On Sun, Jan 25, 2015 at 12:25 AM, Kay Diederichs
kay.diederi...@uni-konstanz.de wrote:
Here, I subtracted the Phenix and Refmac entries from the total Phenix
count, because it seems likely that Phenix was used for other purposes than
refinement.
Actually, based on my skimming of methods
On Wed, Jan 21, 2015 at 10:17 AM, Keller, Jacob kell...@janelia.hhmi.org
wrote:
I see your point about not knowing that it’s a chloride, but I think you
would agree that it is certainly more likely a chloride than map-noise, and
perhaps more likely than water as well. Would you agree that
On Wed, Jan 21, 2015 at 12:16 AM, Engin Özkan eoz...@uchicago.edu wrote:
Carbon in chloride's coordination sphere? To me, it looks like you have
serious vdW violations, and neither water nor chloride could go there.
Halides can interact with carbon too - discussed in Dauter Dauter (2001)
-
On Wed, Jan 21, 2015 at 9:05 AM, Keller, Jacob kell...@janelia.hhmi.org
wrote:
Not sure why there is this level of suspicion about the poor halide when
waters generally get assigned so haphazardly. I would say that there are
probably more “wrong” waters in the PDB than wrong chlorides, but
On Wed, Jan 21, 2015 at 12:24 PM, Keller, Jacob kell...@janelia.hhmi.org
wrote:
I think this will probably never happen, but maybe there could be a
confidence value associated with each atom in structures a posteriori,
although it might be difficult to find the right automatable criteria
On Wed, Dec 31, 2014 at 10:11 AM, Faisal Tarique faisaltari...@gmail.com
wrote:
I request you to please tell me the three letter code for pyridoxine..
You can find the appropriate residue code for any molecule previously
deposited in the PDB - which includes pyridoxine - by simply searching
On Mon, Dec 8, 2014 at 7:24 PM, Keller, Jacob kell...@janelia.hhmi.org
wrote:
FYI, sometimes native nucleotides can make it through protein
purifications if binding is tight.
This is especially true for G-proteins, since tight binding to GDP is an
essential part of their function. I don't
On Thu, Nov 6, 2014 at 5:20 PM, Oliver Clarke oc2...@columbia.edu wrote:
I wonder if a solution might be to create new residues containing alkyl
chains of various lengths, named something like U01, U02, U(n), where N is
the length of the alkyl chain that fits the density. Sort of similar to
On Wed, Oct 29, 2014 at 8:53 PM, luzuok luzuo...@126.com wrote:
I think it is better for COOT to solve this issue.
Coot already can be used to solve this issue - I think the automation is
somewhat lacking, but it's vastly preferable to anything involving a text
editor or shell commands.
On Fri, Sep 26, 2014 at 8:17 PM, Kimberly Stanek kas...@virginia.edu
wrote:
Before refinement in phenix the R/Rfree gap is rather small, however even
after one round of refinement I am finding that this gap increases to
almost 0.06. I have a feeling that the high symmetry present has
The tests that output twinning fractions are *not* diagnostic for twinning;
they merely estimate what the twin fraction would be if the data were in
fact twinned, which can only be decided on the basis of abnormal intensity
statistics. (Any version of Xtriage since July should state this more
In Python scripting (Calculate menu):
set_rotation_centre(x, y, z)
I assume there's a Scheme equivalent.
-Nat
On Tue, Sep 9, 2014 at 1:17 PM, Alejandro Virrueta
alejandro.virru...@yale.edu wrote:
Does anyone knowhow to move the center pointer to a specific x,y,z
coordinate? Or to place
On Thu, Sep 4, 2014 at 4:05 PM, CPMAS Chen cpmas...@gmail.com wrote:
Do you guys have some recommendation of the criteria? phenix reported
anomalous measurability, CCP4/aimless has RCRanom. Sometimes, they are not
consistent.
