Hi folks:
Is there a simple way to attach partially occupied solvent sites with a
specific conformer when dealing with multiple conformations of side chains or
nucleotides, for purposes of PDB deposition? (In this case the resolution is
quite high.)
Thanks.
Bill
William G. Scott
It looks like it should be doing the right thing, i.e.,
zsh-% otool -L qtrview
qtrview:
@executable_path/../Frameworks/QtWebKit.framework/Versions/4/QtWebKit
(compatibility version 4.9.0, current version 4.9.3)
Presumably then it was running Linux?
On Nov 20, 2012, at 7:39 AM, George M. Sheldrick
gshe...@shelx.uni-ac.gwdg.de wrote:
I have never understood why Macs are so popular, although in this part
of the world they are appreciably more expensive. My vintage 2005 Dell
laptop does not have the
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
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 those
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.
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 this dependency...
…then it could make
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
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?
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,
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
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
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
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 is
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
Two very low-brow suggestions that might help:
1. Do a round of idealization in Refmac, to tighten up the geometry as
much as possible. Then return to your current approach.
2. Try using phenix.refine (with the same mtz, test reflections, latest
PDB, etc). The difference can sometimes be
I always Look on the Bright Side of Life, so I take a certain solace in
the fact that while this may be true, most postdoc positions pay about as
well as my job, if not better.
On Wed, September 30, 2009 5:52 pm, Artem Evdokimov wrote:
I personally am not peeved at all, but I am getting
No, just California Dollars, which I think are on a par with those printed
in Zimbabwe prior to April 12th.
On Wed, September 30, 2009 8:27 pm, aaleshin wrote:
Are the salaries compared in orders of magnitude?
Or you mean other pays?
On Sep 30, 2009, at 8:30 PM, William Scott wrote:
I
Is it the gui or mosflm itself that crashes? The new gui is dependent
upon a number of external dependencies, so you are at the mercy of the
stability of those. The old gui still works fine, at least last time I
checked.
On Thu, July 30, 2009 4:40 pm, Marius Schmidt wrote:
We have a little
When I do this with /bin/zsh, it does the right thing. The source command
in the bltwish shell gives me ccp4i.
When I run the commands interactively in bash or sh (which is bash on os
x), the command
exec ${CCP4I_TCLTK}/bltwish $0 -- ${1+$@}
terminates the shell session instead of turning it
On Sun, July 26, 2009 5:38 pm, Edward A. Berry wrote:
William Scott wrote:
..
So I think your process is getting killed before you look at the cat in
the box. If it is a question of ${CCP4I_TCLTK} not getting assigned,
the
error you should see looks like this:
bash: /bltwish: No such file
On Sun, July 26, 2009 6:07 pm, William Scott wrote:
On Sun, July 26, 2009 5:38 pm, Edward A. Berry wrote:
William Scott wrote:
..
So I think your process is getting killed before you look at the cat in
the box. If it is a question of ${CCP4I_TCLTK} not getting assigned,
the
error you
Dear protein.chemist:
Try elbow.builder or phenix.elbow or whatever it is currently called.
It will optimize the geometry.
Good.luck
Bill.Scott
On Tue, July 21, 2009 1:23 pm, protein.chemist protein.chemist wrote:
Dear All,
What is the best way to find the coordinates of a ligand.
I
% fink describe ccp4
Information about 9170 packages read in 3 seconds.
snip
Invoke optional ccp4i gui for the first run using sudo ccp4i
on 10.4, or sudo /bin/zsh followed by source /sw/bin/init.sh ;ccp4i
on 10.5 to permit global configuration. Thereafter, you can invoke
Hi folks:
A colleague of mine here is doing small angle X-ray scattering at SSRL
and finding his samples are suffering significant radiation damage.
He asked me for advice as to what potential radical scavengers might
be useful. I told him to take 10 mg of ascorbic acid and to call me in
The answer to this was to ensure that the file
/etc/hosts
is present and contains the line
127.0.0.1 localhost
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On May 16, 2009, at 6:38 AM, Sebastiano Pasqualato wrote:
hi there,
I'm using ccp4 installed via fink
I just did the same today.
Those that are missing from the 4-03 patch (at least the src version)
included:
scala.f
version.fh
refmac5.tcl
scalepack2mtz.com
dtrek2mtz.com
pname2.com
import_scaled.script
also there was a tcl++ fix
William G. Scott
Contact info:
Hi Paula:
Here is more info:
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/CCP4-6.1.0_on_Ubuntu_Ibex
(There is no reason why you would have to do step 1.)
