Dear Ruby,
With this information I can give some more concrete hints:
- Add the sugar (monosaccharide, disaccharide?) that the lectin is
supposed to bind to your crystallization trials.
- Try different protein concentrations: 10 mg/ml, 100 mg/ml. In the
latter case you may have to dilute your
Hi Anita,
I do not have much experience with detergents, but spherulites like you
showed often occur with proteins. Unfortunately, these things usually do
not diffract. On the other hand, they occur often in conditions close to
good crystallization conditions, so in your case I would try to
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Dear Kalyan,
the reason why you cannot read in the .res-file is that you don't have
RESI-cards. They are required by coot.
For the same reason your PDB-file does not contain any information
that would allow coot to refine the coordinates.
As far as
Hi,
I've generally used PRODRG to create paramater files for any ligands I
add during refinement with CCP4 and/or PHENIX. I've been trying READYSET
from PHENIX as it greatly helps refining some metal ion positions. But
when I use READYSET, any ligand I add (in this case EDO or ethylene
glycol)
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Hi Chris,
If the absence/ presence of hydrogens in the coordinate file made a
difference in the refinement, I guess some parameter setting for the
refinement program is awkward. Did you refine with riding hydrogens in
both cases? Hydrogens can and
Hi Tim,
Yeah, riding hydrogens have always been on. I guess I need some more
investigation.
Chris
On Mon, 2012-05-07 at 15:36 +0200, Tim Gruene wrote:
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Hi Chris,
If the absence/ presence of hydrogens in the coordinate file made a
Hi Chris,
- there is Phenix mailing list for Phenix-related questions. Please check
http://www.phenix-online.org/
- the data resolution of 2.5A does not mean hydrogen atoms are not present
in the crystal. There are methods to account for them. For details see (and
references therein):
On
Anita,
To answer a lot of your questions, you need to provide some more information
about your protein, at least some of its biophysical characteristics (size,
oligomeric state, an integral membrane protein, etc.). Just because you are
using detergents does not mean all your problems are
Jacob,
The main reason why it is not common practice to saturate every crystal
with every heavy metal under the sun is radiation damage. X-ray
absorption increases very rapidly with atomic number (third power), so
on the order of 100 mM of heavy atom is usually enough to cut your
crystal's
Dear Pavel,
I would try both options and see how it works.Thanks for time
RegardsRajesh
Date: Sat, 5 May 2012 13:39:42 -0700
Subject: Re: [ccp4bb] NCS on ligands
From: pafon...@gmail.com
To: ccp4...@hotmail.com
CC: CCP4BB@jiscmail.ac.uk
Hi Rajesh,
I guess they could (in most programs), but the
Dear all,
I'd like some suggestions/opinions about the sense of an experiment
proposed by a collaborator expert in saxs.
In few words, he wants to collect SAXS data on a suspension of protein
xtals to investigate low resolution periodicity of the xtal (more details
below).
The experiment requires
That sounds like powder diffraction.
On 05/07/12 12:30, anna anna wrote:
Dear all,
I'd like some suggestions/opinions about the sense of an experiment
proposed by a collaborator expert in saxs.
In few words, he wants to collect SAXS data on a suspension of protein
xtals to investigate low
It might be that the bulk solvent correction is nullifying the interior
of the ferritin structure, and there should be a way to tell the refinement
software not to treat the interior as solvent. Perhaps then you might find
your Fe? Also, I would think there should be some powder-like diffraction
Dear Anna,
I once modified CNS to refine two solvent regions of ferritin, one inside and
one outside the shell. Perhaps this can be done in Phenix now. If you want to
locate magnetite particles in this way, you should collect data to as low a
resolution as you can (may need to move backstop),
James Holton wrote:
In general, a Bijvoet ratio of 3% or so is needed to solve a structure (the
current world record is 0.5% and lots of multiplicity). The above web page
will also tell you how many crystals you need if you type in their size in all
three dimensions. but this estimate
Hi Anna,
There has been some nice single crystal SAXS work done, check out J. Mol. Biol
(1998) 284, 1439-1452 Imaging RNA and Dynamic Protein Segments with
Low-resolution Virus Crystallography: Experimental Design, Data Processing and
Implications of Electron Density Maps by Tsuruta et al.
