Hi,
every time you run phenix.refine it may exclude some reflections from
refinement per Read 1999 (Acta Cryst. (1999). D55, 1759-1764). Usually the
number of reflections omitted ranges from none to just a few, however, this
may be just enough to make the resolution statistics look slightly
Dear All,
What follows below is not very specific to the particular program
(STAIRSANISO) nor the original questions, but nonetheless, I believe it is
relevant.
In the past, performing any adjustments to the diffraction data intended
for solving and refining atomic models was more or less
Hi Jorge, it'd take about 1 hour of my time to put together a cctbx-based
script to do that, or about 2 hours to make an end-user program in Phenix
that'll be available in tomorrow's build. But I'm not sure how of general
interest this might be to warrant investing time into this. So here is an
Hello Jan,
you can convert your cryo-EM problem into crystallographic one by
FT'ing your map into a set of structure factors "Fobs" and then giving the
atomic model and MTZ with these "Fobs" to CheckMyBlob. If it's cool enough,
it should not make much difference if your "Fobs" come from X-ray or
Hi Liliana,
a few things to consider:
0) There is a Phenix mailing list for Phenix specific questions (phenixbb);
1) Bin completeness depends on (obviously) how binning is done (number of
reflections per bin or number of bins or binning in d^2 or d^3 spacing or
log-binning etc etc etc) -- all
Hi Ketul,
CCmask evaluates the cross-correlation between your experimental map and
the map that is calculated from the model. If you look at the formula, the
map calculated from the model involves, among other things, atomic
coordinates, B factors, and occupancies. This means that even if the
Hi All,
I believe it depends on the resolution. At sufficiently low resolution, it
may not be too unreasonable to assume that the main chain atoms of a
residue have the same B factors, and its side chain atoms also share the
same B factor (different from the main chain). Why? Simply because your
Hi Kay,
to address "(...) not elsewhere (...)", in Phenix GUI go to Tools then down
to "Search PDB symmetry...". I've never used it myself nor do I know who
added it in Phenix but from the description it looks like what you're
looking for. Let us know if you have any problems with it.
All the
Hi Matt,
Im wondering about occupancy refinements - both what's going on under the
> hood and what are best practices.
>
since you are quoting Phenix I suggest this bit of reading that is somewhat
relevant to your questions:
Hi Rob,
the fundamental property of crystallographic or cryo-em maps -- the
presence of high density points -- is what skewness depicts. So I can't see
why the idea of using skewness to quantify maps would be any different for
x-ray vs cryo-em. I've just downloaded a cryo-EM map for this (PDB:
Hi Matt,
I believe figure 3 here:
https://www.nature.com/articles/s41467-018-06957-w
is relevant to your question.
Pavel
On Tue, Sep 5, 2023 at 11:32 AM Matt McLeod wrote:
> Hi all,
>
> I am trying to get some insight in the accuracy/precision of occupancy
> refinements. I have done some
Hi Jon,
not really the answer to your question but.. This may be very tricky to do
because what you look at is not an electron density map but its Fourier
image of finite resolution phased by crystal model (that has errors), plus
experimental errors, and missing F000 (which is not measured as part
Hi Stuart,
the answer, I think, is here:
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
Pavel
On Wed, Feb 15, 2023 at 8:37 AM Stuart McQuarrie <
974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:
> I fit a large cyclic ligand cA6 (cylic
Nukri,
IMO, the idea of cross-discipline meetings is great conceptually, at least
for reasons you pointed out, but utopical in practice. When we attend our
field-specific meetings we meet colleagues we know, we talk to
collaborators from the past or find new ones, we have things in common that
we
Hi Rams,
phenix.match_maps
will superpose maps and models. Totally general: target/moving boxes (unit
cells) and symmetry can be different, gridding can be different too.
I can help off list should you need any assistance!
Pavel
On Wed, Jan 25, 2023 at 6:30 AM Subramanian, Ramaswamy
wrote:
>
> This is best illustrated by Ramachandran "outliers",
> which are perfectly supported by electron density.
>
Indeed, and 3NOQ is one of my favorite examples of that, an outlier isn't
necessarily equates to wrong! However, I think torsion angles (eg, phi/psi)
are much more flexible than
Dear community,
I’m looking for an example of a crystal structure where a large group of
atoms (as large as a whole chain or even a domain) have more than one
distinct conformation that would require modeling of such chain/domain as
more than one individual copy, with each copy having partial
Hi James,
- Where exactly inside the blob of density do you place these dummy atoms?