The measurability isn't always useful - it's definitely correlated
On Tue, Aug 12, 2014 at 10:28 PM, Keller, Jacob kell...@janelia.hhmi.org
wrote:
A somewhat similar question, with a quick answer I hope: when programs
output CC's of 1/2 datasets, are several random halvings compared/averaged,
and if not, does this make a difference, or are the scores so
On Wed, Jul 23, 2014 at 3:25 AM, MARTYN SYMMONS
martainn_oshioma...@btinternet.com wrote:
The practice at the PDB after deposition used to be to remove water
alternate position indicators - although obviously to keep their partial
occupancies.
This has not been my experience - see for
On Wed, Jul 9, 2014 at 5:14 PM, Chris Fage cdf...@gmail.com wrote:
Despite modelling completely into great electron density, Rwork/Rfree
stalled at ~38%/44% during refinement of my 2.0-angstrom structure
(P212121, 4 monomers per asymmetric unit). Xtriage suggested twinning,
with |L| = 0.419,
On Thu, Jul 3, 2014 at 7:50 AM, Nat Echols nathaniel.ech...@gmail.com
wrote:
On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de
wrote:
yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL
intensities as amplitudes, producing very different output
On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de
wrote:
yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL
intensities as amplitudes, producing very different output statistics,
compared both to the XDS statistics and to an mtz file with amplitudes
On Tue, Jul 1, 2014 at 3:10 PM, Katherine Sippel katherine.sip...@gmail.com
wrote:
My google-fu has failed me once again so I am turning to the collective
knowledge of the bb. I'm working on a blobology challenge at the moment and
have hit a wall. Is anyone aware of an ion that coordinates to
On Fri, May 16, 2014 at 7:12 AM, esse...@helix.nih.gov wrote:
Short of storing images, which is the ultimate preservation of primary
information, I have always been puzzled by the fact that the PDB only
stores
unique reflections i.e. no Friedel pairs even when provided. Is this
outdated
On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.uk
wrote:
It seems to me that the Wikipedia mechanism works wonderfully well. One
rule is that you can't make assertions yourself, only report pre-existing
material that is attributable to a reliable published source.
as unreliable since a
misconduct investigation by the University of Alabama at Birmingham has
concluded that it
was, more likely than not, faked [1]
[1] http://www.nature.com/news/2009/091222/full/462970a.html
On 15 May 2014 18:00, Nat Echols nathaniel.ech...@gmail.com wrote:
On Thu, May 15
On Wed, May 14, 2014 at 10:26 AM, Mark Wilson mwilso...@unl.edu wrote:
Getting to Eric's point about an impasse, if the PDB will not claim the
authority to safeguard the integrity of their holdings (as per their
quoted statement in Bernhard's message below), then who can?
I think this may in
On Tue, May 13, 2014 at 9:20 PM, Felix Frolow mbfro...@post.tau.ac.ilwrote:
Phenix does even more, it adds TER after ions and ligands, so again manual
messing is needed.
However they may have a jiffy to fix it.
phenix.sort_hetatms will remove them for you, although why this problem
was
On Wed, Apr 23, 2014 at 8:43 AM, Cygler, Miroslaw
miroslaw.cyg...@usask.cawrote:
I have inquired at Schrodinger about the licensing for PyMol. I was
surprised by their answer. The access to PyMol is only through a yearly
licence. They do not offer the option of purchasing the software and
On Wed, Apr 23, 2014 at 6:15 AM, World light bsub...@btk.fi wrote:
This discussion is very informative to fresher like me. Moreover, with
most of the reading suggested in this discussion I read about the
positively charged metal ions like Na, Ca, Mg and many more. I am curious
about Cl in
On Mon, Apr 21, 2014 at 3:36 PM, Faisal Tarique faisaltari...@gmail.comwrote:
Just in the continuation of my previous mail i again want to ask few
question on the metalloprotiens..Apart from factors like occupancy, B
factor, coordination sphere and metal ion-ligand distances to distinguish
Mg
On Fri, Apr 4, 2014 at 1:57 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
A more up-to-date reason is that programs calculate R values very
differently. If you take a PDB file refined with program X and put it
into program Y you easily get discrepancies greater than 5%.
