The phosphorus absorption edge is about 5.8Å.
I've had much better luck with 5-Br-U for anomalous phasing.
Molecular replacement with sub-structural fragments can also work:
<https://scottlab.ucsc.edu/scottlab/reprints/2010_Scott_Methods.pdf>
Yours sincerely,
William G. Scott
Pro
homebrew heavy-handedly wiped out coocanvas v. 2 when upgrading.
I made a temp fix with a sym link as follows:
ln -s /usr/local/Cellar/goocanvas/3.0.0/lib/libgoocanvas-3.0.9.dylib
/usr/local/lib/libgoocanvas-2.0.9.dylib
your path prefix will be different, but you get the idea.
> On Sep 30,
ct be solved
without resorting to isomorphous replacement, by simply using a small subset of
modeled duplexes for molecular replacement.
cf: https://doi.org/10.1016/j.ymeth.2010.06.011 It might be worth a try.
RNA perhaps inspires hatred because it habitually and bitterly mocks us in
silence
I’ve compiled it, but am having trouble with the GUI. This is not a big sur
problem per se, but rather is the newer GTK+3 X-windows-independent interface.
When we get it working, it will be a much nicer mac interface.
Apple threw OpenGL under the bus in the last couple of OS updates.
> On
Which ones?
All of the binaries in $CBIN I have say "Mach-O 64-bit executable x86_64” So
that is unlikely the issue.
I haven’t installed Catalina yet, as I only have one computer that is new
enough. But one of the changes is they have locked down much of the file
system, and are urging
After reflecting on this a bit, I rejected anything dealing with glide planes,
and although I initially thought I had something good involving a screw axis of
evil, I decided it, too, would probably be lost in translation, not to mention
a bit dated.
Perhaps something more current, involving
s as
much a legacy as his many exceptional contributions to science.
Yours sincerely,
William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http://scottla
positive charge, and O has a
partial negative
charge. (If you think about it, all pi-stacking interactions, from the point
of view of classical
electrostatics, would be somewhat repulsive.)
Good luck with this, and let us know of the outcome.
Bill
William G. Scott
Director, Program
Hi Barry:
It is an X11.app bug that has persisted for years now. (It isn’t specific to
coot).
Briefly, this happens unless you uncheck the checkbox for “Displays have
Separate Spaces” in System Preferences>Mission Control
William G. Scott
Director, Program in Biochemistry and Molecu
coot --no-graphics
William G. Scott
http://scottlab.ucsc.edu
> On Jul 28, 2017, at 1:34 PM, Reza Khayat <rkha...@ccny.cuny.edu> wrote:
>
> Hi,
>
> Is it possible to run Coot without the use of GUI? We have some Coot scripts
> for a pipeline and we’d like to do
a multitude of fruitful and
productive collaborations throughout a period most normal people would consider
retirement. He passed away on Thursday at age 87 from an opportunistic
infection while combatting lymphoma.
William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center
benefit to the
scientific community.
Yours faithfully,
William G. Scott
Director, Program in Biochemistry and Molecular Biology
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
What’s the job situation in Europe looking like for refugee scientists these
days?
William G. Scott
Director, Program in Biochemistry and Molecular Biology
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
More regarding" XQuartz upgrade breaks Coot” from people who know more than I
do (which admittedly is most everyone, but I digress …):
>
> Today's Topics:
>
> 1. Xquartz 2.7.10-rc2 breakage (Jack Howarth)
> 2. fink-0.41.0-101 du_sk.t build failure (Patrick Carmack)
>
>
>
On May 20, 2015, at 5:38 AM, Randy Read rj...@cam.ac.uk wrote:
Thanks, as always, to everyone for a thoughtful discussion!
Alternatively, as a scientific community, perhaps it is finally time for us to
untwist Clippy, bending him backwards and forwards until he snaps at those
horrid beady
On May 18, 2015, at 4:31 AM, Nicolas Soler nso...@mrc-lmb.cam.ac.uk wrote:
You just have to learn the (easy) equation syntax
or just use this:
http://www.macupdate.com/app/mac/18172/tex-fog
William G. Scott
http://scottlab.ucsc.edu/~wgscott
Glad it works!