>
> Where? At the peaks.
>
Peaks? This means you need to have atomic resolution data and also blobs
representing ordered atoms, so you actually have peaks!
> What I usually do is pick peaks, put atoms at the
Hi James,
I like your approach with dummy atoms and occupancy refinement. Dealing
with actual maps sounds like hell to me indeed (especially given that we
deal with weighted Fourier maps!). Reading this as someone who immediately
translates this into a computer code (in my mind), a few things
Hi,
this can be a start:
http://cci.lbl.gov/docs/cctbx/doc_maps_boxing/
There are a lot of boxing options: with and without masking (with many
masking options: smooth masks, etc), around atom selection, per NCS etc..
Pavel
On Fri, Aug 5, 2022 at 2:30 AM Evgenii Osipov wrote:
> Dear CCP4
For some perhaps relevant discussion please see Appendix B here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096492/pdf/d-74-00531.pdf
Pavel
On Sat, Jul 16, 2022 at 6:17 AM Marcin Wojdyr wrote:
> On Thu, Jul 14, 2022 at 3:15 AM Pavel Afonine wrote:
>
> > Map values are calc
Hi Ravikumar,
next nightly build of Phenix (dev-4661 and up, likely becomes available
tomorrow) found in the usual place
https://phenix-online.org/download/nightly_builds.cgi?show_all=1
will contain the new command line program
called phenix.map_values_along_line.
The program inputs the map
Hi Ravikumar,
this can be easily done in CCTBX, but requires knowing CCTBX and Python
scripting. I can write a script-example for you, if interested, or feel
free to give it a try yourself and let me know if you need any help.
Pavel
On Wed, Jul 13, 2022 at 11:19 AM Ravikumar wrote:
>
> Dear
Hi,
Phenix has a collection of tools like this:
phenix.cif_as_mtz
phenix.cif_as_pdb
phenix.pdb_as_cif
phenix.mtz_as_cif
Pavel
On Tue, Apr 19, 2022 at 7:52 AM Marcin Wojdyr wrote:
> Plenty of options. I'll add one maintained by me. Type:
> gemmi convert file.cif file.pdb
> or use it here:
>
It's April 1st today, isn't it? -;)
On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley
wrote:
> Coot 1
>
> 18 years after the release of Coot 0 it's time that I actually released
> Coot 1.
>
> Coot 1 is a major change beyond Coot 0. It has required a lot of writing
> and rewriting [1]
> and has been
For the record, occupancy refinement scenario you're looking for is
described here:
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
Cheers,
Pavel
On Thu, Mar 3, 2022 at 7:09 AM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
Hi All,
who produced this file? If phenix.refine added water with chain S given
that protein chains named S were already in that model, then it is a bug
that I need to fix.
Cheers,
Pavel
On Thu, Dec 30, 2021 at 11:05 AM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> I
Hi Reza,
If you think about it this way... Validation is making sure that the model
makes sense, data make sense and model-to-data fit make sense, then the
answer to your question is obvious: in your case you do not have
experimental data (at least in a way we used to think of it) and so then of
Hi,
if I understood your question correctly, then one of 13 scenarios described
here:
http://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
fits your situation and you should be able to handle it in refinement all
right.
For more specific advice please
One more:
BraggNet: integrating Bragg peaks using neural networks
B. Sullivan, R. Archibald, J. Azadmanesh, V. G. Vandavasi, P. S. Langan, L.
Coates, V. Lynch and P. Langan
J. Appl. Cryst. (2019). 52, 854-863
Pavel
On Tue, Aug 3, 2021 at 4:53 AM Thorn, Dr. Andrea <
andrea.th...@uni-hamburg.de>
Andrea,
you may want to include this one:
Using support vector machines to improve elemental ion identification in
macromolecular crystal structures. Morshed N, Echols N, Adams PD Acta
Cryst. D71, 1147-58 (2015).
Pavel
On Tue, Aug 3, 2021 at 4:53 AM Thorn, Dr. Andrea <
Hi Frank,
phenix.pdb.biomt_reconstruction command should do it.
