DM is kind of past tense (unless you are dealing with multicrystal averaging)
-- I'd use parrot or shelxe instead (both pretty fast and automated). NCS
operators as input do not seem to be in fashion these days, so you might have
to put up with heavy atoms or partial MR models...
I would not
Hi Krisztian,
I have seen refmac fall over in a similar situation (low-ish res,
partially floppy model) during TLS refinement. You could try to rescue
it by
- using fixed TLS parameters from a previous (successful) refinement
- setting initial B-values to a fixed value
- including the peptide in
Hi all,
I have three datasets with same space-group and identical cell dimensions
which I want to merge together. I remember that this was discussed in the
blog some time back. Nevertheless, I can use some help!
Thanks in advance,
ARKO
--
*ARKA CHAKRABORTY*
*CAS in Crystallography and
Do you still have the unmerged files?
In that case just feed them to pointless and redo scala/etc..
If you only 3 merged data sets, you will have to use combat to convert
the mtz files into an fake unmerged format then put them through
pointless/scala to get relative scales and merge them..
There are several ways to skin a cat. If you have processed your data
with XDS, XSCALE can also do the job (you have to think of the unit cell
parameters of the merged data set though - the default may not
necessarily what you wish to have), and I am certain other data frame
processing suites
Hi
I'd have to say that I *really* like using Phil Evan's new program
Aimless rather than Scala - not sure if it's in CCP4 yet but it is
available from his own ftp site for a number of platforms -
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
(I think).
In my hands it's faster and more
Thanks judit, well one problem here would be that if you cant feed in
operators, that you got say from the map correlations with
something like GETAX, and you only have two sites (one per monomer) thats not
enough to define a two-fold... same goes
of course if you dont have a model (because you
Thanks for the clarification. Thanksrajesh
From: hofkristall...@gmail.com
To: ccp4...@hotmail.com; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] bias removal server
Date: Tue, 20 Dec 2011 22:41:10 -0800
I am not sure this service is maintained anymore, but given that with automated
model
Some recently released PDB entries (for instance 3u57) have structure
factor files that contain map coefficients. We think this is a really good
idea because it means that final maps as interpreted by the
crystallographer will then be archived and available.
But there is a problem converting
The patch in
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;325e1870.1112 solves the
problem with 3u57.
A few days ago I read the interesting paper
http://journals.iucr.org/d/issues/2011/01/00/dz5216/dz5216bdy.html referring to
a crystal structure containing a diselenide bond; I
Thanks for this. I have recently updated the CCP4-supplied dictionary to
include standard mmCIF, exchange dictionary, plus extra CCP4 items. This will
be in the next release.
I was about to update cif2mtz to recognise these extra columns. Will look at
what you have done, may save me a job.
Hi,
The solution provided by Mr. Dodson worked out well! Also it was nice to
learn about the other options available.
Thanks a lot!
ARKO
On Wed, Dec 21, 2011 at 5:13 PM, harry powell ha...@mrc-lmb.cam.ac.ukwrote:
Hi
I'd have to say that I *really* like using Phil Evan's new program
Hi,
would like to apologize for addressing Dr. Dodson incorrrectly...it was
purely unintentional...
regards.
ARKO
On Wed, Dec 21, 2011 at 5:13 PM, harry powell ha...@mrc-lmb.cam.ac.ukwrote:
Hi
I'd have to say that I *really* like using Phil Evan's new program
Aimless rather than
hello,
I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or
UBUNTO. Does anyone have an opinion about the best linux version to upgrade to
for not only CCP4 but also for general robustness and for the best standard
apps..Thanks
Paul
Dr. Paul Kraft
Structural Biologist
On Wed, Dec 21, 2011 at 2:29 PM, Paul Kraft haresea...@yahoo.com wrote:
hello,
I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora
or UBUNTO. Does anyone have an opinion about the best linux version to
centos 6
Opinions? You want opinions? On this mailing list? This one ought to
keep us going until the new year.
As for Fedora v. Ubuntu, my opinion is that Fedora is better for a
centrally managed system, whereas Ubuntu is perhaps more convenient for
a single owner-operator.
Fedora uses the RPM
On Wednesday, 21 December 2011, Paul Kraft wrote:
hello,
I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or
UBUNTO. Does anyone have an opinion about the best linux version to upgrade
to for not only CCP4 but also for general robustness and for the best
standard
Paul,
Wait a while, and then CENTOS 6 (or not wait a while). In my opinion neither of
your choices are as stable as CENTOS. The big drawback is that CENTOS does not
have the latest gadgets - but gadgets and stability are mutually exclusive, by
definition. I have lately been annoyed because I
The price of stability is that you don't get all the latest stuff. In SL6.1,
the current version of Firefox is 3.6.24, and the image rendering is SLOW. I
am wondering if I want to go back that far in time.
Not out of the box, but the latest ffx works in centos6. I think there
are third party
Hi Fellows,
I am looking for some advice re LN2 autofill. I want to automatically refill
an open special-use foam Dewar
on the crystal harvesting robot from an unpressurized secondary storage
Dewar. We found this system
http://www.norhof.com/fillingexample.html
and it seems to do what we need
Dear all,
A post-doctoral position is available in the Structural Biology and
Biophysics group at Pfizer's research labs in Groton, Connecticut (USA).
To apply, please go to www.pfizer.com/careers and search for job ID
959727.
Job Focus
The successful candidate for this position
On Wed, 2011-12-21 at 15:40 -0500, Sabuj Pattanayek wrote:
On Wed, Dec 21, 2011 at 2:29 PM, Paul Kraft haresea...@yahoo.com wrote:
hello,
I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora
or UBUNTO. Does anyone have an opinion about the best linux version to
FWIW, I use RHEL 5 = CentOS 5 and recently upgraded to 6.
Everything I use (not crystallographic software) works fine
except vmware workstation currently does not work on it,
Tried upgrading to vmware workstation v8? Compat guide :
Fedora releases are supported for about a year from initial release.
Red Hat Enterprise, Centos and Scientific Linux are all supported for
about 5 years.
--
===
All Things Serve the Beam
I tried the bookend drop method. It didn't work for me but hopefully it
will benefit other people.
There is only one thing I need to add to the detailed protocol from Martyn.
I had trouble not cutting through the plastic slides. Even I could do it,
it was impossible to peel a layer up. So in the
On 12/22/2011 06:56 AM, David Schuller wrote:
Fedora releases are supported for about a year from initial release.
Red Hat Enterprise, Centos and Scientific Linux are all supported for
about 5 years.
Ubuntu has long term support distributions as well:
Starting with Ubuntu 12.04 LTS [...]
I am adding solvent molecules into unmodelled blobs of density in Coot.
When I am finished, I merge molecules, then save my coordinates. For some
reason Coot is saving two copies of each molecule that I have modelled and
assigns them different chain ID's. I notice this when I open it in PyMol
and
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