Are your environment variables like
$CINCL
and
$CCP4
defined?
These usually get set up by sourcing the $CCP4/include/ccp4-setup.X file
appropriate for your shell.
michael nelson wrote:
Sorry folks, but I have been very frustrated to get
mosflm and imosflm to work.
I have get around with
What is the operating system? These things are system-dependent...
On Wed, 12 Dec 2007 15:42:39 -0500
Robert Grant [EMAIL PROTECTED] wrote:
It would appear that an environmental variable involving a library
path is missing or wrong but I have not been able to figure out what
it
On Fri, 7 Dec 2007 13:22:03 -0500
[EMAIL PROTECTED] wrote:
CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK wrote on 12/07/2007 12:43:55
PM:
could anyone drop the name of a source for those tweezer-like clamps
whose
ends fit perfectly around a Nunc/CryoCap cryovial? one
Coot mutates RNA the same way it does DNA and proteins. (Make sure you
have the one-letter code, not the CNS convention).
O also does this.
Green, Todd wrote:
Hello all,
I have models of poly-U RNA that I would like to mutate to other bases. Is
there a program that I can use to mutate the
Dear Ray:
The Crystal Screen I is based on a screen that was developed over a period of
years in Sung-Hou Kim's lab, and is heavily weighted with conditions that were
successful for obtaining the protein crystals that were particular to his lab
at that time (which was when I was a graduate
Juergen Bosch wrote:
@Bill,
how about your experience with 10.5 ?
Dear Apple Customer,
Apple is pleased to report that a shipment for the following order
is on its way to you.
The following products shipped on 10/26/2007.
Product # Product Description QtyExt
Go to the jiscmail page and follow the directions.
On Thu, 20 Sep 2007 16:31:07 +0200
Anat Bashan [EMAIL PROTECTED] wrote:
unsubscibe
On Thu, 20 Sep 2007 17:23:05 +0100
R. J. Lewis [EMAIL PROTECTED] wrote:
a large signalling complex called the 'stressosome' from B. subtilis.
-
If you decide to go for the human form of this signalling complex, I am an
over-producing strain.
Hi folks:
Is there a simple way (or a standard format) that would enable me to
display electron density calculated from a QM program and to compare
it with experimental density?
Thanks.
Bill
William G. Scott
contact info: http://chemistry.ucsc.edu/~wgscott
Did you make your plt file on the intel mac? I've noticed that ones I made on
ppc give that error on my otherwise functional xplot84driver (in the fink
package).
I tried byte-swapping with dd but to no avail.
I guess this is still the cutting edge of 1984 software?
Bill
On Thu, 6 Sep 2007
Hi Bryan:
I think the question is hard to answer because the idea of bad phases is
not particularly well-understood (at least by me).
Good phases give you a nice map.
Weak phases give you a map that is weakly interpretable, but often can
be improved by solvent flattening, NCS averaging, and so
Hi Sam:
You can define a SMILES string, put that in coot, and it will create
coordinates.
Similarly, within phenix, you can do this with elbow.builder and then optimize
is either with built-in forcefields or with an external QM program. It will
give you a reasonable (usually) cif file that
Try
phenix.xtriage
Jobichen Chacko wrote:
Dear All,
Can you please inform me the programs available to find whether a crystal
is twinned and also the data reduction programs for twinned crystals.
Thanks in advance.
Jobi
From: CCP4 bulletin board on
Dear Compatriots:
Is there any chance that ccp4 and coot might allow gmane.org to
archive mail? The jiscmail archives are almost unusable, and ready
access to previous postings helps everyone.
http://news.gmane.org/
Here's an example:
http://news.gmane.org/gmane.comp.shells.zsh.user
On Fri, 24 Aug 2007 14:40:13 -0600
Michel Fodje [EMAIL PROTECTED] wrote:
The mathematics works but doesn't necessarily mean the current
interpretation of the mathematics has any resemblance to what actually
happens in reality.
Sure, it does. Crystallography is traditionally
Sorry for the repost, but I think my question got lost in the earlier
thread.
I've found
$CCP4/x-windows/ipdisp/src/pack_c.c, pack_f.f and so forth, but they
apparently don't build by default, and when I try to, I get
You need to make mosflm-bits in the library for the image-packing stuff
One can only assume that there is 2 schools of thought -
1) water is part of the problem of model building
2) water is the solution to residual reduction.