Sorry, but I couldn't figure out how to append the link using my iPod
while undergoing mind-numbing boredom in an interminable
On Jan 6, 2009, at 7:10 PM, William Scott wrote:
(There is no reason why you would have to do step 1.)
Sorry, that should have been no reason ... to do step THREE.
Hi Citizens:
When compiling ccp4 on OS X v. 10.4.11, I get the following failure
for libmmmdb.dylib:
It works fine on 10.5.5, and mmdb v. 1.19 itself (used for coot)
compiles fine under the same conditions.
gcc -dynamiclib -flat_namespace -undefined suppress -fPIC -fno-common -
Does ccp4i work?
On Thu, December 11, 2008 8:06 pm, Jayashankar wrote:
since its a same coot problem,
i have one more,
i am using mac 10.5 leopord osx the thing is, i dont get any pop upped
table even after i do a translate and do a real space refinement .
is it a bug or is it a
Yo Thierry:
The periplasmic domain of the aspartate receptor, in the absence of
ligand, 1lih, is a dimer, but crystallizes as a monomer in the sense
that there is one monomer per asymmetric unit. There is a disulphide
bond between two Cys36 that maintains it as a dimer (and indeed
Hi Anna:
I think the main thing to emphasize in summary is that any of the
options various people have suggested would be far more than adequate
to do refinement or model building with coot. In my limited personal
experience, unless you have something as big as the ribosome, you
won't
The main differences aren't cosmetic, but rather free accessibility of
updates and distributions, as well as attitude aka philosophy.
Advantages of Ubuntu include frequent OS updates, debian-based package
management system (which admittedly is a matter of taste, but it is
one of the
Friends,
I recently followed William Scott page and followed his advice to
install
fink and crystallographic softwares...
But out of my curiosity i once tried to install arpwarp as per the
instructions and it was done successfully,
no problem,
but whenever i open a new terminal window,i see
Hi Folks:
I just found out that in a couple of weeks I am going to be teaching a
graduate student-level enzymology course.
Can anyone recommend a good text, and possibly good websites authored
by people who are predisposed to consider plagiarism the highest form
of complement?
Many
Glad it worked.
I should have written
sudo /bin/bash
or
sudo /bin/zsh
or
sudo /bin/tcsh
followed by sourcing the appropriate startup script.
However, if I run the tcsh command, I get this error:
limit: stacksize: Can't remove limit (Invalid argument)
oddly, this does not happen with a
coot
On Aug 12, 2008, at 3:35 PM, Raja Dey wrote:
Dear Friends,
Does anyone can refer a reliable program for
building 3D model of a double stranded straight DNA from sequence?
Thanking you in advance...
Raja
Wikipedia claims Hasselbach is a misspelling:
http://en.wikipedia.org/wiki/Henderson-Hasselbalch_equation
Since Wikipedia has now replaced the social consensus as the final
arbiter of truth ...
On Aug 7, 2008, at 3:22 PM, Juergen Bosch wrote:
Just on a side note, can someone clarify why
Hill Road
Menlo Park, CA 945025-7015
Phone: 650 926 2992
Fax: 650 926 3292
On Jul 31, 2008, at 4:09 PM, William Scott wrote:
Hi folks:
I am hoping there is a simple answer I have overlooked to the
following question. I have a pdb file in it that has multiple
residues that have the same
Refmac should be able to do this without moving stuff too much. CNS
(no simulated annealing) also can do this kind of thing. If it
becomes problematic, you can restrain the backbone. You can also do
this via coot (which uses refmac I am pretty sure).
William G. Scott
Contact info:
Hi Patrick:
I'm afraid all the insidious stupidness originates from moi. Anyway,
the machine hosting this thing has a roached power supply, thanks to
the fact that the University electrical supply resembles that produced
by, in terms of its stability and reliability, an underfed gerbil-
My favorite is the elbow builder in phenix. You give it a smiles
string and it will build (and optionally, optimize either classically
or quantum-mechanically) your small molecule structure.
http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
Date: Mon, 14 Jul 2008 15:22:52 -0700 (PDT)
From: Martin.Laurberg [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: DNA/RNA base stacking restraint add-on to CNS avaliable.