It sounds like they finally fixed an X11 bug that has been quite problematic
these last few years.
Bill
William G. Scott
http://scottlab.ucsc.edu/~wgscott
On May 14, 2015, at 9:06 PM, Xiao Lei xiaolei...@gmail.com wrote:
Dear William,
I installed the X11 2.7.8_rc1
knowledge.
All the best,
Bill
William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http://scottlab.ucsc.edu/~wgscott
On Apr 24, 2015, at 12:52 AM, Robbie
Hi Jeorge:
My Luddite approach to such things:
grep -v ANISOU original.pdbiso_only.pdb
HTH,
Bill
William G. Scott
http://scottlab.ucsc.edu/~wgscott
On Apr 24, 2015, at 8:54 AM, jeorgemarley thomas kirtswab...@gmail.com
wrote:
Dear All,
Here is the CCP4 version 6.5
sarcasm and strange verb tenses.)
If anyone has a good source for successful examples or templates, I would be
incredibly grateful.
Many thanks in advance.
Bill
William G. Scott
http://scottlab.ucsc.edu/~wgscott
to materialize.
YMMV,
Bill
William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http://scottlab.ucsc.edu/~wgscott
On Mar 17, 2015, at 4:30 PM, Cygler, Miroslaw
On Mar 13, 2015, at 12:42 PM, Petr Leiman petr.lei...@epfl.ch wrote:
this is how we are supposed to use CCP4 today anyway.
I’ve never been big on doing what I am told I am supposed to do, so I have been
using this:
use this to put it at the end of the path:
ccp4_first_in_path=0
or this
— enzymology. Hopefully this will be something to
get a start with.
Bill
William G. Scott
Director, Program in Biochemistry and Molecular Biology
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
On Mar 11, 2015, at 11:13 AM, Keller, Jacob kell...@janelia.hhmi.org wrote:
Somebody sent me a pdf with such a mind-picture which describes the origin of
the anomalous effect as arising from broken centrosymmetry of the anomalous
atoms themselves:
(p. 8) Under normal conditions,
On Feb 26, 2015, at 4:51 PM, Srivastava, Dhiraj dhiraj-srivast...@uiowa.edu
wrote:
Hi
I have a protein with two substrate. when I am doing the binding studies
with the two substrate separately, I am finding one of the substrate to have
similar kd and Km. however the km and kd values
CCP4 has a number of such utilities, such as pdbset.
http://www.ccp4.ac.uk/html/pdbset.html
You can find others by looking here:
http://www.ccp4.ac.uk/html/FUNCTION.html
HTH,
William G. Scott
http://scottlab.ucsc.edu/~wgscott
On Oct 7, 2014, at 11:01 AM, Sasha Pausch sashapau
On Oct 6, 2014, at 12:04 PM, Sasha Pausch sashapau...@gmail.com wrote:
Hello All,
I would like to know how to change the nomenclature of bases (for example
from Ad to DA for adenosine triphosphate) in PDB file.
perl -pi -e ‘s|Ad|DA|g’ your.pdb
On Sep 2, 2014, at 9:10 PM, Avisek Mondal avisekmonda...@gmail.com wrote:
please can you send me this paper... i can not subscribe it from my lab...
Acta Cryst. (2014). F70, 1296-1302[ doi:10.1107/S2053230X14014381 ]
No problem: http://tinyurl.com/n3gurpe
On Jun 1, 2014, at 10:08 PM, Eze Chivi ezech...@outlook.com.ar wrote:
Hello, when I refine my structure, I see negative density around the
disulfide bond. I have 7 copies per ASU, and I can see this density in many
of them. In some cases, I see positive density also (negative in the center
in that case
would probably be significant. The map image quality, after all, is what we
are after, not beautiful Table 1 statistics.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
corrupted.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http://scottlab.ucsc.edu/scottlab/
On Apr 2, 2014, at 8:58 AM, Yamei Yu ymyux...@gmail.com
On Mar 28, 2014, at 10:29 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote:
Hi,
Does the ccp4 suite work with the latest OSX 10.9.2 operating system? Are
there any known problems?
Mirek
As far as I can tell, it works fine.
