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
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. Work
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
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, ref
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 int
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 too
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 menti
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 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 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
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
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 monomer
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 sup
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 apprec
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 d
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 wer
...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 b
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 Fri, 2011-09-30 at 10:17 -0500, Craig A. Bingman wrote:
> This is quite different than being explicitly optimized to express
> mammalian proteins.
Sure - what I meant was optimized codon usage. I guess to answer the
original question, one could use rare codon calculator
http://nihserver.mbi.uc
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 b
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 p
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 "database
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
t
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 facto
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 or else - it
> doesn't matter, since the phase will dominate anyway) will highly bias
> the map towards the model.
DFc,
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, 2011-10-12 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 $CCP4_LI
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 ev
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
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
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 t
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 c
end has god doing to the tower builders of Babel.
The russian translation of Kernighan&Ritchie was my first programming
book, and seemingly the only one I ever needed.
--
Ed Pozharski
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
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 residue_end> ?
> That's a useful feature in O, but could not find it so far
> 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.
>
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
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.
2
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
outp
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 fo
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 dire
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 a
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, su
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 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 synchrot
one systematic analysis of pdb (even better data
> sets collected on one of the synchrotrons) to see the seriousness of
> the problem? I suspect the problem is much more serious than it is
> perceived.
>
> Before you provide sufficient evidence everybody will have their
> opinio
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_US&formkey=dHh4cjdLZGZrSEpUOG9kV2hkb3ZXNHc6MQ
--
Oh, suddenly throwing a giraffe into a volcano t
hat shall we gain by such a vote? I may be misunderstanding what you
> have in mind, of course :-) .
>
>
> With best wishes,
>
> Gerard.
>
> --
> On Thu, Oct 27, 2011 at 12:08:24PM -0400, Ed Pozharski wrote:
> > I am curious as to what the c
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 ske
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 in
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 l
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
ctors
> 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, 2011-10-31 at 15:57 +, Ivan Shabalin wrote:
> >> As a result,
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).
D
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
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, 2011-11-07 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
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, plea
s openmp-enabled. You can also try passing
> > the --static-exe flag (to configure.py), in which case the executable is
> > static and can be relocated without any headaches. This works with
> > certain compilers.
> >
> > Let me know if there are any problems!
> >
>
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 sal
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
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 exampl
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 pa
On Fri, 2011-11-18 at 06:34 -0800, xaravich ivan wrote:
> Ok, now I do not have an easy access to crystallization robot, so I
> was hoping if someone here have ever used the 96 well plates for
> manually setting drops with much lower solution/sample volumes
> (0.1-0.2micro litres).
>
The best we
Did anyone ever seen a ligand molecule (or water, maybe) moved into a
symmetry-related position upon refinement in refmac? If that is a
feature (e.g. to make sure that non-protein stuff is coordinated to the
spot of the closest contact), how can I disable it?
Cheers,
Ed.
--
Oh, suddenly throwi
The center bit looks very much like phosphate - see what happens if one
is placed there
It may be educational to look at the maps in P1, just to see how much
trouble is caused by "noise accumulation on the symmetry axis"
On Thu, 2011-12-01 at 09:36 +, Martin Montgomery wrote:
> Posting on beh
On Tue, 2011-12-06 at 13:43 -0600, Jacob Keller wrote:
> The question is: "is there a reference in which Rmerge has been
> thoroughly, clearly, and authoritatively discredited as a data
> evaluation metric in the favor of Rmeas, Rpim, etc., and if so, what
> is that reference?"
>
Aren't these suf
On Thu, 2011-12-08 at 17:49 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote:
> I tried to look at all density regions bit by bit, but the density for
> the protein atoms always interfere with my vision. Is it possible to
> mask out
> the density of protein atoms,
Isn't that what difference density map is
Colleagues,
One recurring question on this bb is "I got this blob of density - is it
my ligand or what in the name of pink unicorns this is?" Often, a
screen snapshot is posted, which is very helpful. But it may be better
if those helping out could rotate density around in 3D. Understandably,
p
On Thu, 2011-12-08 at 12:17 +0530, atul kumar wrote:
> I can't build anything in this region,this could be because of
> disordered structure or because of low resolution.
Both, and also the presence of disordered fragment may be the reason the
resolution is low, thus the already mentioned suggesti
There is indeed the phenix.cut_out_density tool (by Tom Terwilliger)
which does a nice job of reducing the size of the output mtz-file (it
shifts the cutout region to the origin and reduces the unit cell).
On the link-versus-attachment issue, certainly the link is preferred,
but the aforementioned
On Fri, 2011-12-09 at 05:45 -0800, Pavel Afonine wrote:
> just a remark: for phenix.refine it does not matter where the flags
> come from and what is the "test"/"work" value since it automatically
> scores the values in the flags array and guesses the right one. Still
> one can imagine corner case,
On Sun, 2011-12-11 at 05:28 +, Yuri Pompeu wrote:
> In refmac however the newly generated refmacX.mtz file contains phase
> info as PHIC calculated from your model. Using this for subsequent
> rounds of refinement results in terrific looking maps as they are now
> biased (even more so) by the i
On Tue, 2011-12-13 at 02:31 +, Yuri Pompeu wrote:
> Hi Ed,
> I just had a chance of looking at your comment more closely.
> You are right it only uses PHIC if in refmacs set up you choose to refine
> "with prior phase information" -AFAIU.
> So what exactly is the info contained in the output
Did you try following these instructions:
http://xray.bmc.uu.se/alwyn/O_to_Go/O_to_Go_frameset.html
?
