Hi Dirk,
this is very interesting! From the list of changes, it appears that in
version 1.6.1, you use a similar idea to implement hydrogen bonds via
DSSP during refinement that I used to stabilize the 4.3 A refinement
of Pol II in complex with TFIIB [1]:
(...)
Could you please give more deta
Hi Daniel,
How do I convert the B-factors from my final structure to full B factors if I
did not use TLS refinement?
a non-ccp4 tool:
if you have PHENIX installed then:
1) if your PDB file has TLS matrices in its header and residual
B-factors in ATOM records, then:
phenix.tls model.pdb c
Hi Francois,
a non-ccp4 tool:
if you have PHENIX installed then:
iotbx.pdb.box_around_molecule model.pdb
will do it (if I correctly understood you question).
You can also specify a buffer region around a molecule:
iotbx.pdb.box_around_molecule model.pdb --buffer-layer=5
Pavel.
On 3/24/10
Hi Regina,
this subject was discussed on PHENIX bulletin board some time ago:
http://www.phenix-online.org/pipermail/phenixbb/2009-December/003074.html
I think this answers your question; please let me know otherwise.
Also, I'm not sure what you mean by "(except that refinement will fail
if t
Hi Karthik,
you can use this:
http://cci.lbl.gov/servers/cctbx/explore_symmetry.html
and you may find this useful too:
http://cci.lbl.gov/servers/index.html
Pavel.
On 3/16/10 5:11 PM, Karthik S wrote:
Hi, I was looking around for programs that display space group
symmetry information and c
Hello,
the guess about ripples is most likely correct. Just do this simple
experiment: place one iodine in a middle of a cubic box and compute
F-calc map. You will see mazing picture! At least I enjoyed. You
will see a number of concentric shells of density around iodine,
positive and neg
Hi Salameh,
there is PHENIX bulletin board where PHENIX-specific issues are discussed:
http://www.phenix-online.org/mailman/listinfo/phenixbb
Anyway, regarding your question:
> In every refinement round the wxc and wcu are out of control,
> although I
> modify the def file and change the values
Hi Alejandro,
you may be can do it using CCTBX tools (that come with PHENIX). This will
require some simple scripting in Python. Let me know if you are interested and
need any help.
Pavel.
- Original Message -
From: Alejandro Buschiazzo
Date: Monday, March 8, 2010 5:51 pm
Subject:
On 2/26/10 8:35 AM, Gerard DVD Kleywegt wrote:
Nope - LSQMAN would still be looking for stretches of sequentially
ordered residues and would only match atoms with identical names (" CB
" with " CB ", for instance).
--G
PS: Brownie points for the non-phenix solution, though!
A non-CCP4 (PHE
CP4 programs ... .
With best wishes,
Gerard.
--
On Thu, Feb 18, 2010 at 03:53:02PM -0800, Pavel Afonine wrote:
Hi Ivan,
two ways (at least) to do it in PHENIX:
- phenix.refine always computes anomalous difference Fourier map (provided
that your input data file contain
Hi Ivan,
two ways (at least) to do it in PHENIX:
- phenix.refine always computes anomalous difference Fourier map
(provided that your input data file contains Fobs(+) and Fobs(-)). The
command below will do it:
phenix.refine model.pdb data.mtz strategy=none
main.number_of_macro_cycles=0 out
But you are correct that refmac should allow the residuals to go negative.
This is what phenix.refine does when you do combined TLS + individual
isotropic ADP refinement.
Pavel.
Hi Jon,
These few rotamers which I fix in Coot, validate in Phenix, refine in
Refmac, and validate again in Phenix keep getting pushed into areas that
are not favored. I would love to hear some ideas as I'm out and this
model
is otherwise done.
did you try refining it in Phenix with or wit
Dear Ed,
Tightly restrained refinement will be equivalent to
torsion angle parametrization, since bonds and angles are essentially
fixed (but dihedrals are not).
Simply not true. Think why -:) Hint: in restrained refinement the weight
applies to all terms - bonds, angles, torsions, etc... S
Hi Ed,
DISCLAIMER: When I say "grouped B-factor refinement" I mean CNS-style,
Bmain/Bside refinement. Not to be confused with more general "domain
B-factor refinement" where single B-factor is assigned to some part of
the structure.
