On Thu, 2011-11-17 at 11:10 +, Eleanor Dodson wrote:
If you dont like it - delete it..
Eleanor
I know. But what I want is to skip the calculation in some cases when
the map is not needed. This currently is impossible without modifying
the refmac code.
Ian provides an excellent example
On Thu, 2011-11-17 at 14:03 -0600, Yi-Liang Liu wrote:
Hi CCP4ers,
I know it is not quiet related to CCP4. I am now working on a protein-protein
complex system. I am wondering which kits I should try in a higher priority?
I appreciate everyone's suggestions, and maybe there are some papers
On Wed, 2011-11-16 at 09:26 +, Tom Murray-Rust wrote:
That way you should be able to
quickly identify any hits that are due to salt, and which are likely
to be your protein.
Just a footnote to Tom's excellent comment:
It is possible to have actual protein crystals to grow alongside salt
Is there some way to make refmac *not* to produce the output mtz file,
i.e. skip the whole FWT/DELFWT calculation altogether?
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
Could anyone point me towards instructions on how to get/build
parallelized phaser binary on linux? I searched around but so far found
nothing. The latest updated phaser binary doesn't seem to be
parallelized.
Apologies if this has been resolved before - just point at the relevant
thread,
problems!
BW, Gabor
On Nov 8 2011, Ed Pozharski wrote:
Could anyone point me towards instructions on how to get/build
parallelized phaser binary on linux? I searched around but so far found
nothing. The latest updated phaser binary doesn't seem to be
parallelized.
Apologies
On Mon, 2011-11-07 at 05:19 +, Sam Arnosti wrote:
Hi everyone
I have a protein that is extraordinarily stable at PH=3.0 or even 2.0.
I want to crystallize it in the low PH and compare the differences between
the crystals in regular PH and low PH.
I was wondering how people set up
If you post the cad input file, it should be easy to pinpoint the
problem. As it stands, you are either:
1) Including Miller indices as merged columns - they get done
automatically, so if you specify them, you get the duplicate labels
2) You actually do have the same name for the two columns in
On Mon, 2011-10-31 at 15:57 +, Ivan Shabalin wrote:
As a result, red peeks around Se are significantly lower, Se B-factors are a
bit smaller (like 25.6 and 23.1), and Rf is lowered by a bit more than 0.1%
with the same input files.
Hope others will comment to clarify my confusion:
It
factor are blurred out by the much wider
B-factor Gaussian. It doesn't hurt to model the atoms form factors
properly, but in almost all cases of MX, some other source of error is
more important.
-James Holton
MAD Scientist
On 11/1/2011 6:55 AM, Ed Pozharski wrote:
On Mon, 2011-10
For reasons I cannot explain even to myself I chose to use the PDBe to
deposit the next structure (instead of RCSB). Curiosity may be one.
This is a protein-DNA complex refined with latest refmac/coot and it
uses (I presume) the modern naming convention (i.e. DA/DT/DG/DC for
nucleotide names).
I am absolutely sure this has been discussed before, and I have just
re-convinced myself that refmac reports the number of reflections in
just the working set, and not the total number of reflections. So my
question is
Is there a reason why the PDB ADIT tool imports the Nwork from the
refmac pdb
On Thu, 2011-10-27 at 20:46 -0500, Jacob Keller wrote:
I went back to using
the original mtz from scala
Curious. What were you using - the refmac output mtz? Just for the
record - the refmac output mtz contains *modified* amplitudes, and Garib
said many times it should not be used as the
Just to verify, is this by any chance *unrestrained* refinement?
On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Kenneth A. Satyshur,
what is your weight set to? If it is set to 'auto', try setting it to a
specific value and lower
On Thu, 2011-10-27 at 15:36 +0200, George M. Sheldrick wrote:
In non-continuous mode, the goniometer has
to accelerate at the start of a frame and decellerate at the end, then
wait for
the frame to be read.
Someone should be able to confirm this, but I was under impression that
at
is much more serious than it is
perceived.