This is actually
On Fri, Apr 4, 2014 at 9:36 AM, Alastair Fyfe af...@ucsc.edu wrote:
The topic brings up a question that I've been wondering about for some
time, perhaps someone can enlighten me. Why is it not standard practice to
deposit map coefficients along with structure factors ? Unlike image
On Fri, Apr 4, 2014 at 10:39 AM, Alastair Fyfe af...@ucsc.edu wrote:
Reconstructing the refinement may be necessary in some cases but there
are other applications (pdb-wide map statistics, development of map
analysis tools, quick model vs map checks) where access to the depositor's
final map
On Tue, Mar 18, 2014 at 6:59 PM, Remie Fawaz-Touma remiefa...@gmail.comwrote:
how do you place the pointer if there is no bond there? (just density) I
am trying to connect 2 sugars creating 2 bonds to one oxygen that I have to
add (oxygen does not exist now).
On my Mac, I can change the
On Thu, Mar 6, 2014 at 11:45 AM, Keller, Jacob kell...@janelia.hhmi.orgwrote:
I was curious whether there has been a rigorous evaluation of ion binding
sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine
that there is a considerably broad spectrum of habits and rigor in
On Tue, Feb 18, 2014 at 8:19 AM, Jan van Agthoven janc...@gmail.com wrote:
I'm filling out my table for NSMB, about a structure of protein ligand
bound to a receptor. They ask for 3 different lines regarding number
of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water.
Does my protein ligand
One comment (not a complaint) on all this: it seems like the same questions
get asked over and over again. If there is a good place for a general
crystallography FAQ list it is well past time for one to be put together -
or maybe it just needs to be better advertised? At a minimum, for instance:
On Mon, Dec 16, 2013 at 1:36 PM, Xiao, Junyu jx...@mail.ucsd.edu wrote:
Dear all, sorry if this topic does not interest you. I wonder whether
anyone has experience with freezing crystals grown in ~0.2 M Magnesium
Formate. Garman and Mitchell suggested that A major anomaly is solution
44, 0.2
On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp hofkristall...@gmail.comwrote:
Hmmm….does that mean that the journals are now the ultimate authority of
what stays in the PDB?
I find this slightly irritating and worthy of change.
http://www.wwpdb.org/UAB.html
It is the current wwPDB
On Tue, Nov 5, 2013 at 12:22 AM, Bernhard Rupp hofkristall...@gmail.comwrote:
Given their otherwise almost paranoid sensitivity to ultimate author
authority
(resulting in things like still having 2hr0 etc in the bank because
certain authors go AWOL or ignore major issues)
In defense of the
On Wed, Oct 23, 2013 at 1:10 PM, Kristin Low kristin@queensu.ca wrote:
I’m looking at upgrading my current laptop to a newer MacBook Pro. I’m
torn as to whether I need integrated vs discrete graphics for structural
biology, including molecular modelling, especially since the latest
On Thu, Oct 17, 2013 at 6:51 AM, Lucas lucasbleic...@gmail.com wrote:
I wonder if there's a list of problematic structures somewhere that I
could use for that practice? Apart from a few ones I'm aware of because of
(bad) publicity, what I usually do is an advanced search on PDB for entries
On Wed, Oct 9, 2013 at 6:56 PM, Marco Lolicato chimbio...@gmail.com wrote:
Anyway, for those reasons and more, I was wondering if maybe is nowadays
needed to revisit the peer-review process.
Apologies for the lengthy response, but I really do think the current
publication system is broken,
Levitt also contributed to DEN refinement (Schroder et al. 2007, 2010).
-Nat
On Wed, Oct 9, 2013 at 2:29 PM, Boaz Shaanan bshaa...@bgu.ac.il wrote:
Good point. Now since you mentioned contributions of the recent Nobel
laureates to crystallography Mike Levitt also had a significant
On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry ber...@upstate.eduwrote:
If you refine once in phenix you can use phenix.cc_star to calculate cc*
and compare with R and R-free; from the output mtz file and your unmerged
.sca file.
FYI, this should also work with structures refined in
On Wed, Aug 7, 2013 at 12:54 PM, James Stroud xtald...@gmail.com wrote:
All that needs to happen is that the community agree on
1. What is the finite set of essential/useful attributes of macromolecular
structural data.