- In general you are free to decide what you name a doma
Hi Jose Antonio Cuesta Seijo,
- at 3.1A I would try 1) refining individual isotropic ADPs, 2) combined
strategy of refining TLS+individual isotropic ADPs, 3) combined strategy
of refining TLS+group isotropic ADPs with one or two definable isotropic
B-factor per residue. Look at Rfree and Rfree
Hello,
1. The reduction in number of parameters is not that significant. On
average, you have some 8 atoms per residue, and thus 32 parameters with
individual B-factors (4 per atom). With grouped B-factors you have 26,
about 20% difference. While it sounds like a lot (hey, I just removed
2000
Hi Kelly,
since you mentioned you tried refinement in phenix.refine:
I guess I know what the problem is, but I wouldn't tell before I'm sure.
Could you send me the two PDB files: before and after refinement (to my
email, not to the whole bb), and specify which residue/ligand is in
trouble? If
Hi,
for example, these qualities below will tell me something about your model:
1. Rfree, Rwork overall and shown in resolution shells;
2. Geometry statistics:
- overall rmsd's bonds, angles, ...;
- Molprobity statistics/scores;
- histograms of deviations from ideal bonds, angels, ...;
Hi Miri,
you can do this (and more) using a tool from PHENIX:
phenix.superpose_pdbs [pdb_file_fixed] [pdb_file_moving] [parameter_file]
A couple of examples:
phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and
name CA" selection_moving="chain B and name CA"
phenix.superp
Hi Sara,
- what you observe should not happen since phenix.refine uses riding
model for H atoms. The hydrogen's B-factors are automatically inherited
from the atoms these hydrogens are bonded to. For example, in X-H bond
the B-factor of X should be equal to B-factor of H.
- make sure you are
Hi Daniel,
you can find an example here:
Acta Cryst. (2008). D64, 515-524
Iterative-build OMIT maps: map improvement by iterative model building
and refinement without model bias.
T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, N. W.
Moriarty, P. D. Adams, R. J. Read, P. H. Zwart a
Hi Feng,
just my speculations (of course, the respective authors of the program
you use may provide you with a better answer):
In terms of refinement results, all pairs of numbers below look the same
to me (regardless the refinement program used):
0.192/0.250
0.191/0.247
0.202/0.254
0.194/0
Hi Mohd,
- if it is a regular peptide bond then they are linked automatically and
this problem should never happen, otherwise there must be something not
right with your input PDB file.
- check in .geo file if this particular bond is restrained;
If you send me (and not to the whole bb) the P
Polygon ideas, is:
"very well done, but have another look at this couple of Ramachandran
outliers and also consider loosening up the geometry a bit".
;-)
A.
On Dec 14, 2009, at 17:04, Pavel Afonine wrote:
Hi,
the exact answer to your question is here:
http://cci.lbl.gov/~afon
Hi,
the exact answer to your question is here:
http://cci.lbl.gov/~afonine/for_ak/validation.pdf
In particular, your question below is spelled out is discussed staring
from slide #2.
Pavel.
On 12/14/09 7:50 AM, rui wrote:
Hi, All,
I have a general question for refinement. I tried to refi
Most of these structures can be easily identified as very suspicious in
a few seconds using POLYGON tool (Acta Cryst. D65, 297-300 (2009)); see
pictures here (courtesy of Sacha Urzhumtsev):
http://cci.lbl.gov/~afonine/fakes/Murthy-polygon-1.pdf
Pavel.
P.S. POLYGON tool is available as part of
yn F. Symmons
Cambridge
'Chan fhiosrach mur feòraich.' Gaelic proverb - Nothing asked, nothing
learned.
--------
*From:* Pavel Afonine
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Wednesday, 2 December, 2009 22:52:45
Hi Pankaj,
if you are refining in phenix.refine:
- is automatic ordered solvent (water) update is turned on;
- you can try weight optimization: "optimize_wxc=true optimize_wxu=true";
- is NCS available. Use it if so.
In fact, the Rworks seems fine, but the gap Rfree-Rwork seems large.
