Hmm I am not sure about directly importing the .x files into
pointless, but you could run them through scalepack in P1 and write
out no merge original index, pointless can read that.
Best wishes,
Graeme
2011/11/17 wangping...@sina.com:
Dear Graeme,
I processed my data with HKL2000, How
Dear Jacob,
You may find useful this web site by Marjorie Harding about metal coordination
sites in proteins
http://tanna.bch.ed.ac.uk/
best regards
Stefano Benini, Ph.D.
Assistant Professor
http://pro.unibz.it/staff2/sbenini/
Bio-organic Chemistry Laboratory
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Hi Ed,
you can probably set hklout to /dev/null in order to not produce the
output mtz-file, but this would not prevent refmac5 from doing the
calculations.
Tim
On 11/17/2011 06:44 AM, Ed Pozharski wrote:
Is there some way to make refmac *not* to
Dear Jacob,
for NH4+, you would expect a (partial) tetrahedral coordination with
typical H-bond distances of ~2.9 A. For Na+, you would expect a
(partial) octahedral coordination with Metal-to-ligand distances of ~2.4
A (see Harding, Acta Cryst., D62, 678-682 (2006); Harding, Acta Cryst.,
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Dear all, dear Phil,
how can a dataset be merged if the space group is unknown? Does
pointless require the Friedel pairs present in the file, too?
Tim
On 11/17/2011 08:34 AM, Graeme Winter wrote:
Dear Ping,
You need the unmerged data for this -
Dear colleagues,
I am suddenly having a problem with starting the ccp4 Interface. Logged on as a
normal user (username, group users) the Interface window pops up but hangs
almost immediately (the top bar says CCP4Interface 2.1.0, the only program
tab shown is Coordinate Utilities and the
Aaagh - you merge the POINT group!
Not the spacegroup...
Eleanor
On 11/17/2011 09:32 AM, Tim Gruene wrote:
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Dear all, dear Phil,
how can a dataset be merged if the space group is unknown? Does
pointless require the Friedel pairs present in
If you dont like it - delete it..
Eleanor
On 11/17/2011 09:29 AM, Tim Gruene wrote:
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Hi Ed,
you can probably set hklout to /dev/null in order to not produce the
output mtz-file, but this would not prevent refmac5 from doing the
calculations.
Tim
It doesn't matter about running scalepack in P1 - just set the nomerge
option and read that sca file into pointless.
Infuriationly - that file does NOT have the cell or the wavelength in
the header so you have to add that by hand in the GUI
Eleanor
On 11/17/2011 09:03 AM, Graeme Winter wrote:
Hi all,
Has anyone observed 'odd' arginine residues, missing the NH1 atom; and possibly
related.. very close Chlorine-arginine (NH1 again) distances.
I have a 1.3Å structure and am having trouble getting my head around some very
odd density features.
I have 2 molecules in the assym. with the
Yes - I have seen something similar at a lower resolution, but very
ugly! I tried to model it as a solvent molecule - possible but not too
convincing..
Cl should give an anomalous signal - try a DANO map and see what it shows..
Eleanor
On 11/17/2011 11:09 AM, Dean Derbyshire wrote:
Hi all,
I was wondering yesterday why one would do this and I'm sure the original
poster has a particular reason for it - I just don't understand it.
Are you burning CPU cycles for benchmarking proposes and don't want to bias the
result based on slow hard discs or SSD's ?
Jürgen
On Nov 17, 2011, at
I can think of at least one good reason: you might want to optimise
the weights using different starting values. In that case there's no
need to look at the maps until the end. But as Eleanor says you can
always delete them. I would do the weight optimisation with a
customised script, so this
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Dear Eleanor,
Sorry, but I don't see how your comment answers any of my two questions.
Tim
On 11/17/2011 12:10 PM, Eleanor Dodson wrote:
Aaagh - you merge the POINT group!
Not the spacegroup...
Eleanor
On 11/17/2011 09:32 AM, Tim
I also have seen similar. I was thinking it was potentially some kind
of radiation damage? Is there a good paper which examines what
chemistries are seen in rad damage?
Jacob
On Thu, Nov 17, 2011 at 5:39 AM, Eleanor Dodson c...@ysbl.york.ac.uk wrote:
Yes - I have seen something similar at a
Hi Jacob,
A couple of years ago, I put together a list of papers that touch on radiation
damage:
http://www.p212121.com/2009/11/17/ultimate-list-on-cryocrystallography-radiation-damage/
To answer your question more directly - see pg. 40 of the following paper:
On Thu, 2011-11-17 at 11:10 +, Eleanor Dodson wrote:
If you dont like it - delete it..
Eleanor
I know. But what I want is to skip the calculation in some cases when
the map is not needed. This currently is impossible without modifying
the refmac code.
Ian provides an excellent example
Hi all,
Sorry for the off-topic question, but I wanted to find out anyone's experience
with using magnetic anti-flag beads (Sigma). I have been having a problem with
the anti-flag antibody leaching from the beads during low pH elution ( which
shouldn't be happening I am thinking) and was
Hi CCP4ers,
I know it is not quiet related to CCP4. I am now working on a protein-protein
complex system. I am wondering which kits I should try in a higher priority? I
appreciate everyone's suggestions, and maybe there are some papers I can read
first.
Lucas
Hi,
I worked on a crystal sensitive to radiation damage, So I need to merge
many crystal to obtain complete dataset, Does anyone know such program that
can tell crystal orientation after first frame exposure.
Thank you in advance.
--
Thank you very much and all the best,
Yanwu Huo
Postdoctoral
All the currently used diffraction image processing programs can tell the
crystal orientation from a single diffraction image.
Some programs like d*TREK can calculate new orientations for the crystal if the
crystal is mounted on a reasonable goniometer such as the Rigaku Kappa
goniostat or the
If it's the M1 antibody, you can elute with EDTA + Flag peptide.
You could also try a little higher pH like 3.5.
Ho Leung Ng
University of Hawaii at Manoa
Assistant Professor, Department of Chemistry
holeung...@hawaii.edu
On Thu, Nov 17, 2011 at 2:00 PM, CCP4BB automatic digest system
There is at least one paper describing the success of PEG precipitants
for complexes, but I can't find the reference right now.
Ho
Ho Leung Ng
University of Hawaii at Manoa
Assistant Professor, Department of Chemistry
holeung...@hawaii.edu
Ho Leung Ng wrote:
There is at least one paper describing the success of PEG precipitants
for complexes, but I can't find the reference right now.
Is this it?
http://scripts.iucr.org/cgi-bin/paper?S0021889802013973
J. Appl. Cryst. (2002). 35, 674-676[ doi:10.1107/S0021889802013973 ]
On Thu, 2011-11-17 at 14:03 -0600, Yi-Liang Liu wrote:
Hi CCP4ers,
I know it is not quiet related to CCP4. I am now working on a protein-protein
complex system. I am wondering which kits I should try in a higher priority?
I appreciate everyone's suggestions, and maybe there are some papers
I would recommend Qiagen's ProComplex and JCSG+, and Emerald's Precipitant
Synergy.
- Original Message -
From: Ho Leung Ng [mailto:h...@hawaii.edu]
Sent: Thursday, November 17, 2011 07:23 PM
To: CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Protein-Protein Complex
Yanwu,
I surmise from your question that you are inquiring how to go about collecting
from many crystals optimally. Merging data ex post facto is a totally different
kettle of fish.
In my opinion, the most robust way to go about this is to use a kappa
goniometer as Jim suggested (I am most
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