Hi Phil:
I've found few, if any advantages. I fear for the future.
I've had problems getting coot to run stereo due to the X11 implementation in
10.7. Apart from that, no major problems with crystallographic software.
Lion greedily uses memory, and any computer I have with less than 4 gig of
On Sep 9, 2011, at 11:09 AM, William Scott wrote:
> (nothing us usual in of itself)
I forgot to mention how delightful the spelling auto-"correction" feature can
be. (It should have read "nothing unusual in and of itself").
That, at least, can be turned off.
On Sep 28, 2011, at 7:15 AM, Artem Evdokimov wrote:
> Are you indeed referring to the oil-filled high voltage transformer core in
> the older model generators?
Yes.
> (Newer ones tend to use solid state voltage multipliers).
That sounds much more sane.
> I recall that there were issues with th
> opinion on the virtues of different OS environments for two days
It might be of interest to look back on the original poster's question, because
all she asked were a few questions about a specific computer (HP Z210 8 GB
with a low end Quadro Nvidia 400 512 MB) running "any Linux", and a sp
Hi Citizens:
Try not to laugh.
I have an embarrassingly simple MAD phasing question:
Why is it that F" in this picture isn't required to be vertical (purely
imaginary)?
http://www.doe-mbi.ucla.edu/~sawaya/tutorials/Phasing/phase.gif
(Similarly in the Harker diagram of the intersection of phas
Thanks for the overwhelming response. I think I probably didn't phrase the
question quite right, but I pieced together an answer to the question I wanted
to ask, which hopefully is right.
On Oct 13, 2010, at 1:14 PM, SHEPARD William wrote:
> It is very simple, the structure factor for the ano
Two ideas:
1. Create a file in your home directory called ~/.curlrc
and in it put the following line:
-P - ftp
2. Use wget
first, install wget with fink
Then put the line
DownloadMethod: wget
into the file
/sw/etc/fink.conf (or /sw64/etc/fink.conf ).
I use wget. It seems to be mor
What other cations are present? Any divalent cations like Mg++ or Ca++?
The Ksp of magnesium phosphate is about 10^-24, so even if you have a very
small amount present, say as a contaminant with citrate or EDTA, it will
crystallize.
On Feb 21, 2011, at 1:22 PM, Yibin Lin wrote:
> Dear all,
Until tcl/tk gets ported, this might tide you over:
http://www.readpixel.com/remotetap/index.html
It is a VNC display optimized for iPod/iPhone/iPad use.
-- Bill
-
On Feb 25, 2011, at 11:54 AM, Jacob Keller wrote:
> Hello All,
>
> is there a ccp4 app for iphones yet
Yeah, I know what you mean. That Zalman 3D LCD monitor put me back almost
$300, and the mac mini I hooked it to, nearly another $600. My SGIs only cost
$12K each in 1998.
On Jun 9, 2011, at 9:43 AM, Mayer, Mark (NIH/NICHD) [E] wrote:
> The sad thing is, although Macs are great crystallograph
Yeah, it was a totally delightful interaction. So much for the Ubuntu spread
the love of humanity theme.
They have successfully migrated from figure 3 to figure 2:
http://bandcamp.tv/linux-demotivators/
As for BLT, my sense (being the unfortunate maintainer for it on fink) is that
it is dead
On Aug 17, 2011, at 3:25 PM, Harry wrote:
> Hi Bill
>
> I don't think this includes BLT, does it?
No. That was what I was trying to say (apparently not very well, sorry!):
>
> On 17 Aug 2011, at 22:33, William Scott wrote:
>
>> if CCP4 could free itself of
Dear Colleagues:
If you know of anyone who might be interested in an assistant professor
position, would you please be kind enough to bring the following advertisement
to their attention?
http://www.nature.com/naturejobs/science/jobs/154054-Assistant-Professor
Many thanks.
Bill Scott
Hi Allen:
I have a smaller Zalman monitor, but I defined buttons to set the screen size
(and toggle stereo) like this:
coot_toolbar_button("FullScreen", "set_graphics_window_size(1680,999)",
"gtk-network")
Making the vertical dimension an odd number seems to be required to ensure that
stereo
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 it
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
d bad practise from the client service. Is this
> directly Apple support or some Apple dealer?
>
> Serge.
>
>
> Le 9 févr. 07 à 00:04, William Scott a écrit :
>
>> Hi folks:
>>
>> Sorry this is a wee bit off topic, but since I am more likely to
>> get
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,
That'
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,
That explains my one counterexample -- the LCD panel needing replacement.
Anyway, they just made $658 on two hard drives, so they should be more
gleeful.
That, and they just made $350 on a memory upgrade that I would have had
for free had I bought a Macbook 4 days later.
But I got them back:
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
re
Oh, I should add that I wrote a shell script to try to work around the
NAMOT modelling bug. It relies on having cns in your $PATH:
http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/fix_namot
Please forgive the profanity in the comments.