Insignif
Hi,
you can do similar thing (that is resulting in similar outcome) in
phenix.refine by increasing the weight on ADP restraints term. Example:
increase "wu" or decrease "wxu_scale". Although I believe a regular
refinement of individual isotropic ADPs should normally work just fine
at 3A resol
Hi Jason,
yes, technically you can refine each residue as a rigid body in
phenix.refine (as Fred explained), but:
- why wouldn't you consider a more sensible (in my opinion) strategy
running a combined refinement job that contains rigid body refinement of
bigger rigid domains, SA in Cartesia
Hi Tommi,
Apologies, i know this is not phenix bb but since i am here (and not
subscr. there)
no need to apologize! You can just subscribe to it:
http://www.phenix-online.org/mailman/listinfo/phenixbb
how to control rigid body ref positions in phenix.refine, i am trying
to do very low res ch
Hi Alexandra,
the answers are in these papers and references mentioned in these papers
(list below is of course incomplete, but following the references inside
of these papers will give you the full picture):
# Jiang, J.-S. & Brunger, A. T. (1994). J. Mol. Biol. 243, 100-115.
"Protein hydrat
Alexandra,
one of many possible options to do this:
If you have the latest PHENIX installed
(http://www.phenix-online.org/download/nightly_builds.cgi), then you can
use "Reflection file editor" from the main GUI to do what you want.
Pavel.
On 11/17/09 9:49 AM, Alexandra Deaconescu wrote:
Hi Fred,
you can do all this in PHENIX, using command line or the GUI.
- GUI: from main PHENIX GUI click on "Comprehensive validation", the
rest should be obvious.
- also, all these values are computed and available after any
phenix.refine run using PHENIX GUI.
- command line: type "phenix
Dear Partha,
I didn't really want to enter this discussion, and I might be totally
wrong writing it Saturday midnight... but...
I guess "open source" means what it means: the source code available to
anyone, right?
Latest or not latest... I guess that would be an additional decoration
to t
A few remarks:
I still believe that this is related to the max. likelihood vs.
conjugated gradients and FFT vs. full summation Fourier and bulk
solvent treatment in those programs.
- "max. likelihood" is a refinement target function, and "conjugated
gradients" is an optimization method.
-
Hi Tommi,
if the map shows some density for that loop, I would try two programs
(those I'm familiar with):
1) phenix.fit_loops (need to have PHENIX for this):
http://www.phenix-online.org/documentation/fit_loops.htm
http://www.phenix-online.org/
2) Xpleo:
http://smb.slac.stanford.edu/~vdbedem
Hi Matthias,
a few suggestions:
- use TLSMD server to define TLS groups;
- before using TLSMD do some group ADP refinement with one or two
refinable ADP per residue (you can do it in phenix.refine), so you get
less biased ADPs from previous restrained B-factor refinement;
- just out of curiosi
Hi,
you can try it in PHENIX:
- phenix.refine outputs such map by default (if input data file contains
Fobs+ and Fobs-);
- you can use a Create Maps option from main PHENIX GUI.
Pavel.
On 10/26/09 11:10 AM, Sergii Buth wrote:
Hello everybody!
I am faced with a problem of calculating an ano
It would be redundant to list the group definitions for the third
option in the PDB header; but isn't it equally redundant to list the
R/Rfree and geometry statistics in the headers since they're in the
log files as well?
Correct. The log file has everything because it is the log file and so
Hi Pete,
when you ask phenix.refine to do group ADP (B-factor) refinement, there
are three possible options:
- phenix.refine refines one isotropic B per residue (done by default);
- phenix.refine refines two isotropic B per residue;
- phenix.refine refines one isotropic B per user-defined grou
Hi Katja,
a possible option:
from main PHENIX GUI select "Comprehensive validation". For example, it
will do:
- all Molprobity checks;
- draw POLYGON picture (Acta Cryst. D65, 297-300 (2009) Crystallographic
model quality at a glance.);
- show all kinds of stereochenistry rmsds;
- real-spac
Hi Sivia,
you say the resolution is 1.8A, and your R-work=0.19 and R-free=0.27.
