intensities! What about maps and
R-factors? I guess you still need F to compute them (I realize you can
compute R(I) but this is not what people are used to do in general), and if
that's the case then I->F is still inevitable (at least for some purpos
t being able
> to proove it, I doubt that this the case, which lead me to the below
> claim that we don,t necessarily want to reach the global minimum of the
> target function.
>
> Of course an acceptable structure actually may have a target value
> representing a global min
Hi Tim,
you don't necessarily want to find the global minimum (...)
this contradicts the definition of crystallographic structure refinement.
If finding the global minimum is not what you ultimately want then either
the refinement target or model parameterization are poor.
Clearly, given comple
101 - 200 of 636 matches
Mail list logo
