On Fri, 2013-02-08 at 09:13 -0500, Edward A. Berry wrote:
> I like to take a 5-sec 180* oscillation which gives plenty of
> spots in a nice pattern for a salt crystal
Second that
It also confuses bystanders really well - what a strange diffraction
pattern - half salt (small unit cell) / half pr
Patrick,
Something related:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Conditions_prone_to_salt_crystallization
Truth be told, we recently had a major breakthrough with the peg/fluoride
condition I came to consider a useless salt crystal generator. So tables like
these are un
Try this
http://www.mac-forums.com/forums/os-x-apps-games/239657-gedit-command-not-found-terminal.html
Original message
From: LISA
Date:
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] gedit on mac terminal
Hi all,
I installed gedit on my mac applications. But i can not use
Article in the Tables is the answer to my question about the latest
Engh&Huber parameters. These still don't match Fig.6 from Fisher, but I
am OK with using Tables for my internal purposes.
Thanks to Mitchell and Dale for prompt response.
Cheers,
Ed.
--
After much deep and profound brain thin
To what extent "modern" geometric restraints have been upgraded over
original Engh&Huber? And where I can find a consensus set of values
(with variances)?
For example, Fisher et al., Acta D68:800 discusses how histidine angles
change with protonation, and refers to Engh&Huber when it says that
On Thu, 2012-12-13 at 17:50 +, Theresa Hsu wrote:
> Being a beginner crystallographer, may I ask a basic question? On how
> many occasions does it make a *biological* difference between having a
> structure at 1.42 and 1.6 A?
And your definition of "biological difference" is exactly what? Ev
On 12/10/2012 08:45 PM, Yuri Pompeu wrote:
hello everyone,
I have collected data on a problematic crystal. (first mistake...)
Images spanning phi angles 45-80 look ok and usable, also images 229-279 are
usable (index well and merge well too).
How can I combine the 2 separate .mtz files from Mosf
On Wed, 2012-12-05 at 17:02 +0100, Robbie Joosten wrote:
> Does 128A come before or after 128?
Robbie,
shouldn't it simply depend on which residue record comes first in the
pdb file?
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Francois,
I did not realize Phil Evans is god (perhaps a minor one as he did not
yet earn a capital G).
I do concur that insertion code is evil. I had to re-refine an old
antibody structure recently and it messes up coot sequence window and
breaks refmac bond restraints. Evil, evil,.evil.
Chee
On Tue, 2012-11-27 at 21:46 -0800, William G. Scott wrote:
> Are Mg++ ions ever observed to chelate primary amines?
MESPEUS reports, for example, 13 structure where magnesium is
coordinated by a lysine. 7 with arginines and a bunch of asn/gln side
chains as well. It does not prove, of course, th
On 11/22/2012 03:40 AM, Wei Feng wrote:
Dear all
An ice ring is found in the raw image files and the resolution range
is from 3.70-3.57A.
I want to remove this ice ring by excluding the reolution bin.
Can anyone tell me how to do?
Thanks a lot !
Wei Feng
iMosflm has the ice ring exclusion o
On Mon, 2012-11-12 at 13:47 -0500, Ed Pozharski wrote:
> Does anyone know of a tool that would generate a protein molecule
> backbone from a set of phi/psi angles?
>
For the record.
Thanks to all who responded. Here is what I found out:
1. MOLEMAN works best. The most cumbersome p
On 11/17/2012 03:04 PM, Rex Palmer wrote:
I would like to specify a target atom in a pdb file and then isolate
all atoms within a given distance of the target. The selected atoms
are then to be placed in a new pdb file.
AWKward BASHing:
#! /bin/bash
read x y z <<<$(awk '{if(substr($0,1,4)=="A
On 11/16/2012 12:54 PM, Kendall Nettles wrote:
I wouldn't go into the lab and say "did you cryo-cool those crystals yet?" or
"check out this nice crystal. Its ready for vitrification".
If we speak the way scientific articles are written...
By Bernard Dixon, published in New Scientist, 11 A
Does anyone know of a tool that would generate a protein molecule
backbone from a set of phi/psi angles?
I actually had written my own code to do this eons ago, but those were
days of Matlab. My actual question is if in a particular protein the
conformational change observed upon substrate bindin
OK, here we go again.