Hi all,
I was wondering if anyone knows how to convert the P21221 to P21212
spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
got a correct MR solution in P21221 spacegroup. I have a script file that
runs with scalepack but was wondering if there is an easier way to do it
On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
Hi all,
I was wondering if anyone knows how to convert the P21221 to P21212
spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
got a correct MR solution in P21221 spacegroup.
Shya:
Scaling is done in a point group,
Hi,
My case is old b is changed to c (scenario 2 as you explained) or hkl is
changed to hlk. Thanks for the help
Shya
On Mon, May 7, 2012 at 4:33 PM, Ethan Merritt merr...@u.washington.eduwrote:
On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
Hi all,
I was wondering if anyone knows
On 5/7/12 4:09 PM, Shya Biswas wrote:
Hi all,
I was wondering if anyone knows how to convert the P21221 to P21212
spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but
I got a correct MR solution in P21221 spacegroup. I have a script file
that runs with scalepack but was
Anna
Interesting.
Yes, the cryo-em might be the way to go to see if some structures (i.e. not
just spheres) within the protein shell are aligned.
The SAXS study does make some sense. If the magnetic particles have some
alignment this should manifest itself in the SAXS pattern, with the
On Monday, May 07, 2012 01:42:58 pm Shya Biswas wrote:
Hi,
My case is old b is changed to c (scenario 2 as you explained) or hkl is
changed to hlk. Thanks for the help
hkl - hkl gives an inverted coordinate system. You don't want that.
Ethan
Shya
On Mon, May 7, 2012 at 4:33
Is it true that HKL adopts the naming convention of putting the screw axes
first and then naming abc if possible, whereas CCP4 just makes the cell
abc? E.g., would HKL ever output by default a p22121 dataset, or would it
automatically be p21212?
JPK
On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt
HKL or most probably SCALEPACK know nothing above point group if you do not
tell it.
But even in GUI one can use hkl matrix with the needed transformation matrix
:-\
What is nice about it that it will never let you to change the handedness of
the data, so anomalous signal is safe…
FF
Dr Felix
Forget to tell that all is done in the menu Macros : - (
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel:
The program that does the indexing in HKL is Denzo. Denzo doesn't care
about the space group. It cares about the point group (cf. Ethan's
point) and the cell dimensions, because it integrates the data without
regard to the symmetry expressed in the intensities - however it does
take notice
If one make a proper transformation :-/ and supply a correct space group,
absent reflections will be printed in the end of scale.log
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel
Acta
Why do you like P21212 better than P22121?
JPK
On Mon, May 7, 2012 at 4:00 PM, Phil Jeffrey pjeff...@princeton.edu wrote:
The program that does the indexing in HKL is Denzo. Denzo doesn't care
about the space group. It cares about the point group (cf. Ethan's point)
and the cell
On Monday, May 07, 2012 02:00:43 pm Phil Jeffrey wrote:
On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt
Scaling is done in a point group, not a space group.
My quibble with this statement is that the output reflection data from
Scalepack differs depending on what space group you tell it,
Hi Matt,
It worked really well in HKL 2000 reindex option, sorry about the confusion
before, I wanted hkl to lhk. as you pointed out the second one gave me what
I wanted.
thanks,
Shya
On Mon, May 7, 2012 at 4:47 PM, Matthew Franklin mfrank...@nysbc.orgwrote:
On 5/7/12 4:09 PM, Shya Biswas
Hi,
i just repeated the MR using the reindexed dataset (hkl to lhk) and it gave
me the right solution.
thanks,
Shya
On Mon, May 7, 2012 at 5:39 PM, Edward A. Berry ber...@upstate.edu wrote:
Now given that the MR soluiton was obtained in the (preparing to duck)
nonstandard setting, what is the
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