Before you provide sufficient evidence everybody will have their
opinion.
Garib
On 27 Oct 2011, at 17:08, Ed Pozharski wrote:
I am curious as to what the collective opinion on the raw data
deposition actually is across the cross-section
Sorry, the results in a pie-chart form are available here (but the
spreadsheet may be useful too if you want to see what is meant by
other)
https://docs.google.com/spreadsheet/viewanalytics?hl=en_USformkey=dHh4cjdLZGZrSEpUOG9kV2hkb3ZXNHc6MQ
--
Oh, suddenly throwing a giraffe into a volcano to
wishes,
Gerard.
--
On Thu, Oct 27, 2011 at 12:08:24PM -0400, Ed Pozharski wrote:
I am curious as to what the collective opinion on the raw data
deposition actually is across the cross-section of the macromolecular
crystallography community subscribed to the bb. So
Dear Adrian,
thank you - this is most helpful in assessing why we do or don't need to
deposit the raw data.
However:
And let me say that, as this bb hardly reaches ALL practicing MM
crystallographers, but only those with an interest in techniques, the
results AND discussion are heavily
On Wed, 2011-10-26 at 10:33 +0200, Tim Gruene wrote:
with every python script one has to distribute a specific python
version
... and with every program one has to distribute binaries for every
platform... more food for my prejudice against software ;-)
This really is not about python, it's
This thread may be relevant
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg18422.html
On Wed, 2011-10-26 at 15:06 +1000, khuchtumur bumerdene wrote:
Hello,
Does anyone know where I could download frm2frm utility from Bruker?
Is it even possible to do so?
--
Hurry up before we all
On Wed, 2011-10-26 at 10:15 -0400, Ke, Jiyuan wrote:
flat sheet option
IIUC, the set command in pymol allows per-selection application, i.e. if
you try this in the command line instead of checking the option in the
menu
set cartoon_flat_sheets, 0, blah
where blah is your selection.
--
Oh,
Assuming you are dealing with a pure twist, isn't the polar rotation
angle reported by lsqkab or superpose what you are looking for?
On Thu, 2011-10-27 at 04:16 +, Debajyoti Dutta wrote:
Hi all,
Does anybody know of any software to calculate the twist angle between
two monomers in a
On Mon, 2011-10-24 at 18:18 +0530, faisal tarique wrote:
Hello everyone
Is there any online server which could convert 3D structure of a
protein into 2D image, the way program molscript does ?
--
Regards
Faisal
School of Life Sciences
JNU
One option is to directly access
As Sabine said, you need to make sure that the monomer is defined as DNA
type. The best way to figure out how to do this is to look at the
standard monomer library for nucleotide, e.g.
$CCP4_LIB/data/monomers/d/DA.cif.
On Sun, 2011-10-23 at 18:44 -0400, zhang yu wrote:
Hi Sabine,
Thanks for
On Wed, 2011-10-19 at 12:20 +0100, Leonid Sazanov wrote:
Hi,
If I have two somewhat different overlayed models, is it possible in
COOT to replace part of one model by another?
Similarly to O command: merge_atoms from_molecule residue_start
residue_end to_molecule residue_start ?
That's a
My question is - is it necessary that we deposit a structure, which
PISA predicted as most probable assembly in PDB as an
asymmetric unit biological assembly or can we deposit a dimer
(asymmetric unit) and give explanation for the biological assembly
according to what PISA predicted.
As
Why not do the molecular replacement - 6kDa is rather small but it most
likely will work
On Wed, 2011-10-19 at 06:13 -0700, Afshan Begum wrote:
Hello CCP4 user
I have collected a data set 2.1 for my complex. Actually after first
run of Rafmac i can see the density for my inhibitor but the
On Wed, 2011-10-19 at 12:45 -0500, Jacob Keller wrote:
Is there an
alternative water-picker in the gui?
watertidy is not a water-picker
--
I'd jump in myself, if I weren't so good at whistling.