This has been argued ad nauseam, see for example
http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19738.html
or
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20268.html
(hard to believe we have gone more than a year without another version
of "what to do with diso
On Fri, 2012-11-09 at 15:12 +0100, Ulrich Zander wrote:
> Does anybody have a suggestion for a protein/ligand combination that
> could be used for that and that is commercially available?
Perhaps lysozyme complexed with some sugar?
--
Bullseye! Excellent shot, Maurice.
On Wed, 2012-11-07 at 11:29 -0600, SD Y wrote:
> https://www.dropbox.com/s/4jd6gdor87ab9lj/Zn-coordination.png
Your sigma level of 6.5 seems a bit low, so maybe it is a different
metal. But on your main question - yes, metal binding proteins do pick
up metals from the media. Once metal is coord
On Wed, 2012-11-07 at 16:04 +0200, Eva Bligt-Lindén wrote:
> To my knowledge the protein is not a
> surface-tension-reducing-protein and there is no detergent in the
> sample.
However your observations indicate that your sample has reduced surface
tension. When you say that "to your knowledg
On 11/03/2012 12:06 PM, Xiaodi Yu wrote:
how common it is that electrostatic interactions are involved in
intra-molecular interactions, particularly in intrinsically disordered
proteins?
It's impossible to answer your question unless you define what you mean
by "degree of commonality".
If you
On Tue, 2012-10-30 at 16:12 +, Peter Hsu wrote:
> I'm wondering, since I lack activity at this pH point, would it lead
> to no binding of a substrate analog?
Not necessarily. You should check pH dependence of the Km - it might be
that lower activity is primarily due to reduction in kcat. Bin
On Thu, 2012-10-25 at 11:34 +0100, Eleanor Dodson wrote:
> You can use superpose LSQKAB to fit various residues by number..
> Eleanor
Eleanor is absolutely right.
Coot has Calculate->LSQ superpose option for that.
I feel what needs to be reiterated is that "CCP4 superpose" uses SSM -
secondar
On 10/19/2012 10:37 PM, Acoot Brett wrote:
Will you please explain to me why the protein salt bridge can still
exist in the high salt concentration as used in the crystallization
condition?
You are saying it as if there is some fundamental law of nature that
says that salt bridges cannot be
On 09/12/2012 06:41 PM, Cosmo Z Buffalo wrote:
is it possible to force Aimless and Pointless to generate statistics
in a space group other than the one it predicts?
yes, but it's pointless to force Pointless
And if so, how would I do this?
I assume you mean doing it from imosflm. If so, go
On 07/06/2012 09:40 AM, Andrew Pannifer wrote:
Hi,
Is there a way to ask peakmax to output the volume of each electron
density peak that it detects (or is there a reasonably straightforward
way to do this via an alternative command line runnable approach?)
Cheers,
Alan
There might be a
Your question is way to broad to be answered in a reasonable time/space.
As for books (plenty of options exist beyond these)
There is a 1976 classic
http://www.amazon.com/Protein-Crystallography-Molecular-Biology-Series/dp/0121083500
And of course there is a more recent highly recommended
htt
Tim,
I did not understand your objection against solution 1 - is it because
it is not automated? You can sort the results by max. Ident so that
you can sroll down to the limit you set yourself.
More that it does not generate a list of PDB IDs. What I want to do is
to find every structure of
Silly question.
Say I want to find every structure in the PDB with the exact sequence or
with perhaps 1-2 mutations. I know of two ways of doing this.
1. Go to NCBI BLAST and run the sequence against the PDB subset. The
resulting list will have identities listed, so manual parsing is doable
On Tue, 2012-06-19 at 11:07 -0500, Jacob Keller wrote:
> What extra insight does the full-length protein give, i.e., why not
> just chuck it?
>
It proves that the N-terminus does not have a strong influence on the
rest of the structure. Other words, it's OK to draw conclusions about
the full-len
On Tue, 2012-06-19 at 17:31 +0200, Robbie Joosten wrote:
> What if the displacement is a translation and a rotation?