I'm a bit of an atheist when it comes to all supernatural phenomenon,
whether deities, water molecules floating 4.5 Å in outer space,
ccp4 J. P. Abrahams pack_c.c compression offers. At the
I used this when I was a postdoc but had forgotten about this. It doesn't
build (?) as far as I can tell in the default ccp4 install. I found it,
and a fortran program, in the ipdisp directory, tried make and got this
rather
I've often wondered whether it would be more fair to report R-factors with
and without waters, since waters can be used to beautify statistics. I
also think providing pdb coordinates and Fobs with experimental phases as
supplementary information in a standard format to be supplied
automatically to
No one knows definitively if this was fabricated.
Well, at least one person does.
But I agree, it is important to keep in mind that the proper venue for
determining guilt or innocence in the case of fraud is the court system.
Until fairly recently, the idea of presumed innocence and the
On Thu, 16 Aug 2007, Clemens Vonrhein wrote:
Maybe we should contact Google to let them do it for us ;-)
Better yet, simply download your images to a computer that uses ATT as an
internet service provider. All the information will be automatically
copied and stored by the
Link to the advertisement:
http://chemistry.ucsc.edu/~wgscott/temp/RNAad.pdf
The Department of Molecular, Cell and Developmental Biology at the
University of California, Santa Cruz invites
applications for a tenure-track faculty position. We seek candidates
whose research centers on
Most of us register on the CCP4 bb with our own names. If we say
something stupid, it damages our reputation in front of our peers. A
similar approach can be used for the Wiki. Control access, and limit it
only to people who register with their own name and who are registered to
the ccp4 bb.
This is usually pretty easy with sftools. You need to feed in the cell
and space group interactively, and then it should give you the option to
write the output as mtz.
Ryan Watkins wrote:
Hello Colleagues,
I'm trying to convert a cns cv file to a CCP4 mtz file. I have only
Fobs and SigFs.
It might be worth it to try phaser
Wu, Mousheng wrote:
hi, everyone!
I am struggling with my crystal structure in a very big unit cell. my
protein is about 16KDa. probably there are about 20 molecules in the
asymmetric unit. I tried to use molecular replacement to solve the
structure.
Hi Kendall:
I have this installed:
zsh-% fink list libpng3-shlibs
Information about 7316 packages read in 2 seconds.
i libpng3-shlibs 1:1.2.18-1 Shared libraries for
libpng3 package
so be sure it (the libpng3 package) is updated to that version.
Bill
Kendall Nettles
It just takes ATT and the NSA a bit of time to de-encrypt it. Eventually
you will wind up on the Do not Fly list.
Douglas L. Theobald wrote:
S/MIME signed/encrypted messages started crashing my Mail app long
ago, after one of the first updates to 10.4. I probably sent in a
couple dozen of
It can also ppt out your protein, if it is bound to the DNA.
You could also DNase and RNase the bejesus out of it, and temporarily
unfold the protein to aid in release of the nucleic acids. Then you need
to get rid of these evil enzymes before you put back your nucleic acid of
choice.
Pavan
Dear Fellow Compatriots:
A few pre-coffee random observations from the field offices of Dr. Cranky:
1. No mention of Resonant Scattering in the index of JJ Sakurai Adv.
Quantum Mechanics (1967, 1987 revision), which I used in (blush) 1989,
although the phenomenon is discussed, with many
Fink shouldn't touch anything else. If in doubt,
sudo mv /sw /sw.keep
and you have effectively hidden it.
Did you use my ubuntu coot debian, or os x stand-alone?
I may have made a mistake packaging these. I never tried the fit protein
script (since none of my recent enzymes contained amino
That's cool. It runs in the browser, and you can stick it right into a
Keynote Slide and it runs in that too.
BTW there is something wrong with crick1953.qtz. It says webkit finds it
to be unsafe.
So how do morons like me learn to do this?
Maneesh Yadav wrote:
While we are on the subject of
Try using phenix, which is the successor to CNS.
phenix.refine foo.mtz bar.pdb
and Bob's your uncle.
http://www.phenix-online.org/
jean wrote:
Thank you all for your suggestions. Unfortunately I am still stuck with
the
segmentation fault problem.
The swap partition is mounted fine.
It's guessing time, but it looks like you don't have write permission to
the directory in which ccp4i/refmac is trying to direct the output file
(or maybe the directory no longer exists, etc).