Here is the distribution of R-factors for structures in PDB
deposited at similar resolution (in range between 1.75A and 1.85A):
Histogram of Rwork
for all model in PDB at resolution 1.75-1.85:
0.114 - 0.130
Hi Armando,
high R-factor at low resolution is likely to be due to poor bulk solvent
model. Some relevant reading:
Jiang, J.-S. & Brunger, A. T. (1994). J. Mol. Biol. 243, 100-115.
"Protein hydration observed by X-ray diffraction. Solvation properties
of penicillopepsin and neuraminidase cry
Hi Fred,
may be it's written somewhere and I simply missed it: will the channel
broadcast in French or/and in English (or any other language options)?
I very quickly glanced through the web site (I understand French) and it
doesn't say anything about it.
And yes, good idea of course (if ava
Hello Vandana, so you are saying your Rfree=27.7 and Rwork=27.0.
Let's stop shaking the air with throwing out hypothesis (someone, likely
you, will need to verify them and this is some work) and start with the
simplest option -- look in PDB at the structures deposited at similar
resolution as
Hi,
POLYGON tool is your friend here:
Acta Cryst. (2009). D65, 297-300
Crystallographic model quality at a glance
L. Urzhumtseva, P. V. Afonine, P. D. Adams and A. Urzhumtsev
Pavel.
On 10/9/09 12:28 AM, Vandana Kukshal wrote:
hi
i am solving one structure
in which after refinement i got R
I guess
phenix.elbow
or/and
phenix.ready_set
can do it
Pavel.
On 10/8/09 7:11 AM, RK Singh wrote:
Dear All,
I would like to request to send me a working and correct
cif file for NAD. I obtained the same from Prodrg and ebi.
But seems to have an issues around O1N-PN-O2N
O3-PN-O5.
Thanks
With
Hi Carl,
the R-factors seem reasonable given the resolution... Try running
phenix.validate from the latest version: it will do all Molprobity
analysis, compute map CC for each residue, draw POLYGON image, and do
many other validation staff. That might help to spot if there is
anything not right.
Hi Jason,
I just replied to very similar question to someone in person.
Your options are:
- all about SA omit maps and more:
http://www.phenix-online.org/documentation/autobuild.htm
ask Tom Terwilliger should you have any questions.
- also, a good thing to check (the best actually; this option
On 10/5/09 9:46 AM, Ben Spiller wrote:
For the refinement case, do others think that Fcalcs become
anisotropic? Or that the liklihood method developed by Read and
others is superior even at late stages?
FYI:
In phenix.refine (or CNS) the total model structure factor is defined as:
Fmodel
Hi Katja,
you may consider trying this:
http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/
but PLEASE do not deposit "corrected" data to PDB.
Also, I would just try to refine the structure and see how it goes (see
if you really need to use the above tool).
Pavel.
On 10/5/09 8:21 AM, Katja Sch
Hi Peter,
sorry for not answering exactly your question... but since this is
relevant I reply anyway:
The latest version of phenix.refine has an option "fix_rotamers=true",
that automatically fixes all side chain rotamers by going
residue-by-residue and choosing the best one based on density
Hi Ben,
On 9/24/09 8:15 AM, Ben Flath wrote:
I will reprocess my data and try and use the UCLA anisotropy server (open to
suggestions here).
once you solved and refined your structure, it would be great if you
deposit to PDB your original data (not manipulated by, for example,
anisotrop
Hi Edward,
if I correctly understood this, you should be able to do it in
phenix.refine using constrained occupancy groups:
http://www.phenix-online.org/documentation/nightlies/1.4-173/refinement.htm#anch20
Please let me know if you have questions. If you send me the PDB file
and indicate th
Hi Matt,
I would do this:
- obtain as good as possible refined model (to assert the noise level is
low) (I presume you refine anisotropic ADPs, include H atoms, constantly
update ordered solvent, etc...);
- remove the ligand (all conformations);
- compute mFo-DFc and 2mFo-DFc average kick map
Hi Karthik,
in phenix.refine there is a parameter for this:
ignore_zero_occupancy_atoms=True
It tells phenix.refine: "Yes, please, do not include atoms with zero
occupancy factors into mask calculation (that is: ignore such atoms
while computing the mask)". This is what I had in mind when int
This is why phenix.refine by default outputs both maps: 2mFo-DFc
"filled" and not "filled", and it is the best to look at both keeping in
mind all pros and cons of each of them.