Julian, King of Lemurs
Not sure where you quoting this from. I am looking at the official
documentation here
http://www.ccp4.ac.uk/html/watertidy.html
which clearly states
This program has two purposes.
1. It moves the H2O coordinates to the symmetry related position
nearest to the host molecule.
On Wed, 2011-10-19 at 20:17 +0100, Jyotica Batra wrote:
Dear users,
Are there any programs to calculate percentage of buried surface area that is
polar vs nonpolar?
Thanks in advance
Thanks!
Jyotica
Surface Racer includes breakdown by atom type (polar vs nonpolar) in the
output:
.
The russian translation of KernighanRitchie was my first programming
book, and seemingly the only one I ever needed.
--
Ed Pozharski epozh...@umaryland.edu
University of Maryland - Baltimore
On Tue, 2011-10-18 at 18:17 +0100, Gerard Bricogne wrote:
it would be of the greatest value to that
investigator to be able to double-check how reliable some features of
that
structure (especially its ligands) actually are.
Certainly, one could argue here that the current PDB policy that
Selecting a test set that minimizes Rfree is so wrong on so many levels.
Unless, of course, the only thing I know about Rfree is that it is the
magic number that I need to make small by all means necessary.
By using a simple genetic algorithm, I managed to get Rfree for a
well-refined model as
Did you check for twinning? The most radical approach is to reprocess
in P1 and see what R-values you get
On Mon, 2011-10-17 at 15:09 -0200, Napoleão Valadares wrote:
Hi there!
I got crystals from some synthetic peptides I bought, they are 30
residues long and are supposed to form a
On Sat, 2011-10-15 at 11:48 +0300, Nicholas M Glykos wrote:
For structures with a small number of reflections, the
statistical
noise in the 5% sets can be very significant indeed. We have seen
differences between Rfree values obtained from different sets
reaching
up to 4%.
This
This is a follow up (or a digression) to James comparing test set to
missing reflections. I also heard this issue mentioned before but was
always too lazy to actually pursue it.
So.
The role of the test set is to prevent overfitting. Let's say I have
the final model and I monitored the Rfree
On Fri, 2011-10-14 at 13:07 -0700, Nat Echols wrote:
You should enter the statistics for the model and data that you
actually deposit, not statistics for some other model that you might
have had at one point but which the PDB will never see.
If you read my post carefully, you'll see that I
On Fri, 2011-10-14 at 23:41 +0100, Phil Evans wrote:
I just tried refining a finished structure turning off the FreeR
set, in Refmac, and I have to say I can barely see any difference
between the two sets of coordinates.
The amplitude of the shift, I presume, depends on the resolution and
data
On Wed, 2011-10-12 at 18:18 -0700, Paul Smith wrote:
and have heard some good things about Bio-rad
Personally, my experience with Biorad was very positive. For instance,
we had the switch valve motor burn out and they sent us the motor for
$150 or so while they could have charged us full price
On Thu, 2011-10-13 at 11:25 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote:
Dear All,
For all monomers (3 letter) used in COOT, where can i find the full names of
the
whole library? Many thanks
stephen
Assuming that you have ccp4 configured, you can use this one-liner
find
On Tue, 2011-10-11 at 15:24 +, Bruno KLAHOLZ wrote:
However, once you have determined and refined your structure it may be
worth predicting the intensity of these spots and put them back for
map calculation,
REFMAC does this by default, because
expected value of unknown structure factors
On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote:
better, but not always. What about say 80% or so complete dataset?
Filling in 20% of Fcalc (or DFcalc or bin-averaged Fobs or else - it
doesn't matter, since the phase will dominate anyway) will highly bias
the map towards the model.
On Tue, 2011-10-11 at 11:54 -0700, Pavel Afonine wrote:
Yep, that was the point - sometimes it is good to do, and sometimes it
is not, and
Do you have a real life example of Fobs=0 being better? You make it
sound as if it's 50/50 situation.
--
Hurry up before we all come back to our senses!