Pavel
On Tue, May 25, 2021 at 12:44 PM Frank von Delft <
frank.vonde...@cmd.ox.ac.uk> wrote:
> Hello all - this presumably has a really simple solution:
>
> For a PDB file with a (correct) biomolecular assembly record (REMARK
>
Hi Dhiraj,
I have structure with bent DNA. I am trying to refine the structure
> using phenix. do I need to turn off the DNA secondary structure restraints
> during refinement?
>
probably not, unless you have reasons to do so otherwise.
P.S.: There is a Phenix mailing list for Phenix
Hi,
as others pointed out electron rich elements tend to amplify imperfections
visible in Fo-Fc maps. Consider:
- refining occupancy of Fe, the site may be partially occupied;
- refining f' and f'' if data are anomalous;
- surrounding histidines may 'see' this Fe as a nonbonded interaction and
Hi Wajahat,
first off, there is a dedicated mailing list for Phenix specific questions (
http://phenix-online.org/).
You need to run more than one refinement cycle before you try making sense
of R factors.
Pavel
On Wed, Jan 20, 2021 at 10:05 AM Wajahat ali khan
wrote:
> Dear all,
>
>
> I
Rama-Z is implemented in CCTBX meaning it is available to CCP4 and Phenix.
Also it is reported in validation and refinement in Phenix (you get the
number every time you run real- or reciprocal-space refinement!).
Pavel
On Mon, Jan 18, 2021 at 1:58 PM Boaz Shaanan wrote:
> Hi,
> Will it be
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
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
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
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 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
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
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
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:
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
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
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.
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:
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
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
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
Yet another way is:
phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and and
resseq 1:10 and name CA" selection_moving="chain B and resseq 1:10 and name
CA"
or using the GUI.
Pavel
On Tue, Sep 17, 2019 at 8:06 AM Folmer Fredslund wrote:
> Dear Kyle,
>
> As other non-CCP4
for obvious issues like this one!
Pavel
On Fri, Aug 30, 2019 at 7:59 AM Pavel Afonine wrote:
> Please send me log file off-list and that may be a start. -Thanks!
> Pavel
>
> On Fri, Aug 30, 2019 at 6:48 AM Tung Thanh Dinh wrote:
>
>> After phasing with phenix, i clicked on the
Please send me log file off-list and that may be a start. -Thanks!
Pavel
On Fri, Aug 30, 2019 at 6:48 AM Tung Thanh Dinh wrote:
> After phasing with phenix, i clicked on the phenix.refine ribbon. Since
> then for every macrocycle of refinement, r-work and r-free values are
> always the same. Is
Hi Ivan,
> My conclusion is that "no fill-in" option might be tried at some
> stages, but with caution, especially for datasets with poor low res
> completeness.
>
I'm guessing you really meant *high*, not low. More or less repeating what
others said already.. Correcting for low res
For the record, phenix.refine always produces two versions of 2mFo-DFc
maps, with and without filling in missing Fobs. The one that opens in Coot
by default is the "filled" map, but you can always load the other one for
comparisons.
Pavel
On Tue, Aug 6, 2019 at 8:34 AM Ivan Shabalin
wrote:
>
Hard to see from a static image, but could it be an alternative
conformation?
Pavel
On Tue, Jul 9, 2019 at 2:32 AM Lumbini Yadav wrote:
> Dear all,
>
>
>
> We have found a huge Fo-Fc density close to cysteine residue (see attached
> image) in the structure with resolution of 1.2A. In the
Hi Sam Tang,
Sorry for a naive question. Is there any circumstances where one may wish
> to refine to a lower resolution? For example if one has a dataset processed
> to 2 A, is there any good reasons for he/she to refine to only, say 2.5 A?
>
yes, certainly. For example, when information
Hi Jonathan,
send me files off list and I will have a look. From your description it
isn't clear to me what the problem is. You need to add H or D or H and D
only once (and phenix.ready_set is the right tool to do it!), then just do
refinement and all should work. Coot indeed may not play well
Hi Jonathan,
this may also be a result of too strong SS bond restraints or/and
inaccurate SS bond restraints parameters or/and disorder (in some fraction
of unit cells there is no SS bond). More on the topic:
"Disulfide bond restraints" here:
Hi Andre,
here is the link to cctbx-based code that computes Uhkl according to your
formula below, using model mean B and F000 that accounts for atomic model
and bulk-solvent:
https://www.dropbox.com/sh/g7sp7pqxst4ldj0/AAD1whlVD2mvAGoRa5jOF-fla?dl=0
I leave it up to you to read and understand
Hi Andre,
> - Is there any macromolecular crystallography software that can compute
> Uhkl as above, or equivalent?