Dear all,
A DNA/RNA base stacking restraint add-on to CNS version 1.21 is
avaliable
for
Hi Citizens:
I realize this is one of those warranty-violating questions, but is
there a simple way to down-weight figures of merit, or the equivalent
in terms of Hendrickson-Lattman coefficients?
I'm trying to generalize and automate a procedure for solving RNA
structures without
Hi Citizens:
I've taken the liberty of summarizing/anonymizing/interpreting a bit
with the varied and colo[u]rful responses. They fell into three
general categories. Thanks to all who responded and offered sage
advice...
1. The unanimous consensus was that headhunters aren't useful for
Is this true for native aqua gui programs, or just the X11 ones?
On Thu, June 26, 2008 1:50 pm, eortlund wrote:
Hi Everyone,
I am writing everyone just to remind all those who are thinking of
upgrading to 10.5 that currently quad-buffered stereo will not work
for coot, pymol etc... since
Check the purity of the DNA in solution:
A(260 nm)/A(280) = 1.8 for fully deprotected DNA, and you should see a
nice clean simple curve with a peak very close to 260 nm.
Check it on a denaturing gel. Smearing indicates incomplete
deprotection. This is usually the cause of solubility
of necessary unix
knowledge - I will try to circulate it among my colleagues.
Thanks again and all the best.
Eike
On Sat, 2008-05-17 at 08:13 -0700, William Scott wrote:
Hi Eric:
You shouldn't have to source or do anything with the def files.
There seems to be some problems with the ccp4.setup
execute: No such file or directory
bash-3.2#
Raja
- Original Message -
From: William Scott [EMAIL PROTECTED]
Date: Friday, May 16, 2008 10:44 am
Subject: Re: No permission to CCP4I_TOP dir
To: Raja Dey [EMAIL PROTECTED]
The easiest thing is probably to initialize a shell with
sudo
On Fri, May 16, 2008 1:06 pm, Eike Schulz wrote:
Hello everybody,
setenv CCP4_MASTER /usr/local/software/ccp4
setenv CCP4 $CCP4_MASTER/ccp4-6.0.2
For bash, zsh, etc, you need to start with
export
Can someone delete the old address from the ccp4bb? I've tried emailing
but to no avail.
On Fri, May 16, 2008 2:28 pm, [EMAIL PROTECTED] wrote:
Hello,
Your message has been automatically forwarded to my new address which is:
sanjukta.aich at usask.ca (replace at with the @ symbol)
At
the error persists when I try to run refmac from the ccp4i
GUI - it complains not to be able to extract data from an .mtz file.
Did I miss anything important?
Kind regards
Eike
On Fri, 2008-05-16 at 14:37 -0700, William Scott wrote:
On Fri, May 16, 2008 1:06 pm, Eike Schulz wrote:
Hello
,
Modulated Crystals, Crystal Perfection, X-ray Topography,
Interests: ThimbleTack, skateboarding, RAGBRAI, and rollerskating
**
William Scott [EMAIL PROTECTED]
Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK
05/15/2008 12:09
On May 15, 2008, at 12:40 PM, Ed Pozharski wrote:
I was just trying to
protect poor creatures, after all they [hydrogens] only got one
electron to hold on
to (:-)
Ed.
A less radical view (pun intended) suggests two. ;)
On May 14, 2008, at 12:28 PM, Mark Del Campo wrote:
At what refinement resolution or resolution ranges would you call a
structure high resolution vs.
low resolution? I realize that this may boil down to semantics
(e.g. some may classify structures as
medium resolution), but I wanted to get
mosflm is an incredibly great program, not to mention free as in beer...
On May 7, 2008, at 3:07 PM, Chris Waddling wrote:
my frustration at HKL2000 not working
On ubuntu, you can get this in the libg2c package. I agree with James
Stroud. Fire the sysadmin and divvy the salary up amongst those who
really need it. Time to raise the black flag and start slitting throats.
On May 5, 2008, at 12:32 PM, Chris Waddling wrote:
Basically, the newest
Hi:
If anyone needs EDEN (Abraham and Hanna Szöke's density modification
program), the original edencrystallography.org site is gone. As a
quick remedy, I've created (with their permission) a google-code page
here:
http://code.google.com/p/edencrystallography/
The code is GPL-ed, fwiw.