On Wed, 2011-10-05 at 17:36 -0500, Jon Schuermann wrote:
If I'm not mistaken it is caused by /tmp/'username' not existing or
being writable...
Jon
I can't reproduce this behavior by removing writing permissions
from /tmp/$USER. ccp4i starts without a complaint (I guess I'd get into
On Tue, 2011-10-04 at 15:25 -0700, Jun Liao wrote:
I want to calculate the surface curvature for my proteins in a
quantitative way and show the results in a graphics software such as
Pymol
Surface Racer
http://apps.phar.umich.edu/tsodikovlab/index_files/Page756.htm
will output curvature per
On Wed, 2011-10-05 at 10:36 +0800, Jobichen Chacko wrote:
I looked into our previous posts and tried to locate the ccp4.LOCK
file, but I cannot find one in my system.
Curiously, neither can I with the ccp4i currently running. Maybe this
info is outdated, and you should try deleting
On Sun, 2011-10-02 at 15:56 -0500, Jacob Keller wrote:
Transfer them to higher pH, and hope
for the best?
Consider crosslinking your crystals with glutaraldehyde. They will then
became virtually insoluble, although it's possible that you may lose
diffraction at elevated pH.
--
Hurry up
...resisted the temptation to express redundant/easily
objectionable/useless opinion on the virtues of different OS
environments for two days... can't hold any longer... the power of one
ring is too strong... the only useful suggestion on automatic update of
proprietary nvidia drivers has already
On Fri, 2011-09-30 at 10:49 -0400, Patrick Loll wrote:
Has anyone encountered a case in which a construct with the native
sequence expressed poorly (or not at all?) in Rosetta(DE3), but the
corresponding construct with a codon-optimized sequence expressed
well? (The gene in question is from
On Mon, 2011-09-26 at 20:42 +0100, Matthias Zebisch wrote:
However, it is not
possible to use it within CCP4, eg. for a subsequent superposition.
What do you mean by that? Do you get an error when you use the
superpose output pdb with some other program?
--
I'd jump in myself, if I
On Wed, 2011-09-21 at 18:04 +0100, Peter Hsu wrote:
Or is this just a crazy/bad idea?
If there is one thing that I learned about crystallization, is that very
few ideas are so crazy that they are bad (i.e. not worth trying). Well,
if dried seaweed and ground horse hair are good for seeding, I
On Thu, 2011-09-15 at 22:20 -0400, m zhang wrote:
Second is about reusing of Ni-NTA resin. According to Qiagen's
instruction, after using fresh Ni-NTA resin, one only needs to wash
the used Ni resin first with 0.5M NaOH, then with your own buffer.
After that the resin is ready to be reused
On Fri, 2011-09-16 at 15:28 +0530, K Singh wrote:
Dear All,
Can anyone suggest me a protocol for silver-staining the PAGE that is
already stained with Coomassie.
Kris
Just destain it and then use the standard silver-staining protocol. If
for some reason you want to have both stainings
On Fri, 2011-09-16 at 10:08 -0400, Ming wrote:
The methionine has half selenium and half sulfur.
Do you have the evidence that your incorporation ration was 50%?
On a practical side, try giving the SeMET a different chain ID. You can
change it back manually after refinement. Assuming that the
On Fri, 2011-09-16 at 14:10 -0400, Narayanan Ramasubbu wrote:
Dear All:
I would like to know the literature on the crystal structure of
Leukocyte Function-Associated Antigen One (LFA-1, CD11a/CD18).
I have the structure of I domain but not for the entire molecule. I
would greatly appreciate
On Thu, 2011-09-15 at 20:50 +0100, Andrew Purkiss-Trew wrote:
Molecular Dimension do such an adaptor which fits to existing
microscopes.
Do you by any chance know the price? I can seemingly order it through
the website for the hefty price of $0.00, which is too good to be true.