>
I estimate this can take about 10 minutes to script in CCTBX. I can write a
script for you, if interested, and send off list.
> - If not, would it be more correct to use the
Hi Andre,
- How can F(000) be best estimated from the final model, which is not
> necessarily always the most complete or best refined? Should we simply add
> together the number of electrons for all the atoms refined in the
> asymmetric unit (protein + ligands + solvent)?
>
the text here
Hi Ian,
perhaps there are as many answers to this as many subscribers to this list,
but personally "Cysteine with attachment" seems more logic and clear to me
than calling the whole thing a different name. Although I would also
understand arguments like if it is a CYS with an attachment it is not
Also, values in parentheses (high-res shell) depend on how you (the program
you use) do binning. Different programs do it differently and so these
values can vary quite substantially. With a little of trial-and-error
effort choosing the binning one can make these values farther or closer to
P.S.: while on the topic, it might be helpful to you to have a look at this
article ("On the analysis of residual density distributions on an absolute
scale", page 43) available here:
http://phenix-online.org/newsletter/CCN_2012_07.pdf
Pavel
On Tue, Mar 5, 2019 at 10:02 AM Pavel Afon
Hi Sen,
As Pavel mentioned, phenix.f000 will give you F(0,0,0) value, but I don't
> see that information stored and easily calculated from .ccp4 data.
>
phenix.f000 requires atomic model (PDB or mmCIF file) as input, not a map.
If you want bulk-solvent to be added, then you need to give it mean
Hi,
> Unfortunately not all structure
> factor programs will give you that F000.
>
phenix.f000 will give you F(0,0,0) value based on atomic model alone or
atomic model plus bulk-solvent.
Pavel
To unsubscribe from the
Hi,
> Or, alternatively, if anyone has used a different program to refine small
> molecule structures determined by ED, we would be happy to hear about that
> program too.
>
phenix.refine has an option to use electron scattering factors. I can
provide further assistance off-list or on phenix
Hi,
this is why Polder map tool also includes analysis of the map in question
to determine whether it looks like bulk-solvent or something else, as
described in paragraph 5 here:
http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf
This analysis tells you in plain English what you are
Hi Mahesh,
In the current version of phenix.refine contains the separate option for
> refinement: xyz (reciprocal space) and xyz (real space ). What does it
> mean and how it differs from the previous versions which had xyz and real
> space instead.
>
All the same, different name. One refines
Hi,
> Any time you do a thought experiment you make a fake-data data set, the
> "true" phases and "true" amplitudes become the ones you put into the
> simulation process. This is by definition. Is there potential for
> circular reasoning? Of course! But you can do controls:
>
this is so
Hi Markus,
I can only guess without seeing files (and link to files seems to be
broken).. So my guess is that the ligand density is weak enough so FEM
treats it as "near noise" and it wipes it. Polder decides it is likely
ligand because it uses correlations, and so even of two maps are weak but
Hi Almudena,
I wonder to which extent I can trust the positive blobs or polder maps that
> I am generating...
>
the answer to this question is given in corresponding paper that describes
Polder map:
http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf
Based on the analysis described
Now I see the value of storing data in plain text files even more (mind
Shelx or X-plor formats, for example) -;)
On Fri, Nov 9, 2018 at 9:47 PM Clemens Vonrhein
wrote:
> Hi Eleanor,
>
> You could try running the oldest MTZ2VARIOUS binary you can find -
> e.g.
>
> wget
Perhaps
phenix.pdbtools model.pdb rotate=... translate=...
which should work with any PDB or mmCIF file.
Pavel
On Thu, Nov 8, 2018 at 11:36 PM Tim Gruene wrote:
> Dear Kaushik,
>
> you could try moleman2 from the Uppsala Software Factory,
> http://xray.bmc.uu.se/usf/moleman2_man.html - maybe
Clément,
I'm guessing this is because it isn't clear what CCwork/CCfree can tell you
that Rwork/Rfree can not. Needless to say we all more or less have a good
idea about what the ok values for Rwork, Rfree and Rfree-Rwork (as function
of resolution) while it is much less clear (to me at least)
Hi Tony,
I always feel some people are too "greedy" with the resolution they want to
> achieve. I mostly find that extremely high density is a pain to work with
> as it's usually accompanied by many dual, triple conformers, a lot of noise
> in the solvent phase that is often difficult to
Hi Deepanshu,
how complete the data set? What's completeness across resolution zones?