2. What is the syntax of (a) accessing and (b) modifying those
On Wed, Aug 7, 2013 at 2:36 PM, James Stroud xtald...@gmail.com wrote:
Although it is likely the best library for working with structural data,
CCTBX requires a loop just to change a specific chain ID (to the best of my
knowledge):
...
I don't intend to pick on CCTBX specifically (because
On Mon, Aug 5, 2013 at 11:11 AM, Phil Jeffrey pjeff...@princeton.eduwrote:
While alternative programs exist to do almost everything I prefer
something that works well, works quickly, and provides instant visual
feedback. CCP4 and Phenix are stuck in a batch processing paradigm that I
don't
On Mon, Aug 5, 2013 at 12:37 PM, Boaz Shaanan bshaa...@bgu.ac.il wrote:
There seems to be some kind of a gap between users and developers as far
the eagerness to abandon PDB in favour of mmCIF. I myself fully agree with
Jeffrey about the ease of manipulating PDB's during work, particularly
On Mon, Jul 22, 2013 at 10:19 AM, Stefan Gajewski sgajew...@gmail.comwrote:
The maps shows signs of over fitting, the B-factors do not look correct in
my opinion.
What do correct B-factors look like? What refinement strategy did you
use for them?
Note that the R-free value in the 3.4A
On Fri, Jul 12, 2013 at 1:08 AM, Stefan Krimmer
krim...@staff.uni-marburg.de wrote:
in some of my macromolecular crystal structures with resolutions between
1.1 - 1.4 Å, several round positive Fo-Fc electron density blobs are
detectable which show after assignment of a water molecule to these
On Sat, Jun 22, 2013 at 3:18 PM, Frank von Delft
frank.vonde...@sgc.ox.ac.uk wrote:
In what scenarios would these improved estimates make a significant
difference?
Perhaps datasets where a unusually large number of reflections are very
weak, for instance where TNCS is present, or where the
On Thu, Jun 13, 2013 at 8:15 AM, Andrea Edwards edwar...@stanford.eduwrote:
I have some rather (embarrassingly) basic questions to ask. Mainly.. when
deciding the resolution limit, which statistics are the most important? I
have always been taught that the highest resolution bin should be
On Fri, Jun 7, 2013 at 8:37 AM, Pete Meyer pame...@mcw.edu wrote:
On the other hand, programming an implementation of something is a good
way to make sure that you really understand it - even if you end up using
another program.
I would argue that it's not really necessary to understand the
On Mon, Apr 15, 2013 at 11:47 AM, James Holton jmhol...@lbl.gov wrote:
However, I'm sure the day is not far off when phenix.refine or the like
will check if the starting R factor is too high and just automatically
invoke a run of MR to see if something clicks.
I think the latest Phaser code
On Fri, Apr 12, 2013 at 10:27 AM, James Holton jmhol...@lbl.gov wrote:
But, when it comes to GUIs, I have always found them counterproductive.
In my humble opinion, the purpose of computers and other machines is to DO
work for me, not create work for me, and I already have enough buttons to
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
bshaa...@exchange.bgu.ac.ilwrote:
Whichever way the input file for the run is prepared (via GUI or command
line), anybody who doesn't inspect the log file at the end of the run is
doomed and bound to commit senseless errors. I was taught a long
On Thu, Mar 28, 2013 at 11:28 AM, mjvdwo...@netscape.net wrote:
Although it is hard to imagine, there could be a mechanism by
which you make all your data public, immediately when you get it and this
public record shows who owns it.
http://deposit.rcsb.org
(or international equivalent)
The
On Fri, Mar 8, 2013 at 11:38 AM, Raji Edayathumangalam
r...@brandeis.edu wrote:
I am looking for two specific test cases (below) and appreciate anyone
pointing me to known structures/examples for the same.
(1) For a successful case of molecular replacement in which the search model
has an
On Mon, Feb 25, 2013 at 8:02 AM, lei feng spartanfeng...@hotmail.com wrote:
I need your suggestion for slowing down crystallization for my protein
my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but
it crystallize too fast. In 1 hr I can see tons of tiny needles.