Jhon Thomas wrote:
Hi all
I am using CCP4i, and running refmac for the
refinement
Hi Martyn:
I never use the GUI and it scares me, so I probably should just STFU, but
that sort of thing has never kept me from pontificating. I often get
emails from people asking how to do something with the GUI and they don't
believe me, because I've developed a reputation as something of a
One option is to just use the tools available from the pdb (the nucleic
acid database).
http://ndbserver.rutgers.edu
Another is Anna Marie Pyle's program Amigos.
http://www.csb.yale.edu/people/pyle/software
There are a lot of combinations consistent with A and B form helices, so
this might be
Another option might be to bind Hg to a phosphorothioate GTP (I've never
actually tried it).
Stephen Cusack wrote:
Does anyone know of any heavy metal labelled GTP derivatives
and if so where to get them?
thanks
Stephen
--
Probably.
Many others can be solved by molecular replacement, even with a very crude
starting model.
Recently we solved a 142 nucleotide ribozyme dimer, a novel structure with
no useful NCS symmetry, with just a native data set, A-form helical
fragments generated in coot, and an irritable,
Oddly, I have never had this problem with CCP4's data processing program
ipmosflm.
I reinstalled the same version of linux once in an attempt to cure a disk
arbitration problem and ran into the same issue. You have to get the
vender to send you a new file.
yang li wrote:
Hi,All,
Now I am
You would probably be better off using the CentOS5-supplied python, tck,
tk, blt, and so forth (and if they aren't supplied, then consider a linux
distro that provides these things).
Also, if you compile your own ccp4, you can include the latest patches and
direct it to use whatever versions of
Hi Citizens:
What programs/web sites would you recommend for prediction of enzyme
cleavage sites in a protein sequence?
Many thanks.
Bill Scott
Hey, dude, thanks for writing!
I could swear (so to speak) You sat next to me on an 11 hour airplane
flight not too long ago and tried to strike up a similar conversation. I
apologize for being too engrossed in the latest Dawkins book.
However, we encountered a similar structural riddle in need
Please note some of the on-line servers and database resources are
temporally off-line.
Service should resume in a few days
Jianghai Zhu wrote:
Dear all,
Sorry for the non-CCP4 question. Does anybody know where the RAMPAGE
server is now? The links I have (http://mordred.bioc.cam.ac.uk/
Hi Citizens:
Does anyone use an uninterruptible power supply for their X-ray
generator? Here at UCDIY, the electricity supply is pretty sketchy,
and it is hammering our X-ray generator every time someone forgets to
feed the hamster or grease his wheel. If so, how much does such a
thing
shameless-plugWe just solved a 142 nucleotide asymmetric unit of a novel
ribozyme structure using only A-form RNA helical fragments and phaser. I'm
trying to find some time to write the paper but the basic idea is sketched
out in the supplementary material to the paper that comes out March 16th
Dear Eleanor et al:
mmtbx.xtriage, which is part of the full-blown ccp4 install, and
phenix.xtriage, which I think is basically the same thing, are also
options, and run a variety of twinning and other sanity checks.
mmtbx.xtriage --help tells how to run it, fairly painlessly.
All the best,
I would like to find out which journals (that publish structural work) are
OK with placing structures on hold for the full year permitted by the PDB.
American Rifleman, Cosmopolitan, and Dog World
I use this to get the same maps:
http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcover
http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcoverdiff
I used zsh but I think it should work with current versions of bash.
mac minista wrote:
Dear all,
I have noticed
Hi Ibrahim!
I also found another package NAMOT (from Bill's website, thanks Bill); I
managed to install the package on MacOs PPC using fink.
However, I have a problem to run the program: issuing namot on the
command line starts the program for a second (flashing the Gui of Namot) and
My $0.02 (speaking as someone who has not been happy lately with Apple
tech support and customer care).
This strikes me as a completely unacceptable response. Unless I'm
missing something, if the machine is no longer under warranty then you
are simply asking for a fee-for-service repair,
We also currently have a laptop at Apple for repair. The repair center
charges a flat rate of $329, no matter what the repair entails.
We have a similar deal here, but my understanding is that if the actual
cost of parts exceeds $329, you get charged the difference. Since it was a
hard drive,
Put it in 1 ml syringe, seal the end with your finger (use a piece of
parafilm in between if you need it) and then draw out the plunger to
create negative pressure, and your bubbles will go away. Then let it
gravity-drain or very slowly push the contents into an eppindorf tube.
or
Speed-vac
Hi folks:
Sorry this is a wee bit off topic, but since I am more likely to get
a straight answer from people here, I'm going to ask..
I have 2 identical laptops. We bought both for the lab about 2 years
ago. They are G4 ppc. I bought an extra half gig of memory for each
at the time of
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