One problem I have heard (on the ccp4bb) with 10.9.X
I remember seeing an approx (5mm)^3 haemoglobin crystal in the MRC LMB crystal
growing room, and the nucleosome crystals there were almost as big in their
longest dimension.
Bill
On Oct 24, 2013, at 8:33 AM, Tobias Beck tobiasb...@gmail.com wrote:
Dear all,
I was just wondering if anyone
On Sep 4, 2013, at 2:57 PM, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote:
You may need to use the latest available version (5.8) from our LMB site
Hi Garib:
Would it be possible to add a link for the source code, so this could also be
used with Coot?
Thanks.
Bill
Scroll up to see where it started failing.
On Aug 3, 2013, at 11:22 AM, anil kumar anilkumar...@yahoo.co.in wrote:
Dear members,
I am attempting to install ccp4 package in my mac machine. The download of
the files was directed in a temp folder and done via the package manager
On Jul 12, 2013, at 12:57 PM, Mark van der Woerd mjvdwo...@netscape.net wrote:
I just re-wrote our safety plan because we have to renew our radiation
license for our new in-house instrument. On this plan, they ask you to write
a worst-case scenario. For an in-house sealed tube instrument,
resolution you might need.
Good luck.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
That last paragraph is great:
Adam is the author of the book Surviving Your Stupid, Stupid Decision to Go to
Grad School (Broadway Books, 2010)
-- Bill
On Mar 28, 2013, at 9:09 AM, Ian Tickle ianj...@gmail.com wrote:
By coincidence this just landed in my Inbox:
to them
not to have to rely only upon my limited abilities and increasingly obsolete
knowledge.
We should all be able to learn from one anther without fear of reproach.
All the best,
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular
I find that least-squares fitting of RNA in coot is fairly painless, robust and
straightforward. It will move all of the contents of one pdb file, not just
the RNA residues you select to align.
On Mar 14, 2013, at 1:53 PM, Chen Zhao chenzhaoh...@gmail.com wrote:
Dear all,
I am now
,
annoyances and 'features' that have been corrected in 10.8, so I either run
10.8.X or 10.6.8 on my computers in the lab.)
Good luck.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University
It sounds like you have updated the OS system since last updating fink.
Easiest thing is to blow it away and start over. I made some tarballs to
remove the pain:
http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Installing_Fink_on_10.6_and_10.7#Installing_Fink_on_10.8
Or you can just
On Feb 10, 2013, at 8:23 AM, LISA science...@gmail.com wrote:
Hi all,
My mac has the old version of phenix. How can i update to the new verison?
Should I delete the old version and download the new version to install as
the fist time ? Thanks
lisa
You can delete it and download a new
structure?
any suggestion is appreciation.
dengzq
Unless it has some other, more stable structure to compete it out, you will
have this problem persist. Even GTP in solution will do this.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center
Give it the suffix .ccp4
On Dec 7, 2012, at 10:52 AM, Harman, Christine christine.har...@fda.hhs.gov
wrote:
Hi,
Can anyone tell me how to open a CCP4 map in Pymol.
Thanks,
Christine
Hi folks:
Are Mg++ ions ever observed to chelate primary amines?
Are there any examples in crystal structures?
Thanks.
-- Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University
Make your life easier and use CCP4's imosflm
(this is the CCP4 bb after all)
On Nov 18, 2012, at 5:48 PM, 王瑞 wangrui...@gmail.com wrote:
OK,thank you all of you. I have installed one copy of HKL2000 on our
desktop computer. But for my notebook's low 1366*768 resolution, the
HKL2000 can't
Hi folks:I'm trying to get a sense for how frequently this sort of thing occurs:That was a macbook air that served me well for four years, but then self-destructed. (I took it to the Apple store. They generously offered to repair it for $800 or to sell me a new one, and suggested this was normal
On Nov 12, 2012, at 8:13 AM, Michael Roberts mrobert...@talktalk.net wrote:
Dear All,
I would be interested to learn of other crystallographers' experience in
their use of glass capillaries for protein crystal growth and X-ray
diffraction clarity.