Bill
On Sat, 10 Feb 2007, Ibrahim M. Moust
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 notice
> 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
You should try the cci_apps from phenix (specifically phenix.refine)
instead of CNS.
http://www.phenix-online.org/download/cci_apps/
You can use mtz files from ccp4 and you don't have to goof around with
your pdb file. It is also much easier to run.
Jiamu Du wrote:
> Thank you all.
> It seems t
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,
B
Hi Richard:
I just did this using fink's python and other dependencies, but I had to
install pygtkglext-1.0.1 myself.
Now I have to figure out how to test it to see if it works...
If it does, I can make fink install scripts for these packages and put
them into fink.
Bill
Richard Gillilan wro
Dear Jacob, Richard et al:
Thanks. That seems to work.
So, to summarize briefly, using fink on os x, I installed the following:
fink install pygtk2-py25-dev pygtk2-gtk-py25-dev pygtk2-py25 opengl-py25
gtkglext1
(I changed the dependency in
/sw/fink/dists/unstable/main/finkinfo/libs/opengl-py
We 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
in Science.
I
Feed it common substructures and see what happens...
On Mon, 5 Mar 2007, Nat Echols wrote:
> I'm not sure what "in desperation" means. You're trying to solve a
> structure, so all options are open, right? They don't have to be elegant,
> it just has to work. :)
Yes, but
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 c
"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
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 o
Hi Citizens:
What programs/web sites would you recommend for prediction of enzyme
cleavage sites in a protein sequence?
Many thanks.
Bill Scott
Thanks, everyone!
This was a very popular answer: http://us.expasy.org/tools/
peptidecutter/
also
http://www.cbs.dtu.dk/services/NetCorona/
http://www.cbs.dtu.dk/services/NetPicoRNA/
and
If you are interested in the physiological, known cleavage sites, you
may also try one
This is a hard thing to do.
Eric Westhof is one of the masters:
http://www-ibmc.u-strasbg.fr/upr9002/westhof/
[EMAIL PROTECTED] wrote:
> HI ccp4ers, I have to model the structure of a 400nt RNA and I was
> wondering if there was free programs out there, similar to Modeller or
> other 3D predic
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 th
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 a
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, cantan
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
>
> --
>
> ***
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 w
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 Ma
I have a partially cleaved RNA, so I would like to try refining with
two different dinucleotide segments embedded in the model, one of
which has a broken backbone and 2',3'-cyclic phosphate, and the other
with a standard phosphodiester backbone. This should be analogous to
having two confor
Hi Yang Li:
I don't know anything about php, but I think I recognize the problem.
Typically, when you execute a unix command from a scripting language, it's
like doing it in a subshell; the command executes and the subshell exits.
So what you need to do is to figure out how to execute all of your
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
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 fin
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
Hi Junhua:
These are ccp4 bb questions, so don't apologize (or we all will start
having to do so).
All of my room-temperature shipping experiences are pre 9-11-2001, and
involve carrying stuff with me on airplanes, which is now an impossibility
(unless you possess a Saudi diplomatic pouch, but in
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 ac
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 exercise
I think you can do what you want using elbow.builder in phenix with a
smiles string.
You can use something like this to make the cofactor:
http://www.molinspiration.com/cgi-bin/properties
Then use elbow.builder to make the pdb and cif files, and do your
refinements in phenix.
It may be possibl
Try elbow.builder and phenix.refine in the phenix package. It will make
your life much easier.
Jae Hyun wrote:
> Dear all,
>
> I have a decavanadate anion in my structure, and want to refine it. For
> that, I got parameter and topology files from HIC-Up website, and used in
> CNS. But, it gave t
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 wrote
If you have phenix
% cctbx.form_factor_query element=Br wavelength=13474.00 unit=ev
Information from Sasaki table about Br (Z = 35) at 13474.0 ev
fp: -9.48706
fdp: 1.36565
I don't know enough about chooch or gsl to answer your question about what
is going wrong.
Bill
Truc Kim wrote:
> Hello
It just takes AT&T 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
I would happily contribute to this, and migrate anything relevant from my
own stuff. I think this could be a very valuable resource. The PyMOL
wiki is a good example of what could be done. The main requirement for
success I think is having a few dedicated users who want to see it
succeed. We shou
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 wrote:
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 SigF
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 fundam
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 AT&T as an
internet service provider. All the information will be automatically
copied and stored by the NSA
he analogy is flawed, and dangerously so.
We are qualified to judge science, but that does not endow us with
the ability to establish criminal intent, which is paramount in a
fraud case.
Bill
Regards,
Ed.
William Scott wrote:
No one knows definitively if this was fabricated.
Wel
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
> 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,
too
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 crypt
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
Thanks, Graeme.
Is there any advantage to bzip2-ing the individual images rather than making
one bzip2-ed tarball with tar cvfj?
Bill
On Thu, 23 Aug 2007 20:12:26 +0100
"Winter, G (Graeme)" <[EMAIL PROTECTED]> wrote:
Hi Bill,
> It seems it would be good to have available if w
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
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
T
gfortran -o platon platon.f xdrvr.c -lX11 -L/usr/X11R6/lib does the trick.
export NETEXE="open"
lets you use your default web browser.