On Mon, 2011-12-26 at 18:53 +0800, 王瑞 wrote:
> Excuse me, could anyone can tell me how to install O on
> ubuntu11.10 ?Thanks a lot !
I've seen this happening to water molecules as well (in a somewhat
unpredictable fashion). In the latest refmac versions, you can try
harmonic restraints, although these will only slow down the atom drift,
as the target position is updated every cycle.
Perhaps you can use distance restraints agai
On Sun, 2012-01-01 at 12:14 -0600, Dima Klenchin wrote:
> With Garib's help, I have forced the atom into its position by using
> external distance restrains of zero length against the same
> symmetry-related atom. The cause is unclear because the same program
> handles special positions in anoth
On Thu, 2012-01-05 at 20:40 +0800, Zhiyi Wei wrote:
> Is it possible that this two regions has
> different crystal domain arrangement (one is normal and another is
> twinned)?
Absolutely. This will, of course, vary for different crystal systems,
but from what I have seen it appears that a differ
On Fri, 2012-01-06 at 20:40 +0800, LISA wrote:
> Hi all,
>
> I have a DNA binding protein. I get crystals of this protein by
> co-crystallization with different dsDNAs. But all the crystals have
> very poor resolution, about 10-20A. I tried to purify protein-DNA
> complex before setting trays, but
> and R-factor/R-free have a value of 0.328/0.326.
Notice that Rfree The question is, as I only have ~3000 reflections, and the atoms in
> the sequence is around 1000, and each atom there are 4 parameters to
> be refined(X,Y,Z,B-factor, assuming occupancy is 1), so how to refine
> my model to avoi
On Fri, 2012-01-06 at 11:18 -0700, Francis E Reyes wrote:
> I've seen the following question asked: At what resolution is
> (individual,group,one per residue, two per residue,overall)
> appropriate?
My personal opinion is that the individual B-factor refinement with
restraints proper to the resol
On Fri, 2012-01-06 at 10:48 -0800, Ethan Merritt wrote:
> A TLS model is more likely to be
> appropriate.
>
A quick clarification request if I may:
We all seen how well the multi-group TLS models seem to match the
B-factor variation along the chain. Is this in your opinion how such
model may be
On Mon, 2012-01-09 at 10:28 +, Guillaume Gotthard wrote:
> Is there a mean to obtain statistics about R-Sym for deposited
> structures databases ?
1. It's actually quite easy to do on your own if you want. This
one-liner will get you the Rsym
wget http://www.rcsb.org/pdb/files/.pdb?head
On Mon, 2012-01-09 at 18:15 +, Theresa H. Hsu wrote:
> Dear crystallographers
>
> A theoretical question - can sub-angstrom resolution structures only be
> obtained for a limited set of proteins? Is it impossible to achieve for
> membrane proteins and large complexes?
>
> Theresa
On the ma
On Tue, 2012-01-10 at 09:04 +, Colin Nave wrote:
> Yes, I think Ed's analysis is a bit misleading.
I apologize if I misled anyone. Re-reading my post, I can see that it
lacked precision. Indeed, in a perfect monocrystal all the molecules
are lined up perfectly, so I should have emphasized ra
On Tue, 2012-01-10 at 13:25 +, Luca Pellegrini wrote:
> "This is not a reliable map."
There are many reasons why one could get the gap in R-values. As the
proud author of an "unreliable" map myself (3pht), I found that what did
it was that the TLS-refined model was deposited with the full B-f
On Tue, 2012-01-10 at 18:30 +, Theresa H. Hsu wrote:
> Thank you for the interesting replies so far.
>
> Please let me ask a related question - at what resolution should we stop
> efforts to get better diffracting crystals? Are there *biological* questions
> that a model with 1.8-2.0 A resol
On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote:
> Do you have ultra-high resolution? Something I did not…. Are there
> many examples in the pdb of proteins with Li+ refined?
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=het2pdb.html¶m1=_LI
39 in
at 10:23 -0500, Matthew Franklin wrote:
> On 1/12/12 9:42 AM, Ed Pozharski wrote:
> > On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote:
> >> Do you have ultra-high resolution? Something I did not…. Are there
> >> many examples in the pdb of proteins with Li+ refine
On Fri, 2012-01-13 at 10:40 -0800, Ethan Merritt wrote:
> Which of these two statements would be more useful:
> 1) The RMSD for sidechain atoms between apo and holo was 0.678 Å.
> or
> 2) Only two residues exhibited a significant change of
> conformation:
Perhaps the same is true for the back
On Wed, 2012-01-18 at 18:26 +0530, PULSARSTRIAN wrote:
> The Problem is I am not able to get rid of the infamous contamination
> proteins of arnA gene (72 kDa) and glmS gene (67 kDa).
This is only a problem if you plan to have imac purification as your
only step. If the goal is crystallization,
These R-values are reasonable:
http://xray.bmc.uu.se/gerard/supmat/rfree2000/plotter.html
On Mon, 2012-01-23 at 21:48 +, Sam Arnosti wrote:
> Hi every one
>
> I have some crystals in the space group P3121. I collect 180 frames of data.
>
> My crystals do not diffract better than at most 2
I am looking for a program/server that would determine secondary
structure from a pdb file and then output a new pdb file with
HELIX/SHEET records. I have a model for which pymol fails to produce
correct secondary structure. DSSP and STRIDE identify the secondary
structure correctly but I'd need
Consider cross-linking crystals with glutaraldehyde. The caveat here is
that you may end up with the protein conformation that is forced by
lattice, but if the issue is just the fragility, you should be fine. I
assume that crystals simply crack but do not dissolve?
Certainly, as others have said
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