Can
On Wed, Feb 20, 2013 at 12:39 PM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
it has been my experience that homology modelling programs get folds pretty
well, but sometimes the details are pretty obviously bad, like too-close
contacts. One might think that the modelling software would
If SPG buffer is what I think it is, that means you have a significant
concentration of inorganic phosphate, which forms salt crystals when
mixed with divalent metal ions.
-Nat
On Thu, Feb 7, 2013 at 2:24 PM, amro selem amro_selem2...@yahoo.com wrote:
Hallo my colleagues.
i hope every one
On Mon, Feb 4, 2013 at 12:24 PM, Roger Rowlett rrowl...@colgate.edu wrote:
It's possibly a transition metal ion. Zinc is a common adventitious
contaminant of solutions. Typical Zn-O distances (tetrahedral or
pseudo-tetrahedral coordination) are 2.0 A. ICP-OES or ICP-MS of the protein
solution
On Mon, Jan 28, 2013 at 8:04 AM, Antony Oliver
antony.oli...@sussex.ac.uk wrote:
If you don't mind using the ksDSSP implementation, it is already installed
with the phenix suite if you have it.
Correct, but although the method is supposed to be the same, the
output is not, and there are bugs
On Mon, Jan 28, 2013 at 8:39 AM, Robbie Joosten
robbie_joos...@hotmail.com wrote:
DSSP recently went open source with a very liberal license. So you can
consider using the real DSSP now. This may also be the moment to integrate
DSSP in CCP4.
Based on the info here:
On Fri, Jan 25, 2013 at 2:24 AM, Robbie Joosten
robbie_joos...@hotmail.com wrote:
Phenix however needs to deal with the CCP4 type reflection binning. Now the
size of the sets cannot be used which means that you have find a smarter
solution. So I wonder how this is implemented. Does Phenix use
On Thu, Jan 24, 2013 at 10:34 AM, Leonid Sazanov
saza...@mrc-mbu.cam.ac.uk wrote:
Most likely scenario is that Phenix by default assigns Rfree flag as 1, while
ccp4/refmac - as 0.
That would explain your Rfree going down - because your Rfree reflections
were refined by refmac.
According to
On Thu, Jan 24, 2013 at 3:52 PM, Urmi Dhagat udha...@svi.edu.au wrote:
If Rfree reflections are refined my refmac upon switching from phenix to
refmac then does this contaminate the Rfree set ? Should swiching between
refinement programs Phenix and Refmac be avoided?
Repeating what was said
On Tue, Jan 22, 2013 at 9:59 AM, Cara Vaughan
c.vaug...@mail.cryst.bbk.ac.uk wrote:
I've seen from the archive that some people do use the Mac Mini for
crystallography and I've got two questions:
1. Do I need the Quad core or is a Dual core processor enough?
You can survive with the dual, but
On Tue, Jan 22, 2013 at 10:05 PM, James Stroud xtald...@gmail.com wrote:
On Mac v. Linux where calculations come secondary to office-type
calculations, you have to weigh your level of vendor lock-in. Do you run
Libreoffice or Microsoft Office? Inkscape or Illustrator? Gimp or Photoshop?
On Wed, Jan 16, 2013 at 2:53 PM, Roger Rowlett rrowl...@colgate.edu wrote:
When you are a building a metalloenzyme model you should really have some
solid evidence that a metal ion is present by (1) inclusion in the
crystallization medium, (2) direct determination by an analytical technique,
On Mon, Jan 14, 2013 at 11:18 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
I admit not having read all contributions to this thread. I understand
the John Henry Challenge as whether there is an 'automated way of
producing a model from impossible.mtz'. From looking at it and without
having
Subject: Re: [ccp4bb]
Convert cbf to png/tiff? Date: Thu, 10 Jan 2013 12:47:21 -0800
From: Nat Echols nathaniel.ech...@gmail.com To: Frank von
Delft frank.vonde...@sgc.ox.ac.uk
Using any recent Phenix distribution:
labelit.png file_name
For reasons unknown
On Mon, Jan 7, 2013 at 1:28 AM, Xiaopeng Hu huxp...@mail.sysu.edu.cn wrote:
We recently resolved an enzyme/inhibitor complex structure. The enzyme
contains two NCS related active site and we did find extra density in both of
them.However we observed that the two inhbitor moleculors are not
On Thu, Nov 8, 2012 at 12:20 AM, Mark J van Raaij
mjvanra...@cnb.csic.es wrote:
Depends on what you call a solved structure.