That's one fugly interface.
Miller, Mitchell D. wrote:
> What about Ton Spek's Platon / System-S package?
> http://www.cryst.chem.uu.nl/platon/pl00.html
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
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 you
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 15
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
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
Try using
./scalepack2mtz.exam
or
$CCP4/examples/unix/runnable/scalepack2mtz.exam
On Sun, 16 Sep 2007 03:13:08 +
U Sam <[EMAIL PROTECTED]> wrote:
I used to run "scalepack2mtz" succefully. now it is not working. Can
anybody suggest the way to short it out.
%chmod +x scalepa
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.
Try this:
CCP4BB-unsubscribe-request @ JISCMAIL.AC.UK
(get rid of the spaces first)
Aida Baharuddin wrote:
> Dear sir,
>
> I would like to stop from receiving the ccp4i mailing list from
> my [EMAIL PROTECTED] email account.
> Thank you.
>
> Sincerely yours,
> Aida Baharuddin
> Institute of
If R-sleep is to be the "real" validation R-factor, why not just sequester
each of R-sleep and the current R-free, each as a randomly-chosen (but
mutually exclusive) set of reflections, and then proceed as normally with
the other (eg) 80% of the data until the very end of the refinement, using
the
Dear Tiancen Hu:
Two things you need to do:
1. Try refining with cis-proline and see if it fits better.
2. Construct Fo-Fc and Fc-Fo maps (coot makes this very easy). See what they
are telling you.
Best of luck,
Bill Scott
On Thu, 18 Oct 2007 09:35:44 +0800
HTC <[EMAIL PROTECTED]> wrote
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 QtyE
Several people have emailed me about X11 in OS X 10.5. Because I pre-
ordered it, I haven't received it yet, so I have only gotten to enjoy
the migraines vicariously. Hence, i can't really help.
Meanwhile, this looks informative:
http://lists.apple.com/archives/X11-users/2007/Oct/msg00065.h
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 stud
Hi folks:
The build seems to fail almost immediately (using python 2.5.1
provided by the system).
Has anyone had any luck?
Everything else apart from harvest seems to build fine.
Thanks.
Bill Scott
PS: The latest cctbx from the cctbx download site builds flawlessly.
Is there a way to
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
On Fri, 7 Dec 2007 13:22:03 -0500
[EMAIL PROTECTED] wrote:
CCP4 bulletin board 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 very famous
so
A slight variation on this theme is to use 0.5% toluidine blue (in water) as a
stain. A 2 to 5 minute soak followed by destaining in hot water for a few
minutes is all that is required.
On Tue, 11 Dec 2007 12:14:27 -0600
Paul Paukstelis <[EMAIL PROTECTED]> wrote:
Rongjin,
This
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
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
Yes, Virginia, there is a Santa Coot:
http://tinyurl.com/24mchk
This one will work on intel, both 10.4 and 10.5. If there are any problems let
me know.
PPC version to follow in the next few days. It is designed to be stand-alone,
and to inflexibly
install into /usr/local/coot
I used a gtk+2
In general I think they should be ok. Some componenents may slowly oxidize or
otherwise deteriorate, but as long as there is nothing growing in the
solutions, you should be ok. If you experience irreproducibility when you try
to follow up on a successful condition, it is good to keep in mind th
On Fri, 28 Dec 2007 15:55:39 +
Brenda Patterson <[EMAIL PROTECTED]> wrote:
Hello,
I am fairly new to this lark
No problem. With a name like Patterson, your future is guaranteed (unless of
course you see everything in the world with intensity but no phase).
I have a d
Also, the PDB now uses prime (') instead of asterisk (*) for the ribose
numberings, and uses OP1 instead of O1P, and so forth.
Do the new refmac dictionaries have that (I haven't been able to get it to
work in the context of coot).
Garib Murshudov wrote:
> If you take new dictionary with new refm
Hi Jessica:
Thanks for posting these gastroeneterology and dermatology adverts to the CCP4
bulletin board. Many of in macromolecular X-ray crystallography are
contemplating just such a career change, and although the retraining procedure
may take 7 to 10 years, I am sure you would be willing t
Just to add to that, on OS X, if you install the apbs and pymol packages via
fink, everything will be set up for you. I think this is also true of at least
Ubuntu and other debian linux varieties. As far as I am aware, the plugin is
not compatible with the non-X-windows PyMOL on OS X.
On Tue,
Hi Yang Li:
Macromolecular crystal refinement programs use ideal bond lengths and angles.
The simplest ones just assume any carbon-carbon single bond (C-C) is the
same as any other, and use one average value, and any carbon-carbon double
bond (C=C) is the same as any other, and use another averag
Dear Yang Li:
Happy New Year to you, too, (ahead of Feb. 7th).
You certainly owe us no apology; the reverse may not be true.
Your question is an important one, as is what you have written below.
I'm not certain I have a completely satisfactory answer.
The reason is that ideal bond lengths may
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