Pavel.
On 9/15/09 5:22 PM, Peter Zwart wrote:
Application of a elliptical resolution boundary is justified because
Hi Mohd,
here is how using PHENIX tools:
Step 1:
phenix.pdbtools model.pdb keep=backbone
Step 2:
phenix.pdbtools model_backbone_only.pdb --show-adp-statistics
Please let me know if you have questions about the above tools.
Pavel.
On 9/15/09 9:37 AM, Salameh, Mohd A., Ph.D. wrote:
Dear
Hi Sylvia,
although modern MR programs perform rigid body refinement, it may be
worth of giving a try a novel rigid body refinement protocol
implemented in phenix.refine (MZ rigid-body refinement protocol), that
has very high convergence radius:
J. Appl. Cryst. (2009). 42, 607-615. "Automatic
Hi Justin,
may be I mis-understood your question, but can't anisotropic scale
factor that is the part of the total structure factor (as defined in
phenix.refine for example and most likely in the other programs):
Fmodel = scale_overall * exp(-h*U_overall*ht) * (Fcalc_atoms + k_sol *
exp(-B_s
Hi Antonio,
My question is how can I determine which water is needed, which is not
needed?
may be this will give you some clues - here are the approximate criteria
for water picking that are used in automatic water picking and
refinement in phenix.refine:
1) peak at mFo-DFc map is higher
Hi Buz,
phenix.print_sequence model.pdb
will print sequence from input PDB file (although I don't know if it is
a FASTA format).
Pavel.
On 8/13/09 2:34 PM, Buz Barstow wrote:
Hi All,
Does anyone know of a program that can extract the amino sequence of a
protein from a PDB file and output
Hi,
all the errors go into B and so you can get decent R with wrong
structure. Glycosylated proteins have a large component totally
disordered - do you see any sugars?
with B~133 you uj is 3.7A which means that atom is all over the
place and meaningless
As a reviewer I wo
Hi Jiamu,
My question is:
1. How to reduce the B factor to a reasonable level?
3. In the same of similar resolutionIs, is there some other structures
like this situation?
POLYGON tool is (one of) your friend(s) to answer this question (apart
from debatable one about "a reasonable level"):
Hi Peter,
you can also try superposition option in phenix:
phenix.superpose_pdbs [pdb_file_fixed] [pdb_file_moving] [parameter_file]
where optionally you can provide atom selections for "fixed" and "moving".
Pavel.
On 7/5/09 12:33 AM, peter hudson wrote:
Hello all
I superposed the two dif
Use less parameters:
- TLS or group iso ADP with one-two ADP per residue (or better both, as
available in phenix.refine);
- torsion angle space instead of individual xyz;
...
Pavel.
On 4/23/09 2:54 PM, Francis E Reyes wrote:
All
It seems I have a case where I have 5595 reflections but my p
Hi Thiyagarajan,
the latest version of PHENIX has a command line tool called
"phenix.real_space_correlation", that for each atom or residue computes:
- map CC (where a user can define any map types, the default: 2mFo-DFc
and Fc maps),
- 2mFo-DFc map value at atom center,
- mFo-DFc map value
Hi,
if asked, phenix.refine will output X-plor formatted map for any
selected part of your structure:
http://www.phenix-online.org/
Pavel.
On 4/19/09 8:06 AM, JOE CRYSTAL wrote:
Hi,
I want to generate maps only covering atoms in the pdb file. I tried
fft-creat map in ccp4i (output map to
Hi Bernhard,
b) how does PHENIX/refine handle the fobs = 0 reflections in
either case?
phenix.refine outputs two series of maps:
- one pair of (2mFo-DFc, mFo-DFc) maps is computed using original
untouched Fobs;
- and the other pair of (2mFo-DFc, mFo-DFc) maps is computed using
mani
Dear friends,
if the data is of high enough resolution, wouldn't be more reasonable to
attempt anisotropic refinement (constrained with TLS or refining
individual anisotropic ADP), or mixed one - some atoms are isotropic and
some anisotropic, rather than struggle with file conversions and gett
Hi Dale,
1) There is a need for additional validation of structure factor
depositions.