You need to run
source /sw/bin/init.sh
if you use bash or zsh
or
source /sw/bin/init.csh
if you use tcsh.
this will automatically set up the environment variables and then it
will do what you want it to (which is to set up the ccp4 environment
according to whichever shell you might be
Could one or both of you try this with the pre-compiled intel version
that comes from the CNS website? If it works on that, it might be
something introduced in the compiling process for the osx-optimized
version made by David.
Thanks.
Bill
On Apr 23, 2008, at 7:26 AM, Sean Johnson
I think this version of coot tries to set the DISPLAY variable and that
will sabotage launching it in 10.5.2.
May I suggest trying this:
http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Coot-0.5-pre-1-968_for_Intel_10.5_only
On Tue, April 22, 2008 7:53 pm, zhangtao wrote:
Dear All: I
Dear Chris et al,
My guess is something needs ruby built as a build-time dependency, but
coot doesn't require it. In any case, I've got the latest version of
ruby built and anyone who needs it can download it from one of my
servers as described on this page:
http://tinyurl.com/h2lzq
I have
i librsvg22.9.5-11SAX-based render library for
SVG files
i librsvg2-gtk2.9.5-11Enable GTK to use SVG data
i librsvg2-shlibs 2.9.5-11SAX-based render library for
SVG files
Do you have all of those installed? If not, the package
Dear Buz:
Not sure why you have to install ruby. But if you describe the
problem, I might be able to help.
Meanwhile you can use what I pre-compiled:
http://tinyurl.com/h2lzq
This will speed things up by a few orders of magnitude.
Bill
On Apr 17, 2008, at 10:07 AM, Buz Barstow wrote:
This is a gtk+2 phenomenon. Same happens with gimp-2.
On Apr 14, 2008, at 8:36 AM, Andreas Förster wrote:
Hey Klaus,
after I installed coot 0.5 via fink for the first time, I
encountered stalling during startup as well. However, this resolved
itself within a minute. Startup resumed, and
Does this include the customary grieving period?
On Apr 14, 2008, at 2:10 PM, JOE CRYSTAL wrote:
Hi,
Does anyone have information about how long it takes to set up a 96-
well
tray for the crystallization robots available? Besides cost per
tray and
maintenance cost, another important
On Apr 11, 2008, at 3:04 AM, Jim Naismith wrote:
However, does anyone know how to convince editors and non-
xtallographers that 3.45A is valid?
You have to introduce them to the resolution vs. biological interest
trade-off matrix, and how it ought to be diagonaliz(s)ed.
Bill
As opposed to putting McDonald's food into their stomachs?
On Apr 4, 2008, at 9:33 AM, Ezra Peisach wrote:
I saw that toy - Personally, I do not like the idea of encouraging
children to aim a light (low powered led) directly at one's eye...
Ezra
P Hubbard wrote:
I took my 5 year old niece
Sorry, I should have been less cryptic:
On Apr 2, 2008, at 2:13 PM, Jacob Keller wrote:
Forgive the naive questions:
To what do the terms hard and soft refer here?
In inorganic chemistry, hard refers to bonding where the Coulomb
potential dominates, and soft where orbital terms dominate.
Hi Chu-Young:
I would recommend either a PC running Ubuntu Linux (my personal
favorite distribution -- they are all more or less the same thing) or
else Apple Mac OS X, depending upon your other needs, budget, etc.
I've got a lot of propaganda for OS X here: http://xanana.ucsc.edu/xtal
HI Simon:
The X11 guy at Apple is very interested in trying to help. If you
could join the Apple X11 mailing list and document this as carefully
as possible, it would be a real benefit. He's out of town for a few
days but is interested in dealing with this as soon as he returns.
There
In both cases, you have to make sure you are setting up the
environment appropriately for ccp4, unique to the unix shell you are
using.
In the case of the ccp4 package you compile with the aid of the fink
script, at the start of a shell session, you, or your dot file, needs
to issue
That is exactly how it is supposed to work with 10.5. No need to use
an xterm, and it sets the DISPLAY variable automatically. I assume
you have write-permissions in the directory it is trying to make
the .CCP4 directory?
On Mar 25, 2008, at 9:32 AM, Kurt Padilla wrote:
Sue,
If I move my .CCP4 directory out of the way and start ccp4i, it makes
a new one:
zsh-% ccp4i
22:14:16 Creating a home directory for CCP4 at /Users/wgscott/.CCP4
22:14:16 Creating CCP4i shadow area at /Users/wgscott/.CCP4/CCP4I_TOP
22:14:16 Creating shadow subdirectory
Sounds great.