There are many types of glass available
On Oct 18, 2012, at 3:39 PM, Kip Guja k...@pharm.stonybrook.edu wrote:
If the output says: /bin/bash then do
source /Applications/ccp4-6.3.0/bin/ccp4.setup-sh ccp4i
If the output says: /bin/tcsh or /bin/csh then do
source /Applications/ccp4-6.3.0/bin/ccp4.setup-csh ccp4i
You need
Dear Ronan et al:
I apologize if I have missed it, but is there a simple way to obtain the
corresponding changes in the source code for those of us who compile ccp4
ourselves?
I looked on the web site and the ftp site but can't seem to find it.
Many thanks in advance.
Bill
On Oct 8, 2012,
I'd just use a decent shell scripting language (like zsh) in conjunction with a
unix tool like awk. But the gnuplot option sounds ideal.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
On Sep 6, 2012, at 9:00 AM, eugene.krissi...@stfc.ac.uk wrote:
If this does not work for you for any reason, please (re-)read update manual
for details. If that does not help as well, please write to us.
Dear Eugene:
Will there be a way to get the corresponding changes to the source-code?
I completely agree with Harry's observation about the glare screen feature.
I find it is quite literally an almost instant headache. There is an option
with the macbook pro to pay a ransom to get a usable screen, so my wife did.
On my macbook air, I found putting a dull dark grey background
I'm unable to reproduce the error.
Can you try it in a temporary new account that doesn't have anything modified,
and see if it works?
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University
it will work fine. If you can get it from Best Buy
for under $300 and return it within 30 days for a full refund, it might be
worth it.
Either way, let us know.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer
, and Hg++ prefers sulphur to oxygen.
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
On Jul 17, 2012, at 6:25 AM, Felix Frolow wrote:
I will wait for fink version if it will be one… :-\
Does anyone use or want this anymore?
-- Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
If RedHat allows you to install a more current version of glibc, then do that.
If not, switch to something like Ubuntu.
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California
xdrawchem is free and will do this.
On May 31, 2012, at 8:01 PM, Appu kumar wrote:
Dear ccp4 user,
Sorry for offset question, Anyone please tell me
the name of programme which can be used to draw enzyme reaction mechanism (
like Sn1 and Sn2). Your kind help
I thought it was some sort of allegory for tenure-track faculty positions.
-- Bill
On Feb 28, 2012, at 7:16 AM, Gerard Bricogne wrote:
Dear Smita,
For me, your story mostly illustrates the grave dangers of wanting to
own a BMW while still in high school ... ;-) .
With best
This paper is a favorite:http://www.ncbi.nlm.nih.gov/pubmed/2160019
J Mol Biol. 1990 May 5;213(1):159-66.
Crystallization of Escherichia coli catabolite gene activator protein with its
DNA binding site. The use of modular DNA.
On Feb 15, 2012, at 12:06 AM, LISA wrote:
Hi all,
I have
for
a Ph.D. thesis project (especially when combined with an M.D.), and you,
unlike Him, have access to a Sigma catalogue.
All the best,
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University
http://en.wikipedia.org/wiki/Henderson–Hasselbalch_equation
or any intro chemistry text
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California
monitor attached to a $600 mac mini.
I'm sorry this doesn't answer your question, but I think an ancient version of
coot on an ancient computer will just be a world of hurt.
-- Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228
that would be the best way to handle it from a central repository,
allowing the end-user to decide on the fly. The lossless files could somehow be
tagged as such, to avoid confusion.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular
On Oct 5, 2011, at 5:52 PM, Bosch, Juergen wrote:
http://www.apple.com/stevejobs/
May innovation continue to lead the future.
Jürgen
I've been quite saddened about this all evening. Even though we knew it was
coming, it is still incredibly sad, especially at his age (only 56).
Although
On Sep 28, 2011, at 5:26 PM, Jacqueline Vitali wrote:
Dear colleagues,
I need some advice for a new computer.
(1) I have the option of an HP Z210 8 GB with a low end Quadro Nvidia 400
512 MB.
--How does Coot run with this card?
OK
--I am happy with any Linux. However, the
On Sep 22, 2011, at 9:29 AM, Ben Eisenbraun wrote:
Desmond 3.0 Tutorial
2.2 was quite impressive.
(sorry.)
) source of frustration.