PHENIX has tools for this:
1) "phenix.cif_as_mtz" will convert the PDB data file with diffrcation
data into MTZ file. It automatically will figure out if the data are
X-ray: Iobs or Fobs, or Neutr
Hi Bert,
- define NCS selections in your input parameters file "ncs.txt" (just
copy-paste-edit whatever is defined automatically, for example);
- do not forget to use "main.ncs=true";
- turn off automatic NCS detection: "ncs.find_automatically=false".
Example:
phenix.refine model.pdb data.mtz
Sent on behalf of Sacha Urzhumtsev:
Dear Richard,
I answer to the whole CCP4bb since the question was quite general and
the answer may
be interesting for other people.
As already mentioned by Bruno Klaholz, low-resolution reflections are not
only "a few reflections more" but they contain info
Hi Dirk,
thanks a lot for your feedback.
If you refine a macromolecular structure with phenix.refine using TLS
and isotropic B-factors, the resulting PDB file will have the
effective isotropic B-factors and their anisotropic corrections as
ANISOU cards from both the TLS components and the ind
Hi Lisa,
in addition to what Joern suggested, there are two other options:
1) You can run "phenix.metal_coordination" that will create additional
restraints for Mg atoms:
phenix.metal_coordination model.pdb
2) Not the best ways of doing this, but just to mention so you have a
complete list
Hi Ho,
this might be helpful:
R.J. Read, Acta Cryst. (1999). D55, 1759-1764
"Detecting outliers in non-redundant diffraction data".
Pavel.
On 2/13/2009 4:45 PM, Ho-Leung Ng wrote:
Hi Clemens,
Can you elaborate on the effects of improper inclusion of low
resolution (bogus?) reflections?
Dear John,
If by unstable refinement you mean a significant increase of Rfactors
during refinement, then there is a problem in the software you use and
the best thing you can do is to notify the developers of that software
so they can fix the problem.
I can't tell for other software, but I'
Hi Miguel,
there are limits and they are applied to total B-factor:
- minimal Biso should be positive;
- anisotropic ADP matrix is always enforced to be positive definite.
Pavel.
Thanks, it is clear now.
I have a last concern, though. Does phenix impose minimal values to
the refined ADPs? I
Hi Miguel,
Right, but why this happens only in the final bss step ? Why not in
the first one?
It's arbitrary: one can do it every macro-cycle as well. The main idea
is to have a total B-factor in ATOM records written out to a PDB file.
I have noticed the behaviour described by José when I r
Hi Jose,
We have seen that the recent versions of phenix (1.3) the structure
refinement ends with a bulk solvent correction step, something I found
quite unusual (absent in other refinement programs and in older
versions of phenix, 1.24.1).
- the software is evolving and gets better over t
Hi David,
for example:
phenix.refine does it automatically as part of usual refinement; for
illustration, see the picture here:
http://phenix-online.org/documentation/refinement.htm
Cheers,
Pavel.
On 1/20/2009 10:13 AM, David J. Schuller wrote:
I note that in CCP4 6.1.0, arp_waters has been
Hi,
you can do it PHENIX (http://www.phenix-online.org/):
phenix.ramalize model.pdp
and it will give you this list.
Pavel.
PS> You need to have the latest version of PHENIX for this.
On 1/14/2009 10:05 AM, John Pak wrote:
Hi, sorry if this was posted earlier. How can I calculate a
Ramacha
On 1/10/2009 5:14 PM, Ethan A Merritt wrote:
On Saturday 10 January 2009, Bernhard Rupp wrote:
Dear All,
I am getting conflicting comments on the use of
'structure factor amplitude'
vs. just
'structure amplitude'
for |F|.
???
That's just... odd.
|F| is the amplitude of F.
But no
Hi Ed,
I didn't really open a can of worms... Sorry if I did!
But there are many things affecting R-factors not
being reported. Do I have to deposit the bulk solvent mask?