Excellent point. A slight modification of this
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Print_the_shifts_in_individual_atom_positions
will do as follows
grep
just do this one-liner (assuming that your numbering is not messed up
and you have "the first atom")
grep 'ATOM 1' model1.pdb model2.pdb | cut -d: -f 2 | cut -c 31-54 |
awk '{printf "%s ",$0;}' | awk '{print sqrt(($1-$4)^2+($2-$5)^2
+($3-$6)^2);}'
On Tue, 2012-06-19 at 15:04 +, Claudia M
On Tue, 2012-06-19 at 16:43 +0800, LISA wrote:
> Hi all,
>
> does anyone solve their structure by molecular replacement with
> phaser with LLG < 0?
> Thanks
>
> lisa
AFAIU, this means that your estimate of the solvent content is too low.
If you increase that, eventually you should get positive
will be considered a plus.
Please submit your letter of interest, resume and contact information of
3 references to epozh...@rx.umaryland.edu.
--
Ed Pozharski
University of Maryland - Baltimore
On Tue, 2012-06-05 at 15:26 +0530, Faisal Tarique wrote:
> how to proceed with submission, can i show it as a modified residue
> CME or cys in disulfide bond with bme
You can do either. One could potentially argue that cys+bme is more
appropriate since the protein presumably had cysteine which wa
On Mon, 2012-06-04 at 13:11 -0500, Katherine Sippel wrote:
> Though as a disclaimer it was a 1.2 angstrom data set
Which is about 6x more data than 2.2A... Certainly, at atomic
resolution the results of occupancy refinement will be more robust. To
be fair, even at 2.2A such refinement may succee
On Sat, 2012-06-02 at 23:32 -0700, aaleshin wrote:
> Was not Z. Otwinowski first to use it in his scalepack?
Maybe I missed something, but given the hoops I have to jump through to
get Rpim calculated after scalepack (basically take unmerged data to
either the program from Manfred Weiss or SCALA)
> Is it reasonable to refine occupancy in phenix at 2.2 A resolution?
Implementations may differ, but imgo refining occupancy at 2.2A
resolution is not very reasonable under most circumstances, as it will
correlate strongly with the B-factor. A reasonable approach might be to
fix occupancy at d
http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html
http://scripts.iucr.org/cgi-bin/paper?S0021889800018227
Just collect 360 sweep instead of 180 on a non-decaying crystal and see
Rmerge go up due to increase in multiplicity (and enough with redundancy
term - the extra data is not really
s a different issue, but has been much
> improved in the latest versions of the program.
>
> Best wishes,
>
> Graeme
>
> On 25 May 2012 16:12, Ed Pozharski wrote:
> > I should do more digging, but I hope maybe there is a simple explanation
> > and someone has seen
I should do more digging, but I hope maybe there is a simple explanation
and someone has seen this before. On some datasets (collected at SSRL)
I get SCALA reporting average mosaicity of 0.0. This probably happens
at the integration stage, and for this whole set of datasets *always*
happens when
On Fri, 2012-05-25 at 19:01 +0800, LISA wrote:
> try to refine this structure by phenix but failed.
Not that I have an answer to your question, but you have to describe
what you mean by "failed".
Maybe you should try refmac. Will also make your inquiry better suited
for this forum (although it's
On Thu, 2012-05-24 at 14:11 +0200, Eike Schulz wrote:
> Are there other ways to calculate the volume of a protein/complex from
> pdb-coordinates, maybe an alternative to SURFACE/VOLUME?
For a non-ccp4 solution, consider hydropro
http://leonardo.inf.um.es/macromol/programs/hydropro/hydropro.htm
Does anyone know of a (non-commercial) software that can analyze results
of a crystallization screen? What I am looking for is some way to tell
what components/factors favor protein solubility/precipitation based on
binary input (clear drop/precipitate).
I did some googling, but please feel free
On Wed, 2012-05-23 at 18:06 +0300, Nicholas M Glykos wrote:
> It seems that although you are not doubting the importance of maximum
> likelihood for refinement, you do seem to doubt the importance of
> closely
> related probabilistic methods (such as maximum entropy methods) for
> map
> calculat
On Wed, 2012-05-23 at 18:06 +0300, Nicholas M Glykos wrote:
> This is an amplitude modification. It does not change the fact that
> the
> sigmas are not being used in the inversion procedure
Nicholas,
I am not sure I understand this - perhaps we are talking about different
things. Even if by i
On Wed, 2012-05-23 at 10:02 -0500, Pete Meyer wrote:
> bviously
> model and experimental errors do factor into calculation of a
> 2mFo-DFc
> map - but is weight and structure factor calculation part of map
> calculation, or a distinct stage of data processing?