For deposition to the pdb ideally there should be very little clashes like
Nat writes.
But perhaps you are referring to the clash score just after molecular
On Wed, Nov 7, 2012 at 4:02 PM, Meisam Nosrati meisam.nosr...@gmail.com wrote:
I want to know what is considered an acceptable Clash Score for a solved
structure.
The recommendation from MolProbity is less than 10. If you have
low-resolution data and don't have a high-resolution starting
On Tue, Nov 6, 2012 at 12:06 PM, saleem raza mysaleemr...@hotmail.com wrote:
I have to put water molecules in my model but It's difficult to judge that
electron density is for water of something else. How to differentiate
How the electron density look like for metal ions like Ca and Na???
On Tue, Oct 30, 2012 at 12:12 PM, Jim Pflugrath
jim.pflugr...@rigaku.com wrote:
How would you distinguish between a mixture of Ca and Zn in the same
locations?
How often would they be likely to bind in the same place? Some of the
other transition metals are difficult to tell apart, but Ca and
On Tue, Oct 23, 2012 at 9:55 AM, Meindert Lamers
mlam...@mrc-lmb.cam.ac.uk wrote:
Is there any convention on the numbering of residues in a fusion protein?
I have a structure of two domains fused together but would like to keep the
biological numbering intact.
1st domain: residue 200-300
On Tue, Sep 25, 2012 at 6:51 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
I would assume that someone who publishes crystallisation conditions has
given up solving the structure or some other reason to encourage others
to pick up the project, i.e., no, I don't see much point NOT
publishing
On Wed, Sep 12, 2012 at 7:32 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
since this probably comes up a lot in manipulation of pdb/reflection files
and so on, I was curious what people thought would be the best language for
the following: I have some huge (100s MB) tables of
On Wed, Sep 12, 2012 at 12:49 PM, James Stroud xtald...@gmail.com wrote:
Also, python (aka python 2) and python 3000 (aka python 3) are considered
two different languages. It's not reasonable to consider them one language
and then complain that they are incompatible. Python 3 was created as a
On Thu, Aug 23, 2012 at 10:44 AM, Jim Pflugrath
jim.pflugr...@rigaku.com wrote:
Singly-measured reflections should have a sigma from Poisson counting
statistics, so that should not be a problem. A problem might occur if the
X-ray background is exactly zero and the observed (sic) intensity is
On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)?
On Thu, Aug 9, 2012 at 8:14 AM, Quentin Delettre q...@hotmail.fr wrote:
I have seen that in the last Mac Os, X11 have been removed... But can still
be used with some package installation.
I guess it isn't distributed with the OS any more - but it is still available:
On Thu, Aug 9, 2012 at 12:52 PM, Lee, Ting Wai twlee.scie...@gmail.com wrote:
May I ask a very general question? I am going to buy a laptop. I am going to
do a lot of structural biology work on it using programs such as CCP4,
Phenix, Coot and Pymol. Mac or PC, which is better?
See this
On Wed, Aug 1, 2012 at 11:27 AM, Uma Ratu rosiso2...@gmail.com wrote:
The protein is in tetramer form. I define this by using the residue number
(1332) which is 4 x monomer.
After run, Phaser only gave 9 partial solutions, and no solution with all
components. The resulted PDB contains only
On Tue, Jul 24, 2012 at 10:14 AM, Haytham Wahba haytham_wa...@yahoo.com wrote:
1- if i have anomalous peak of unknown heavy atom, How can i identify this
heavy atom in general. (different methods)
2- in my case, i see anomalous peak in heavy atom binding site (without any
soaking).
On Tue, Jul 24, 2012 at 10:33 AM, Ethan Merritt
merr...@u.washington.edu wrote:
As to the home source - no.
