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
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 part
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)==ATOM
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
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 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 knowledge
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
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.
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 -
secondary
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
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
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
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
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 LLG.
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
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
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
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 epozh...@umaryland.edu
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 was
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
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)
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
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
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
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
much
improved in the latest versions of the program.
Best wishes,
Graeme
On 25 May 2012 16:12, Ed Pozharski epozh...@umaryland.edu wrote:
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
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
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
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
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
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
calculation.
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 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 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
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 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, I
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 dont
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 nothing
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 epozh...@umaryland.edu 写道：
On Sun, 2012-04-22 at 12:47 +0530
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
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? Is that
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 solve
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
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
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
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
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+nitrogenl=1
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_remember.txt do
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
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 MR
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?
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:
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
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?
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 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 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 included
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
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
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
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
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
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.
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
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
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.
begin \personal_bias
Sodium malonate is your friend
http://scripts.iucr.org/cgi-bin/paper?fw5004
end
--
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
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 2.0
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
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/atemplate=het2pdb.htmlparam1=_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+ refined?
http://www.ebi.ac.uk/thornton-srv
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
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
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
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
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 matter
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 it
and R-factor/R-free have a value of 0.328/0.326.
Notice that RfreeR. This may be caused by twinning and/or NCS, as the
test set is not truly independent of the working set.
The question is, as I only have ~3000 reflections, and the atoms in
the sequence is around 1000, and each atom there
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
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 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
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
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 another
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 !
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
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
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, so
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
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
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
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
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
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
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