Oh, I see. Sure, when the map co
I may be wrong here (and please by all means correct me), but I think
it's not entirely true that experimental errors are not used in modern
map calculation algorithm. At the very least, the 2mFo-DFc maps are
calibrated to the model error (which can be ideologically seen as the
"error of experimen
On Thu, 2012-05-17 at 15:12 +0100, Paul Emsley wrote:
> In Coot 0.7, to draw a bond between monomers that don't have an
> implicit
> connection due their serial number, you need a LINK record. You can
> add
> a LINK using Extensions -> Modelling.
>
Thanks - is there some way to remove the link
On Thu, 2012-05-17 at 14:13 +0530, Faisal Tarique wrote:
> to make disulphide bond ie to connect cysteine with bme
While I believe that CYS+BME is a correct choice ideologically (you had
cysteine and bme reacted with it), note that you can use CME monomer
(it's listed as peptide in monomer librar
Just a curiosity - I have a dataset at 1.45A for which SCALA reports the
highest resolution shell completeness at 100.1%. I am impressed :-)
--
"Hurry up before we all come back to our senses!"
Julian, King of Lemurs
On Tue, 2012-05-15 at 15:51 +0100, RHYS GRINTER wrote:
> A colleague suggested that sulphate or phosphate could fit at these
> distances, but these ions have not been added at any stage of the
> crystallisation process.
>
I vaguely remember a report about 2-3 years ago at the ACA meeting of
phos
On Tue, 2012-05-15 at 07:27 +0100, Naveed A Nadvi wrote:
> I was wondering if there is any software out there that can be used
> for multiple structure superimposition and output some graphical plot
> of residues based on their deviation from the reference molecule.
And why exactly you cannot acco
On Mon, 2012-05-14 at 13:01 -0400, Bosch, Juergen wrote:
> Although the question was asked for Mosflm I would like to briefly
> p[oint out that you might be able to also rescue your data by using a
> program that does 3D profile fitting e.g. d*trek and XDS.
For the sake of completeness (and nothi
On Sat, 2012-05-12 at 19:28 +0100, Yuri Pompeu wrote:
> Dear community,
> I am probably disturbing a sleeping bear
definitely so
> Reading the thread on hydrogen deposition with the model, I came accross
> several arguments that make sense on their own, but when put together are
> puzzling and
On Sat, 2012-05-12 at 08:48 -0400, Dave Roberts wrote:
> However, I just want to make sure the metal environment is not due to
> the fact that I did something wrong in my refinement script - thus
> making it tetrahedral because it was refined as tetrahedral.
...
> I don't use CCP4 for refinement,
http://mathworld.wolfram.com/StandardDeviation.html
On Tue, 2012-04-24 at 09:13 +0800, Qixu Cai wrote:
> Dear Ed,
>
> Why the variance is the square of standard deviation?
>
> thank you very much!
>
>
> 在 2012年4月23日，20:53，Ed Pozharski 写道：
>
> > On Sun
On Mon, 2012-04-23 at 23:39 +0800, Qixu Cai wrote:
> Dear all,
>
> I have solved a 3.5ang structure with R/Rfree = 0.23/0.32 (refmac5.6 result).
> But when I used sfcheck to validate the coordinates and structure factors, I
> got a high R factor > 0.38 !
>
> Could anybody tell me the reason? I
On Sun, 2012-04-22 at 12:47 +0530, Arka Chakraborty wrote:
> baverage program in ccp4 gave average bfactor of 25.0 for the residue
> but coot is showing 150!
Variance is the square of standard deviation, thus var=150 means
sigmaB~12 in that particular residue. High, but not impossible.
--
I do
Manoj,
while reviewer-bashing is my favorite pastime too (recent gem: "studying
transcription factors will not advance our understanding of mechanistic
enzymology"), you should remember that they are unpaid individuals who
volunteer their time to help you to improve your paper (or so the idea
goes
It seems that this discussion has somehow reached the conclusion that if
a reviewer asks for model/data, there absolutely must be an ulterior
motive to cheat you out of your high profile publication.