Not that many and most of them are reported (at least those that may
affect the R-factor "significantly"). The model
On 12/18/2008 8:23 AM, Ed Pozharski wrote:
Riding hydrogens are *not* part of your model,
The fact that you don't see H in your fo-fc map due to limited
resolution and high level of noise does not mean that H atoms are not
present in actual real structure -:)
Let me ask you this
On 12/18/2008 7:23 AM, Ed Pozharski wrote:
Riding hydrogens are *not* part of your model,
The fact that you don't see H in your fo-fc map due to limited
resolution and high level of noise does not mean that H atoms are not
present in actual real structure -:)
There are definitely some (ma
Hi Jon,
- obviously, the model should not be manipulated once the final
statistics is obtained, or if it is manipulated, then the final
statistics must be re-calculated;
- I can't imagine someone thinking that hydrogens were refined
individually in a X-ray structure say at 2A resolution.
-
This might help:
Acta Cryst. (1997). D53, 540-543
Local Improvement of Electron-Density Maps
Pavel.
PS> It will be implemented in PHENIX sometime in future, but for the
moment you will need to so some scripting.
On 12/8/2008 11:08 AM, Andy Millston wrote:
I am trying to build a model of
27;s! I would suggest
that this is not a good idea!
-- Ian
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Ethan A Merritt
Sent: 14 November 2008 06:06
To: Pavel Afonine
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Choosing TLS groups.
On Thurs
Hi Priya,
- there is a phenix bulletin board :
http://www.phenix-online.org/mailman/listinfo/phenixbb
- you don't tell the resolution of your data so I can't tell you if
25/28 are reasonable values;
- why don't you happy with lower R-factors?
- the maps that phenix.refine creates (2mFo-DFc a
Hi Ian,
All - I was just in a discussion about TLS and one thing that came out
that I hadn't been aware of is that for the Biso restraints Refmac
restrains the difference between the 'residual' Bs, i.e. with the TLS
contributions subtracted, not the 'total' Bs. Now it seems to me that
this isn'
Hi Jason,
- run your model through TLSMD server to identify TLS domains (it will
produce PHENIX friendly TLS groups selections);
http://skuld.bmsc.washington.edu/~tlsmd/
- use these selections for TLS refinement in PHENIX:
http://www.phenix-online.org/documentation/refinement.htm
for example,
Hi Pete,
just a remark:
On 9/25/2008 4:00 PM, Dunten, Pete W. wrote:
I mentioned previously phenix.refine tosses your weak data if IMEAN,
SIGIMEAN are chosen during refinement.
phenix.refine does not automatically remove the data based on sigma (it
does it by user's request only). pheni
Hi Krystle,
you can do it easily in PHENIX: http://phenix-online.org/
Please let me know if you interested and have questions.
Pavel.
On 7/29/2008 1:29 PM, Krystle . wrote:
Hi all,
I am trying to model an alternate conformation in my structure, but
the alternate conformation is a completely
Hi Jinjin Zhang,
yes, it is high indeed. Here is the distribution of R-factors for
structures in PDB at resolution between 1.7 and 1.8A:
Distribution of R-work, resolution 1.7-1.8A
6.00 - 8.50: 1
8.50 - 11.00: 0
11.00 - 13.50:16
13.50 - 16.00: 166
16.00 - 18.50: 1064
18.
Hi Sun,
you may also want to have a look at this paper:
Acta Cryst. (2008). D64, 515-524.
Iterative-build OMIT maps: map improvement by iterative model building
and refinement without model bias.
Pavel.
On 7/25/2008 10:53 PM, Sun Tang wrote:
Hello Everyone,
I have a question about get
Not sure for other software, but in phenix.refine you can request to
output I*mFo-J*DFc map, where I and J are any user specified values.
Pavel.
On 7/7/2008 6:00 PM, Meyer, Peter wrote:
It is redundant, but it adds an additional step if someone wanted to calculate
something like a 3mFO-2DFc
Hi Pete,
phenix.refine outputs it all the time.
Pavel.
On 7/7/2008 7:59 AM, Meyer, Peter wrote:
Slightly off-topic from the original question, but is there a reason that most
programs don't output D for sigma_a coefficients?
Pete
-Original Message-
From: CCP4 bulletin board on beh
501 - 600 of 636 matches
Mail list logo