--
Hurry up
On Thu, 2011-09-15 at 15:10 -0500, Jacob Keller wrote:
Maybe one should do a gradient of
gluteraldehyde concentrations, then plot the deviation of the observed
cross-linked oligomerization from a theoretical null hypothesis?
Right - just do it side-by-side with a protein known to be monomeric
On Wed, 2011-09-14 at 14:06 -0400, Emmanuel Saridakis wrote:
If
not, is there another way to check my point group/spacegroup starting
from
Denzo/Scalepack?
If you are trying to choose the screw axes, you can always look at the
systematic absences. This script may be useful in extracting the
On Tue, 2011-09-13 at 08:55 +, #HEW KAI LI KELLY# wrote:
However, Rfree refused to go down any further and it's still around
30-31%
And you have built the DNA already, right?
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
On Sat, 2011-09-10 at 15:00 +0800, anita p wrote:
Would it be worth while to try and remove glycerol at the last step
which is gel filtration and then set trays in my case?
Sure, assuming that your protein does not become unstable without
glycerol (protein solubility is likely to decrease
The best X-ray related typo I ever seen was the Small angel scattering
- poor little things!
On Fri, 2011-09-09 at 18:23 -0400, Patrick Loll wrote:
Still doesn't beat my all-time favorite, an early Microsoft spell-checker
that changed diffract to defrocked.
I forgot to mention how
On Sat, 2011-09-10 at 08:21 +0200, Miguel Ortiz Lombardía wrote:
A, C and G are RNA nucleotides. T is (mostly) not, its RNA-equivalent
is
uridine phosphate, U.
Right, that was my suspicion. But I thought that RNA bases would be Xr,
not Xd. Plus, refmac does not complain about missing
On Thu, 2011-09-08 at 16:58 +0200, Miguel Ortiz Lombardía wrote:
Perhaps the Nd/DN issue was solved between revisions 3470 and 3628 ?
Indeed. I just built the rev 3633 and it works fine. Autobuild scripts
used to have some problems on Lucid, but this time it worked perfectly.
This evolved
After switching (finally) to 6.2.0 and therefore to Refmac 5.6.0117 I
have found a problem working with DNA that I have not seen with
6.1.13/5.5.0109. Namely,
- if I use the pdb file produced by Coot (0.7.pre-1.3470) that seems to
output DNA as Ad/Td/Gd/Cd no matter what the input names were,
On Tue, 2011-09-06 at 11:51 -0500, Chaudhary, Ritcha wrote:
Do people use regular screens used in macromolecular crystallization
such as Hamptons, wizards etc?
Probably not - I believe short peptides are crystallized mostly via
various evaporation techniques (but I am very curious to hear what
I am almost sure this has been addressed before, so you can go after me
for insufficient googling. However,
1. Is there any *significant* advantage in using 64-bit CCP4 binaries
(primarily speed)?
2. IIUC, the standard CCP4 download results in 32-bit binaries being
run on a 64-bit system.
On Tue, 2011-08-30 at 09:55 -0500, Pete Meyer wrote:
but I'm all in favor of dropping gui's for tasks
that don't involve dealing with graphical data
second that. I was about to say while it is not expected that everyone
practicing crystallography should master the use of command line, but
On Tue, 2011-08-23 at 09:44 -0400, Yamei Yu wrote:
Is there a protein that it could interact
with different proteins by the same part (maybe the same part but in
different conformations?)?
Lysozyme interacts with two antibodies, HyHel-5 and D44.1 via the same
epitope but different set of
On Tue, 2011-08-23 at 11:30 -0600, Francis E Reyes wrote:
What's a way to determining a B-factor to set for all residues of a
model at low resolution (4A)?
Why not refine the overall B-factor? Even at 4A it should still be
legitimate.
--
Oh, suddenly throwing a giraffe into a volcano to make
On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote:
Seems to be a quiet day on the BB
So you need an earthquake :)
This is similar, imho, to the issue of disordered side chains:
On Tue, 2011-08-23 at 12:19 -0700, Tiago Barros wrote:
Does anyone know a program that will check a PDB file for missing
atoms and output a list of the corresponding residues?