On the other hand, it seems like the intent of such reviewer is also
misunderstood as if the only
As Randy pointed out, you should check Patterson map for off-origin
peaks. There is also a small chance that you actually have P2 -
systematic absences may result from tNCS nearly colinear with
crystallographic axis.
On Thu, 2012-04-19 at 14:20 +0800, LISA wrote:
> Hi all,
>
> I am trying to sol
36% solvent sounds too low. Most protein crystals are at ~50%. On the
other hand, if you assume one molecule, your solvent content jumps to
68% - not unheard of, but somewhat high for 1.7A resolution dataset.
But you have a good MR solution, just try to refine/rebuild and see what
you have in th
I always request both the final model and the experimental data
(assuming that they are not yet available directly from the PDB).
Obviously, this is done with assurances of confidentiality.
I don't think it's common though, since I was never asked to provide the
same by reviewers.
What exactly is
On Tue, 2012-04-17 at 17:49 -0400, Uma Ratu wrote:
> In order to have my target .pdb, I need to mutate the residues using
> coot?
Others already recommended CHAINSAW to prepare the model. Note that
coot has a nice feature under Extensions->All molecule... called "[Post
MR] Fill partial residues.
On Tue, 2012-04-17 at 20:03 +0100, Frank von Delft wrote:
> Hi, thanks for all responses. Most people suggested avoiding the
> scenario altogether, which was cute but not the question.
As far as US is concerned, the FAA instructions to air carriers
http://lmgtfy.com/?q=faa+liquid+nitrogen&l=1
On Tue, 2012-04-17 at 11:08 +0200, Dirk Kostrewa wrote:
> The mask bulk solvent correction is more powerful
Just to note that sometimes Babinet solvent correction returns lower
Rfree and thus may be preferred to mask (assuming that the Rfree is the
only thing that matters).
Beginning with 5.6.007
On Wed, 2012-04-04 at 17:31 +0100, Eleanor Dodson wrote:
> I wish Paul, that at least SOME of the great info that coot prints to
> the
> screen then scrolls out of sight could be directed to a
> "very-useful-things-to-remember" box..
>
> Eleanor
>
Won't "coot | tee very_useful_things_to_rememb
Whatever you do, make sure you have enough bottled water before the next
doomsday:
http://en.wikipedia.org/wiki/Year_2038_problem
I am using 64-bit linux almost exclusively for some time now. "XRD
software" works fine, no lingering issues that I can report. ia32-libs
do the trick for 32-bit bin
http://www.ccp4.ac.uk/dist/examples/tutorial/html/heavy-tutorial-mir.html
seems relevant
On Fri, 2012-03-30 at 19:04 +0530, Shanti Pal Gangwar wrote:
> Dear all
>
> I am beginner in crystallography.We have collected a native data of a
> given protein at 2.2A resolution but are unable t solve by
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg19931.html
On Thu, 2012-03-29 at 11:38 -0400, Kumar, Veerendra wrote:
> Dear All
> My lab is planning to buy a new bench top incubator for crystallization.
> I came across this one –
> http://www.tritechresearch.com/DT2-MP-47L.html
>
> This
I suspect Chris is asking for the shortcut to the zone refinement
button, i.e. invoking the manual zone selection. Not sure if there is a
scripting way to do this, nothing obvious.
On Tue, 2012-03-27 at 17:03 +0100, Debreczeni, Judit wrote:
> Yes, look here:
>
> http://strucbio.biologie.uni-kons
works here on 0.7-pre-1 rev 3713
so try downloading the latest version if yours is <3713
On Tue, 2012-03-27 at 14:50 +0100, Morten Grøftehauge wrote:
> set-refine-max-residues
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
On Mon, 2012-03-26 at 11:57 -0600, Matthew Lalonde wrote:
> What parameters should I vary to reproduce crystals in hand plates?