Neither Cu nor Zn has appreciable anomalous signal when excited with a
Cu K-alpha home source.
http://www.bmsc.washington.edu/scatter
An element's emission edge (Cu K-alpha in this
On Mon, Jul 23, 2012 at 9:50 AM, Scott Foy s...@mail.umkc.edu wrote:
We are computationally averaging several homologous protein structures into a
single structure. This of course will lead to a single protein structure that
possesses poor biophysical characteristics of bond lengths, bond
On Fri, Jul 13, 2012 at 2:19 PM, Radisky, Evette S., Ph.D.
radisky.eve...@mayo.edu wrote:
Several have mentioned harvesting in the cold room to reduce evaporation. I
used to do this also as a postdoc, but I worried whether I risked nitrogen
gas poisoning from liquid N2 boil-off, since the cold
On Sun, Jul 8, 2012 at 2:11 PM, James Garnett j.garn...@imperial.ac.uk wrote:
I have found a molecular replacement solution in I212121 using an NMR
structure of the same protein and MR-ROSETTA/PHENIX (PHASER LLG=128
TFZ=12.3), although I can not refine this below R ~45% and Rfree ~50%. The
On Wed, Jun 20, 2012 at 11:13 AM, sonali dhindwal
sonali11dhind...@yahoo.co.in wrote:
I am working on a protein for last so many years and for which i have got
crystal now in a tray which i kept 1 years ago. It diffracts well and
resolution is 2.2A, which is good.
I indexed in HKL2000,
On Tue, Jun 19, 2012 at 8:35 AM, RHYS GRINTER
r.grinte...@research.gla.ac.uk wrote:
There's no significant difference between the high res and low res proteins
in the shared region (amino acid 38+) (r.m.s.d 0.46 A), and the while there
is broken density for the first 38aa from the full length
On Tue, Jun 12, 2012 at 8:53 PM, Frank von Delft
frank.vonde...@sgc.ox.ac.uk wrote:
Finding 111 sites should be feasible without other tricks than very careful
data collection (see below); if you have two or more copies in the ASU, you
may find you need to do what the ribosome guys did, namely
On Sat, May 5, 2012 at 2:23 PM, Pavel Afonine pafon...@gmail.com wrote:
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
On Sat, Apr 7, 2012 at 9:50 AM, Roger Rowlett rrowl...@colgate.edu wrote:
I don't know the state of current software, because I haven't tried
recently, but when I set up my student crystallography workstations a few
years back I noticed many packages (e.g. EPMR, Phaser) that had potentially
On Mon, Apr 2, 2012 at 11:00 AM, Maria Sola i Vilarrubias
msv...@ibmb.csic.es wrote:
About a wrongly fit compound, the reviewer can ask images about the model in
a map calculated at a specific sigma and in different orientations.
This will often be insufficient, I'm afraid. We generally assume
On Fri, Feb 10, 2012 at 12:29 PM, James Stroud xtald...@gmail.com wrote:
How could they not be snapshots of conformations adopted in solution?
Packing billions of copies of an irregularly-shaped protein into a
compact lattice and freezing it to 100K isn't necessarily
representative of solution,
supporting the
physiological crystal structures
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat
Echols
Sent: Friday, February 10, 2012 10:35 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Crystal Structures as Snapshots
On Fri, Feb 10
On Wed, Feb 1, 2012 at 11:17 AM, Dianfan Li l...@tcd.ie wrote:
I am working on a kinase and would like to get an ATP analogue into
the crystals. When soaked with AMP-PCP, the kinase crystals crack in
about 15 min at 4 C.
This isn't too surprising; most kinases undergo global conformational
On Tue, Jan 24, 2012 at 1:38 AM, Adam Ralph adam.ra...@nuim.ie wrote:
CUDA is a set of extensions for C which will allow you to access hardware
accelerators (certain NVidia cards in this case). CUDA has been around for
a
while and there are CUDA libraries for FFT and BLAS.
I have not
On Tue, Jan 24, 2012 at 10:24 AM, Ian Tickle ianj...@gmail.com wrote:
reassuring air of finality! Maybe a Python expert will answer this
but I've often wondered, what happens if as some editors do
(particularly if as I do you have to use different editors at
different times depending on where
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