REFMAC reports a (truncated?) list in the log file. Coot can also
identify missing atoms. I would be pretty sure
On Thu, 2011-08-18 at 17:23 +0100, WENHE ZHONG wrote:
Dear all,
I would like to show the visible metal-residue interaction during the
Morph movie. Anyone knows how to do that in Chimera? Thank you.
King regards,
Wenhe
IIUC, you have worked out how to generate the morph trajectory
On Fri, 2011-08-05 at 15:48 +0100, WENHE ZHONG wrote:
Hi all,
Sorry for a little bit out of topic question. Morph Serve is the only
online server I know to make movie for protein motion. But what I want
to do is to make a movie to show one single side chain flip. It seems
Morph could not do
On Thu, 2011-08-04 at 13:06 +0530, vandana kukshal wrote:
in a PDB with 2 A resolution many atoms of side chan if argenine and
aspartate , lysine and glutamate are missing due to weak electron
density
Aha! Take that, non-believers in the wisdom of the end user! :) Hope
it does not revive
On Thu, 2011-08-04 at 08:10 -0400, james09 pruza wrote:
Refmac is giving the error No reflections in resolution bin??? It
seems there is no SigFP column. I wonder how to fix the problem.
This, of course, depends on the origin of the data. Most data processing
software will include the
On Fri, 2011-07-29 at 20:08 +0100, Yuri wrote:
Dear all,
I have just downloaded and installed the ccp4-6.2.0.
It says all I should do next is source the /setup-scripts/csh/ccp4.setup
file... I have done that, but I cannot launch the program...
Any help is welcome...(it is probably something
On Thu, 2011-07-28 at 05:07 +0100, Sean Seaver wrote:
Spoiler - Fabs like ammonium sulfate.
Not really - in my hands the ammonium sulfate was one hit out of 7.
While Ivan's question is about Fab complexes with protein antigen, I
think it brings up a more general question of protein
On Thu, 2011-07-28 at 14:35 +, Jung-Hoon Lee wrote:
Acta Cryst D63 (2007), 550-554.
I can't believe Cornell has no access to Acta D.
--
Hurry up before we all come back to our senses!
Julian, King of Lemurs
On Wed, 2011-07-27 at 13:42 +0100, Charles Allerston wrote:
I am trying to decide on the many variables I need to consider to
attempt a co-crystal between a protein I work on and a DNA oligo of
~35nt in length.
In my somewhat limited protein:DNA crystallization experience, the less
pure
On Tue, 2011-07-26 at 09:51 -0400, zhang yu wrote:
I would like to have a close look at the reflections. for example, the
average I/sigma for reflections with h+k=2n+1 and reflections with h
+k=2n.
Once you have your reflections listed in a file having h,k,l,f,sigf as
first five columns (e.g.
On Mon, 2011-07-25 at 13:24 -0400, zhang yu wrote:
which software could calculate and output non-crystallography symmetry
operator?
LSQKAB, SUPERPOSE - there are other options, of course
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
I recall using CME some time ago (within last couple of years) without
problems. Also, an alternative approach is to incorporate BME as a
separate residue instead - the disulfide bond will be correctly
identified by refmac. I would think ideologically this is more
appropriate - using a different
Just a general curiosity - did I miss the release announcement for the
6.2.0 version on the bb or is it the CCP4 policy not to make such
announcements? Perhaps the idea is to prevent people rushing to
download the latest release and crushing the server :)
--
I'd jump in myself, if I weren't so
On Fri, 2011-07-15 at 09:26 +0100, Phil Evans wrote:
Ed. You could count them from the unmerged output as you say, or I
could make you a special version of SCALA or Aimless maybe next week
Phil,
that would be fantastic! Hope there is broader interest in such option
(beyond Robbie and
I am looking for a way to output redundancy per individual reflection,
preferably for scala but if that is not possible then maybe for
scalepack.