Thanks in advance.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
and joy,
Bill
On Sep 16, 2011, at 6:33 AM, William G. Scott wrote:
Dear Phil (and everyone):
1. I've now got automated build systems for coot for 10.7.1 and 10.6.8. I
just haven't had a chance to get the 10.6.8 one on line. I'll try to do this
today. (Also, the last few haven't build due
OS X 10.7 enables you to do whole-drive encryption.
Here is a description from Arse Technica:
http://arstechnica.com/apple/reviews/2011/07/mac-os-x-10-7.ars/13
I ain't never tried it myself. 10.7 seems to run slow enough as it is.
-- Bill
On Aug 18, 2011, at 5:34 AM, Andreas Förster wrote:
On Jul 27, 2011, at 6:45 AM, Bosch, Juergen wrote:
But Bill has updated his webpage
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes
On Jul 22, 2011, at 4:24 AM, Xiaoguang Xue wrote:
I noticed that the Fink repository will not run on the Lion system
All the debian utilities work (as does the crystallography software), so it is
just the fink perl wrapper script itself that doesn't work.
Here is a cheap and easy, but
Sorry about this.
Issue the command
sudo perl -pi -e
's|/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6\:/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5\:||g'
/Library/Coot/bin/coot
and that will fix it.
I'll make a new one.
Bill
On Mar 10,
Hi Wataru:
I hope all is well. For the ones you already have grown, try very gently
prying them off with a wedge-shaped needle.
If you can grow more, try using a very thin smooth layer of vacuum grease, and
apply the drop to that. I managed to get RNA crystals to grow that way that
On Dec 20, 2010, at 1:16 PM, jlliu liu wrote:
it is also within hydrogen bonding distance to the main
chain N of another protein residue.
This also strongly suggests it is not Mg2+, which prefers hard ligands such as
charged oxygen, rather than softer ligands like uncharged backbone
On Dec 3, 2010, at 3:11 AM, U US wrote:
Hello CCP4, long time no see! I wanted to show you this article. I've made
over $2k in the past month and I barely work 4 hours a day.
Grad school was the best 13 years of my life, too.
As usual, the Omniscient Wikipedia does a pretty good job of giving the
standard mathematical definition of a vector:
http://en.wikipedia.org/wiki/Vector_space#Definition
If the thing fulfills the axioms, it's a vector. Complex numbers do, as well
as scalars.
It is a bit more
On Oct 14, 2010, at 7:40 AM, Ed Pozharski wrote:
On Thu, 2010-10-14 at 08:41 +0200, Tim Gruene wrote:
This sounds as though you are saying that a single photon interacts
with several
electrons to give rise to a reflection.
Not only with several - it shouldn't be much of an exaggeration to
On Oct 14, 2010, at 2:31 PM, Tim Gruene wrote:
I would like to understand how the notion of a photon being scattered from all
electrons in the crystal lattice explains the observation that radiation
damage
is localised to the size of the beam so that we can move the crystal along and
shoot
On Oct 14, 2010, at 2:28 PM, Jacob Keller wrote:
I have always found this angle independence difficult. Why, if the anomalous
scattering is truly angle-independent, don't we just put the detector at 90
or 180deg and solve the HA substructure by Patterson or direct methods using
the pure
On Oct 13, 2010, at 4:21 PM, Jacob Keller wrote:
While we are on embarrassingly simple questions, I have wondered for a long
time what is the reference phase for reflections? I.e. a given phase of say
45deg is 45deg relative to what? Is it the centrosymmetric phases? Or a
theoretical wave
On Oct 13, 2010, at 3:09 PM, Tim Gruene wrote:
Dear Bill,
The discussion is becoming complicated because of the mixing of notations.
There is a theory or model which describes the atomic scattering factor as
f = f0 + f' +if
from which the structure factor is calculated. That right angle
Hi David:
I think you need to start with the pure 64-bit fink from cvs in order to
get this to work. All the errors are a consequence of using the 32-bit
version. You can't mix them. I have no idea why they still don't have a
binary installer, but they don't.
Email me directly if you need
or the system wish, gives a nicely
working imosflm. And thanks for the fink packages...
Engin
On 7/6/10 6:36 AM, William G. Scott wrote:
Remove both.
