To add to Garibs answer - it is a good idea if your data set is pretty
complete - but can enhance model bias if it is not .
Eleanor
Garib Murshudov wrote:
On 18 Mar 2009, at 01:47, Bernhard Rupp wrote:
I mean *absent* reflections here with fobs=0
Dear All,
Bernhard
There's the related issue of how to optimally treat the *test set*
reflections, i.e. perfectly good measurements but not used (in
refinement that is). The various program authors seem to treat these
quite differently, e.g. Refmac AFAICS treats them exactly like
unobserved for the maps
Herbert J. Bernstein wrote:
Other sciences have struggled with this and seem to have found an answer.
Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html
kind regards,
Klaas
This is a good time to start a major crystallogrpahic image
archiving effort. Money may well be
Dear Garib
Thank you.
After removing SCALE card in the pdb file, refinement
is completed somthly.
Rajakumara
--- Garib Murshudov ga...@ysbl.york.ac.uk wrote:
It seems that something may be wrong with your input
file.
Specifically with the SCALE card in the pdb file.
Could you please
Dear all,
I wanted to use COOT to add a few residues to a the N-term, just simple
fantasy building. It should be straight forward with the
add-terminal-residue command, however COOT insists on a e-density map.
Any idea to overcome this?
Thanks in advance,
Guenter
Dear MOSFLM/IMOSFLM people,
when I start the new version of imosflm I expect it to dump files and to search
all files
starting from the current directory. This doesn't seem to be the case. It
appears it always
starts from MOSDIR. I my imosflm.tcl the line related to STARTDIR is:
set STARTDIR
Dear CCP4 developers,
I just wonder if there will be a fix for this problem. Basically when the first
user is running ccp4i on a linux server and then when the second user tries to
run ccp4i on the same linux server, the second user will only see the fist
user's DirectoriesProjectDir.
Best
Hi I just upgraded to the latest refmac5 . I am looking to merge this
newest refmac5 and its associated dictionaries with my existing ccp4-6.1
installation .
I was wondering where do I copy the latest accompanying dictionary
downloaded from Garib Murshudovs page to.
Thanks in advance
Hari
Apparently it DOES take a rocket scientist to solve this problem. Maybe the
brain surgeons also have a solution?
JPK
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
On Wednesday 18 March 2009 17:04:49 Jacob Keller wrote:
Apparently it DOES take a rocket scientist to solve this problem. Maybe the
brain surgeons also have a solution?
Apparently so: http://www.dclunie.com/medical-image-faq/html/index.html :-) .
--
Dr. ir. Lieven Buts, Postdoctoral Fellow
Actually the radiologists who manage CT and PET scans of brains do have
a solution, called DICOM, see http://medical.nema.org/. If we work
together as a community we should be able to do as well as the
rocket scientists and the brain surgeons' radiologists, perhaps even
better. -- Herbert
Dear Jun Dong,
This is a problem with the new mechanism used in CCP4 to store project
and job data (the CCP4 DBhandler). The quick fix for now is to turn it
off and use the old mechanism for storing the project data. To do this
in the CCP4i interface go to System Administration, select
Have any other Windows users noticed that Refmac5 runs much slower on
the same job when you upgrade from CCP4 6.0.2 to 6.1.1?
Best regards,
Phil Leonard.
--
DISCLAIMER: This e-mail and any attachments are confidential. They may contain
privileged information and are intended for the
Dear all
Before going into and trying to find a technical solution to the
problem it would be good if decide if we need images. As far as I know
if we face with a problem to solve and we know that it is necessary to
solve then we find technical solution to the problem (either from
other
On Wednesday 18 March 2009 09:41:59 Garib Murshudov wrote:
Dear all
Before going into and trying to find a technical solution to the
problem it would be good if decide if we need images. As far as I know
if we face with a problem to solve and we know that it is necessary to
solve then
Hi Garib
Does this answer your question (see final paragraph):
http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html
Best
-- Ian
-Original Message-
From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
Behalf Of Garib Murshudov
Sent: 18 March
Dear CCP4BB,
For further research of a particular structure wouldn't hints on
expressing, purifying and crystalizing the protein often be more
useful than images or amplitudes?
Liz
On 18 Mar 2009, at 17:00, Ethan Merritt wrote:
On Wednesday 18 March 2009 09:41:59 Garib Murshudov
As Herb will attest, the need for keeping images and the various reasons
for it have been discussed ad nauseum and agreed upon in various imgCIF
meetings - I am sure Herb or Andy Howard can provide links to the
documents/recommendations, to put this to rest.
Best, BR
Past ACA Data Standards
You could try something like this (bash/zsh/sh):
alias imosflm='MOSDIR=${PWD} imosflm'
The single quotes are required for it to do the right thing.
Bill
On Mar 18, 2009, at 6:49 AM, James Foadi wrote:
Dear MOSFLM/IMOSFLM people,
when I start the new version of imosflm I expect it to
Hi
I've heard of a tool from the Golden State which could (potentially)
be used for forging diffraction images... I believe it's called
mlfsom.
On 18 Mar 2009, at 17:50, Felix Frolow wrote:
One convincing argument I have:
We will be able to catch fraud ultimately. Fraud is a devastation
There have been excellent examples given for cases in which the original data
would have been very valuable for discussion and understanding. However, it has
always been my understanding that scientists are required to keep the original
data on which their conclusions are based. It is also my
Maybe, but images without experimental context (sequence? ligands?
purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!!
relationship to the other 15 similar datasets) are as good as no
images. And as far as I know, there's no good discussion on the table
for that. At least,
Perhaps we could use Poincare's argument(?), that knowing one cross section
of the universe in all of its detail would allow forward and
back-calculation of all previous states. Then the universe would be its own
lab notebook/ archive, and we would not need to bother with all of these
May be wwPDB should introduce a clause that all structure depositions
(upon release) must allow raw images accessible to anyone upon request
provided the requester pays (for postage and/or CD/DVD - if applicable).
This may be followed until google/NSA will offer free and _reliable_
storage in
expressing, purifying and crystalizing the protein
They are also useful. The NIH PSI initiative for example is trying as
a part of their Protein Structure Knowledgebase to establish a material
repository.
How well this will be generally accepted is another question, and the
storage and
Hi,
Since my mailbox is swimming in 'Images!' emails I would add my irrelevant
two cents:
Image storage does not pay for itself. There has to be a source of funding
for it. Storing, transmitting, etc. of the ever-increasing number of
terabytes costs money, which at the moment no one seems to
Dear Bernhard,
Re-reading your previous message, I can see that I did indeed misread
it, and I apologise for that. Perhaps it was the expression put to rest in
relation to a topic where so much action is needed that made me charge in
the wrong direction.
Although this thread is now
All right: How about then putting in a NIH challenge grant (due April 27)
for image archiving? Who is in?
BR
-Original Message-
From: Gerard Bricogne [mailto:g...@globalphasing.com]
Sent: Wednesday, March 18, 2009 4:12 PM
To: Bernhard Rupp
Cc: 'Gerard Bricogne'; CCP4BB@JISCMAIL.AC.UK
Some of us have already been discussing that possibility.
-- Herbert
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
Hi all,
is there any wisdom on NAD out there? I experience some strange
behaviour of this common cofactor.
With moderately convincing density, probably low occupancy of a
cofactor that came along for the ride from E coli, Refmac5.5.0088
pulls the AN6 atom out of the adenine plane. With my
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