Systematically missing reflections can have systematic impact in real space
(maps). I've seen entire ligands or domains disappear due to missing
low-resolution data.
Just another check-point to consider..
Good
Nonbonded interactions? (if you approach this from classic geometry
restraints used in refinement programs)
Pavel
On Mon, Sep 17, 2018 at 2:09 PM Joel Tyndall
wrote:
> Hi,
>
>
>
> Polar interactions seems to make the most sense. This is what Pymol uses
> as I don’t think it differentiates
>
>
P.S.: all questions are welcome of course, no labeling. It's just some of
them are so orthogonal to common sense that answers my be such as well.
Best,
Pavel
On Sun, Sep 9, 2018 at 9:38 PM Pavel Afonine wrote:
> Hi,
>
> Is there any sever available to create electron density maps fo
Hi,
Is there any sever available to create electron density maps for cryo-em
> structures?
>
The questions are nonsensical. Here is why:
1) In cryo-EM maps are not electron density maps but surfaces representing
electric potential.
2) Creating such a map is essentially carrying on from cryo-EM
Hi Xavier,
> is there some kind of general trend if not consensus as how to refine
> cryo-EM structures?
>
Not really consensus, but my clearly biased contribution to the topic:
I'd say basic common sense for refinement applies:
- optimally sharpen the map (
Hi,
also, it helps to keep in mind that some clashes may actually be valid
interactions that are labeled as 'clashes' by validation software that is
simply not sophisticated enough to distinguish between bad steric clashes
and chemically/physically favorable valid interactions. For an example,
There is an option in phenix.refine to do this, described here:
Automated identification of elemental ions in macromolecular crystal
structures. Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ,
Richardson JS, Terwilliger TC, Adams PD Acta Cryst. D70, 1104-1114 (2014).
Pavel
On
Phenix has its own way to do it which is "Comprehensive validation"
available from the GUI. This includes validation of model, data and
model-to-data fit. It is data-specific: there is one for crystallography
(X-ray or neutron) and one for Cryo-EM. For best results, you need the
latest version
As others suggested, you can use Polder map:
- how-to video tutorial can be found here:
http://www.phenix-online.org/documentation/reference/tutorial_channel.html
- background is described here:
http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf
Pavel
On Tue, Jul 24, 2018 at
It's important to remember that free-R reflections are not only used to
calculate Rfree, but also are used in calculation of m and D scales in
2mFo-DFc and mFo-DFc maps, as well as in likelihood-based refinement
targets. The fact is that you need to have a sufficient amount of free-R
reflections
This should work in latest nightly builds:
phenix.pdbtools model.pdb clear_seg_id=true
If it doesn't please report a bug (on appropriate Phenix lists).
Good luck!
Pavel
On Thu, Jul 5, 2018 at 4:33 AM, Eugene Osipov wrote:
> Hello everyone,
> is there any simple way in CCP4 to clear segid
More re disulfide bonds:
http://www.phenix-online.org/newsletter/CCN_2015_01.pdf#page=13
Pavel
On Tue, Jul 3, 2018 at 11:26 PM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:
> Hi all
>
> I got a structure which has COA in it, and the SH in the tail of COA
> is very close to the SH side chain of
> If I am not wrong, I remember that someone proposed to standardize
> B-factors of protein atoms as “BS = B - Bave”, where Bave is the average
> B-factor of the protein.
This will make some of BS negative (if B
Just in case you find it helpful, you can get 100% complete set of
reflections (Fcalc) in specified resolution range using
phenix.fmodel model.pdb high_res=2.5 low_res=15
or if you leave out low_res it will go all the way up to theoretical limit
of low resolution.
If you have/use cctbx then I
This is discussed, for example, here:
http://www.pnas.org/content/114/12/3103
Also, here I calculated the distribution of map values (scaled in r.m.s.)
for four groups of atoms: main-chain atoms, side-chain oxygen atoms of ASP
and GLU (negatively charged OD1, OD2, OE1, OE2), side chain atoms of
> 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
>
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
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
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
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
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
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