On OS X, 10.6, imosflm uses the tcl/tk supplied with OS X, and the latest
mosflm is in ccp4, so there is no need for any of that. Just use what
Remove both.
On OS X, 10.6, imosflm uses the tcl/tk supplied with OS X, and the latest
mosflm is in ccp4, so there is no need for any of that. Just use what is in
ccp4.
Sorry for this.
On Jul 5, 2010, at 4:34 PM, Engin Özkan wrote:
Hi everybody,
I was doing a regular fink update (OS X
Dear Harry et al:
I'm sorry, I've been immersed in grant renewal/resubmission hell. I obviously
screwed something up in a rush.
Briefly, if you have 10.6.X, ccp4 and OS X have everything you need for a nice,
fully-functioning OS X aqua imosflm gui.
Bill
PS: The 64-bit ccp4 and mosflm work
When searching, avoid the almost overwhelming temptation to spell it as
vile manipulator or you will just wind up with a listing of university
administrators.
Bandaranayake, Rajintha wrote:
Hello all,
Does anyone know where one could purchase cryo-vial tongs/manipulatos with
the plastic
Hi folks:
Sorry about the off-topic nature (so to speak) of this post, especially given
that it is not yet Friday, but I am interested what our community thinks of
this:
http://library.ucsc.edu/sites/default/files/Nature_Faculty_Letter.pdf
Something similar happened with UC and Cell Press a
On May 18, 2010, at 4:13 PM, Jay Pan wrote:
Hello Everyone,
I have a reasonably well fitted electron density map through
molecular replacement. However, there is always some red region left
no matter how hard I tried when the mtz file is loaded into Coot. Is
this because my model is
Although not as dramatic, there is a simple, private, method one can use
to unsubscribe, and it possesses the additional merit of actually doing
what you want:
http://www.ccp4.ac.uk/ccp4bb.php
Colapietro, Anne-Marie wrote:
Please remove me from this list.
Thank you,
Anne-Marie
Yo Hari:
The symbolic link won't solve the problem.
I managed to scrape together a blt for tcltk 8.5 on OSX, so it is possible.
Most of the hacks in turn came from a different Linux distro (gentoo) so it
should be possible on ubuntu.
Here by the way is the patch:
This was done in total despair:
http://sage.ucsc.edu/scottlab/reprints/2008_Scott_ActaCrystD.pdf
Francis E Reyes wrote:
Hi all
I'm in search of literature *detailing* low resolution [4-5A] phasing
protocols. Heck I'll take detailed thesis chapters (since they tend to be
more detailed than
On Feb 28, 2010, at 5:11 PM, Damon Colbert wrote:
I have a persistent Kubuntu 8.10 .. it took a week to work out some
problems. The main one being that with limited space on the thumb drive,
one cannot do a complete update of Kubuntu. Therefore many libraries are
missing and dependancy
On Feb 27, 2010, at 7:10 PM, David Roberts wrote:
I have a quick question about linux for all. Is there anybody running a
windows pc with linux on a bootable cd or bootable drive/flash drive/??? that
works for crystallography apps? I have a colleague who does molecular
dynamics
Dear Rui:
Did you by any chance install an old ppc version of X11 onto an intel machine?
If so, it might be running via Rosetta, which is an emulator provided for
transition, but could account for lousy performance. OS X 10.6 comes with X11
installed by default, so you might have clobbered
You have to make sure the asymmetric unit for the maps is the same as for
your molecule (which it probably isn't). The easiest way is to extend the
map so it covers all the atoms with a few angstrom border. Coot
calculates the map on the fly from the mtz file (I am guessing this is the
On Feb 7, 2010, at 11:13 PM, Wataru Kagawa wrote:
Hi all,
I would like to create a pdb file for a chemical compound (FW ~600) that was
created in our chemistry department. ChemDraw 3D appears capable of doing
this, but I would like to know if there are free alternatives that work great
The easiest thing to do is:
export MOSFLM_WISH=/usr/bin/wish8.4
or
fink install imosflm-aqua
will make sure everything is set up ok for 10.6, where the supplied aqua
TclTK plays well with imosflm.
Yamei Yu wrote:
Hi all,
I use fink to install ccp4-6.1.2 on my Mac OS X 10.6. All
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