From my (admittedly quick) look at the scala manual it seems that I can
use something like UNMERGED output option to exclude outliers and then
would
Fairolniza,
my experience with multiple crystal forms growing from the same drop (I
had 4 that I was able to identify, there could have been more) was that
there were similarities in the way protein molecules packed into
fibers that were subsequently arranged into distinct crystal forms.
You may
Raji,
Assuming that the real space group is P212121, in P21 you will still get
a solution except for the extra NCS which will closely resemble the
extra 2-fold screw. Then you can probably tell if there are any
significant differences between NCS-related copies that justify lower
symmetry space
On Fri, 2011-06-24 at 09:50 +0200, mullapudi edukondalu wrote:
Dear Members,
I have my first data set on one of my protein crystals, that diffract
to 2.7 A, and the space group is I222. According to Mathews
coefficient, there should be 4 molecules in the asymmetric unit. But,
when I run
On Thu, 2011-06-23 at 16:49 +0900, Masaki UNNO wrote:
Dear all
Is it possible to put restraint on only peptide bonds? I would like
to put restraint on O-N bond lengths, Ca-O-N angles, and O=O-N angles.
Could you teach me how to do it, if possible?
Masaki UNNO, Ph.D.
One could create a
On Wed, 2011-06-22 at 14:10 +0200, Petr Kolenko wrote:
Some of them have 2.7 AA contacts to main chain!
it may be a good idea to report this to the PDB, this seems like a
bug.
--
Hurry up before we all come back to our senses!
Julian, King of Lemurs
I have a 3.2A dataset for a protein-DNA complex. The protein is
a homodimer, and the DNA is almost palindromic (except one base pair
in the middle and two or three base pairs at both two ends). It is my
first time solving structures, and unfortunately the resolution is
low. No body in
On Fri, 2011-06-10 at 12:48 -0700, Ethan Merritt wrote:
I don't think that combination makes any sense. Whatever anisotropic
is being described by the TLS parameters can also be fully described
by the individual anisotropic U^ij terms. So the TLS parameters are
entirely redundant, leading
Kay,
The Wikipedia's error propagation article in its Caveats
and Warnings paragraph calls this a Cauchy distribution.
And that sounds strange to me. p.d.f. of the Cauchy distribution is
non-zero for any finite argument, whereas the p.d.f. for the inverse
Gaussian must tend to zero at x-0,
That is, I think that a correct procedure could be to convert model to
structure factor and then obtain intensities squaring the SF.
Does anyone know how can I do?
Use sftools
--
Hurry up before we all come back to our senses!
Julian, King of Lemurs
On Tue, 2011-05-03 at 13:27 +, Jahan Alikhajeh wrote:
term insertion code.
Does anyone know anything about it? what is it used for?
It may be used to follow WuKabat numbering for antibodies. Frankly, it
it is something that can be easily avoided (after all, 32A is simply the
33rd
On Tue, 2011-05-03 at 18:06 +0100, Ian Tickle wrote:
So Ed, it's not just
relevant to the WuKabat numbering for antibodies.
Obviously, it was meant to be an example of use, not the only example.
The idea that
one would _not_ use consistent numbering (and therefore insertion
codes) across
On Mon, 2011-05-02 at 15:48 +0800, anita p wrote:
What are the reasons behind nonreproducibility of protein crystals?
There are many possible reasons. You could start by checking you
protein stock for signs of degradation and preparing it afresh.
--
Hurry up before we all come back to our
Is there any way to download all of the files produced by a BALBES run
on YSBL server at once (as opposed to going through every item
individually)?
A related question is what is a minimal set of files I will actually
need to analyze the solution? refmac_final_result.* and summary.log -
is
On Tue, 2011-04-26 at 08:48 -0400, Peter Randolph wrote:
My PI has mentioned a Mock Dataset made available by the ACA for
various programs (HKL etc) to practice with, but I haven't been able
to find it and was wondering if anyone knew of any,
Thanks,
Peter Randolph
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