You can jailbreak an iPhone/iPod touch and install a whole BSD
subsystem on it. So printing should be possible at some point...
This of course also suggests that iPod touch is a valid research
expense ...
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
Install zsh.
Then invoke it.
Then issue:
autoload -U zmv
alias mmv='noglob zmv -W'
Then you are ready for some fun:
mmv 1105\ A*.osc A*.osc
Then if you decide to make your default shell zsh, you can put that in
your .zshrc file and all you have to remember in the future is mmv
Raja Dey
Syncing directories with unison (use the same version of the program
on all computers) or rsync can help. Lately I've been using svn,
which is I think the best way to deal with this. Setting up a server
on linux is probably easiest. You can do this with any type of file,
by the way, it
NFS is alive and well (even on OS X 10.5), but having separate copies on
different computers and/or an svn server has the additional merits of
being a backup system and one you can use with computers that don't have
static IPs.
David J. Schuller wrote:
Back in the good old days, we were
able
phenix.refine also produces an mtz file by default, and that can be
auto-opened with coot, along with the coordinates.
On Mar 4, 2008, at 7:27 AM, yang li wrote:
Since the map from phenix couldnot be opened by coot directly--or I
donnot know how to--I used refmac to get a mtz map file.
Here is an example:
http://news.gmane.org/gmane.editors.textmate.general
Charles Ballard wrote:
Dear Mark
gmane has an obscure e-mail address function. We would use that.
Charles
On 26 Feb 2008, at 16:58, Mark J. van Raaij wrote:
Dear Charles,
it would perhaps be good to make sure
I agree!
I suggested this about a year ago too. All they need is permission from
ccp4. The current system of archives is hard to use (and for mentally
deficient people like me, impossible).
Bill
Kay Diederichs wrote:
Dear all,
I love CCP4BB, but I hate going on holidays because when I come
Hi Citizenry:
This is worth reading:
http://www.nature.com/nature/journal/v451/n7181/full/451887d.html
Without knowingly doing so, I've short-cited coot and probably other
crystallographic software in this way. I hope one
day to redeem myself.
Bill
Then I used CNS to do annealing, then use refmac to do rigid body
refinement.
That can be why the R-factors went up. Rigid-body subsequent to simulated
annealing will (if anything) undo the refinement ...
Anastassis Perrakis wrote:
Just to point out that I have missed the NCS presence; Lijun
Yes, thanks, that does it for the Terminal.app, but not for any of the
rest. It would be great to have such a feature globally.
mb1pja wrote:
Dear Bill
William Scott wrote
Aqua simply behaves by slightly different rules. Although I am a
slobbering OS X fan, this lack of customizability
I want to thank the very many people who responded to my inquiry. I'm
overwhelmed and really appreciative. I've still got to read through
it all, but a clear (near-unanimous) consensus is emerging.
All the best, and again thanks very much for the help. I really
appreciate it.
Bill
Hi folks:
A colleague has an antibody they would like a crystal structure of,
bound to a peptide. Currently it is a whole antibody. From my
superficial search of the literature, it looks like everyone uses Fab
fragments in such cases. Is this true, and is it stupid to try the
whole
I had learned that Rsym compared symmetry-related reflections within an
image or film (in the context of a rotation exposure), and Rmerge compared
symmetry-related reflections on different images or films with one
another.
Is that wrong?
Bill
Manfred S. Weiss wrote:
Dear Mohd and all others,
This looks promising:
http://www.ccp4.ac.uk/newsletters/newsletter36/13_perl.html
Ezra Peisach wrote:
You may wish to look at the occp4-pm perl package by E. Courcelle and
J.P. Samama (formerly available from ftp://ftp.ipbs.fr/pub/occp4 - but
this no longer works...) I no longer have a copy
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
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
molecules might tend to distort a bond by a couple
hundredths of an Ångstrom.
William Scott wrote:
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
Dear Jinjin:
Malic acid, a diprotic acid, has a pKa of about 3.4 for the first dissociation
and a second at about 5.1. So it is best as a buffer within a pH range of about
2.4 to 6.1, and it at its best around best in the range of 3.4 to 5.1. If the
pH of your solution is indeed 7, then it is
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 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
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
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
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
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