First of all, protein concentration. It also does not hurt diluting
your reservoir since you are getting precipitates. If your goal is to
get bigger crystals (which is
On Mon, 2012-03-26 at 16:30 +0200, herman.schreu...@sanofi.com wrote:
> It is like with Heisenbergs uncertainty principle. Either one has a
> complete model with a number of atoms having a coordinate uncertainty
> of 4-6 Å, or one has a model where the uncertainty of all atoms is
> below say 0.5 Å,
On Mon, 2012-03-26 at 10:17 -0400, Gregory Bowman wrote:
> But what about the issue of resolution? As was previously pointed out,
> at say 3.2 Å resolution, many side chains will fail to fit, but it
> doesn't seem appropriate to trim them all down.
Why is it inappropriate to trim them down? Some
I agree with Eleanor 100%...
In my biased opinion, only the atoms supported by electron density
should be included in deposited models. To satisfy the "but this will
mess up the electrostatic potential coloring" argument (a valid one, of
course), the "projected model" can be deposited alongside w
This may be useful
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera
http://pymol.sourceforge.net/newman/user/S0300movies.html
On Wed, 2012-03-21 at 22:52 +0800, sonali dhindwal wrote:
> Dear All,
>
> My query is slightly out of scope of ccp4.
> I need some suggest
Technically, no. You may be able to exclude nuclear forces, but gravity
certainly isn't included in Maxwell's equations.
The other forces can simply be neglected because their contribution is
negligible when molecular interactions are concerned.
On Wed, 2012-03-21 at 08:42 -0500, David Mueller w
On Wed, 2012-03-21 at 10:16 +0100, Rubén Sánchez Eugenia wrote:
> In Physical Chemistry Van der Waals interacions are defined as all
> type of forces between molecules (or parts of them) excluding covalent
> bonds and electrostatic interactions. So, you are right that the most
> common forces inclu
Scaling up 100nl drops is problematic. What I understand is that it is
not only the different equilibration conditions, but primarily the
amount of protein that gets absorbed on the surface is relatively higher
for small drops. There were some empirical formula for scaling up (i.e.
how much you n
One comment I'd like to add here is that in the presence of
pseudo-translational ncs that is nearly colinear with crystal axes you
will have a significantly higher R-value. This may be a serious problem
with some reviewers when your R~30% on a 2A dataset. It is completely
justified then to have t
On Sat, 2012-03-17 at 08:44 -0400, Hena Dutta wrote:
> I tried with clonezill and it did not work.
There are many problems with what you are trying to do.
1. Windows license is tied to the hardware, thus it's not likely to
work out of the box if you clone the whole drive.
2. Even though it's
By mechanical disruption you mean sonication only or have you tried the
French press?
Assuming that you use sonication, and assuming that you follow a fairly
standard protocol (e.g. something like 10sec pulse/20sec pause on ice
for 3 minutes total), it may be heat not ultrasound that gets to it.
T
On Wed, 2012-03-14 at 09:26 +, Dipankar Manna wrote:
> After running molrep R-factor is around 53% (100% identity), after
> rigid body refinement its showing around 49% and after restrained
> refinement its showing around 47%.
Sounds like you didn't get a solution. With 100% identity MR in m
If you are looking for predicting disulfide bonds, then this may be
useful
http://lmgtfy.com/?q=predict+disulfide+bonds
Cheers,
Ed.
--
Hurry up, before we all come back to our senses!
Julian, King of Lemurs
> 2. How do I fix them? delete the side chains?
Here we go again. Take a look at these threads
http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19738.html
http://phenix-online.org/pipermail/phenixbb/2011-March/016875.html
--
Oh, suddenly throwing a giraffe into a volcano to make water is cra
On Mon, 2012-02-13 at 21:02 +, Theresa H. Hsu wrote:
> Hi all.
>
> When collecting data, is there a specific wavelength to be chosen at
> synchrotron source? Does it make difference between 0.9 and 1.5 A, for
> example? I know it is important for SAD/MAD but how about MIR?
>
> Thank you.
>
On Sun, 2012-02-05 at 22:49 +, Theresa H. Hsu wrote:
> Crystals are from 2 M ammonium sulfate.
Sodium malonate is your friend
http://scripts.iucr.org/cgi-bin/paper?fw5004
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
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
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
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
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,
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
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 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
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 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 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 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 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
101 - 200 of 543 matches
Mail list logo
