If I understand correctly, the only difference between mFo and Fo
map will be weighting in different resolution shells according to
figure-of-merit. While this will presumably downweigh the less reliable
resolution shells, it will hardly make up for the heavy model bias. The
reason you see the
On Thu, 2010-08-26 at 11:35 -0400, Roger Rowlett wrote:
We routinely polish protein preps on Q-sepharose (Mono-Q should be
even better) with at least 10 CV gradients over a narrower range of
NaCl concentrations, maybe 0-0.5 M or even smaller.
Just wanted to add that in my experience the
I don't see what George's attempt to point out that pure-phenix
questions should be asked in phenix bb (and the point itself may be
subject to different opinions) has to do with renaming Moscow streets
and subway stations (unless you thought that the proposition to rename
ccp4bb is serious).
There are many ways to test if the two test sets are identical. For
example (using CCP4i):
Go to Reflection Data Utilities - SF file analysis
and then perform data correlation between your two FreeFlag columns. If
they are identical, the resulting R-factor should be 0 and correlation
Take a look at MAMA from Uppsala Software Factory
http://xray.bmc.uu.se/usf/mama_man.html
It can generate the mask from the PDB file. This will, however, leave
internal cavities belonging to solvent. If you don't want that, the
following MAMA script will fix it giving you the mask of the
PEG solutions contain fragments of all sizes - it is the average size
(however defined by the manufacturer) that is 1000. So technically it
is incorrect to claim that you have PEG1000 molecules bound to your
protein, it is most likely much shorter fragments that can penetrate the
channels in
On Thu, 2010-08-12 at 08:57 +, MARTYN SYMMONS wrote:
Zero occupancy is generally a deprecated way of dealing with missing
density as it is confusing for less experienced user of the
coordinates. I think zero occupancy can be useful during refinement as
the atoms help fill space (or for
Nevertheless, what do you have in mother liquor/protein buffer?
On Thu, 2010-08-12 at 17:24 +0200, wrote:
Dear All,
I am refining structure of protein at 1.7A. It is enzyme with 3
histidine residues in the active site, which are chelating metal (at
the moment I built in calcium but I do
, 1294.
29, 1338.
30, 1382.
31, 1426.
32, 1470.
33, 1514.
34, 1558.
35, 1602.
36, 1646.
37, 1690.
38, 1734.
39, 1778.
40, 1822.
41, 1866.
42, 1910.
43, 1954.
44, 1998.
45, 2042.
46, 2086.
47, 2130.
--- On Thu, 12/8/10, Ed Pozharski epozh
The problem is the unrestrained nature of the grouped b-factor
refinement itself. Read this thread
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg14133.html
In a nutshell, just stick with (properly wighted) individual B-factors.
On Fri, 2010-07-16 at 10:57 -0400, hongjunyu wrote:
Hi，
I
Pure translation NCS?
On Fri, 2010-07-16 at 20:04 +, Marie Lacroix wrote:
Hi everybody,
I just calculated a self rotation function from the data used for
molecular replacement (what by the way did not worked) and saw no peak
at all. Does this not mean that there is only one molecule in
But of course. This is what mixed refinement is for - the easiest was
to get it to work is probably somehow generating anisou records for all
the atoms and then doing something like egrep -v 'ANISOU|HOH' on the
pdb file. Mixed refinement will then refine only the atoms with
pre-existing anisou
Given your unit cell parameters + high Rsym I'd say you have an indexing
problem. If you try P2, what happens? I suspect that you might have
something as simple as incorrect beam center position and while
integration works, scaling fails (the only way you are getting away with
it is by choosing
I just compiled the latest coot (0.6.2-pre-1.3011) on 64-bit Lucid (it
appears that the gtkglext issue is gone). I don't know what you mean by
so many compiling issues. Are you using autobuilder script?
On Sun, 2010-07-11 at 12:28 -0700, Michael Hothorn wrote:
Hi,
can someone point me to a
Several recent posts with decently sized attachments (now in cross eyed
stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky
for me, I can just recycle the old messages:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html
Cheers from the self-appointed thought
netiquette.
Tim
P.S.: I wonder how much traffic this email will induce ;-)
On Fri, Jul 02, 2010 at 09:33:01AM -0400, Ed Pozharski wrote:
Several recent posts with decently sized attachments (now in cross eyed
stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky
for me, I
When refmac encounters new ligand, the default behavior is to report it
in the log file and exit. But it also apparently creates the output
pdb-file (with coordinates the same as the input file). Is there some
way to change this behavior so that no output pb file is generated?
What I need is
http://sw-tools.pdb.org/apps/CIFTr/
On Tue, 2010-06-01 at 15:21 +0200, Christian Engel wrote:
Dear All,
I am looking for a ccp4 program that reads in cif-files and converts
them into pdb-files, including the CRYST1 card. Can anybody suggest a
solution? I didn't find any in ccp4i, e.g. the
http://en.wikipedia.org/wiki/SGI_Octane#Available_Operating_Systems
just googled linux sgi o2
On Tue, 2010-06-01 at 10:18 -0600, Brennan Bonnet wrote:
Hi All,
I just obtained a Silicon Graphics O2 Unix workstation from 1996. I
want to use it for 3D modelling of protein crystals using
You should take a look at DIFFMODE COMPARE keyword in AREAIMOL manual,
it allows for buried surface area calculation (you have to prepare the
two pdb files with complex and receptor only). If you can easily use
command line and scripts (i.e. you are running CCP4 on non-micro$oft
OS), try the
I just checked a recent refmac job and it seems that in the output mtz
the Fobs has indeed changed. what's more interesting, the number of
missing reflections has changed too (disturbingly, it decreased so that
the dataset looks more complete 97.07% to 97.17% in this case).
But if the same
On Tue, 2010-05-18 at 07:03 -0700, Miller, Mitchell D. wrote:
The decrease in missing reflections are due to the fact that
the output file does not include the missing reflections that
are lower resolution than the lowest resolution observed
reflection. Thus, this file is no longer
On Fri, 2010-04-30 at 13:35 +0100, Nicholas Keep wrote:
If anyone has a piece of software that would do this it would be
great.
How about this (this is a single line)
---
grep 'ATOM\|HETATM' file1.pdb file2.pdb |grep -v REMARK | cut -d: -f 2 |
cut -c 13-54 | sort | awk 'BEGIN {FIELDWIDTHS =
On Thu, 2010-04-29 at 16:23 +0530, Jhon Thomas wrote:
This is a strange behaviour of the protein complex.
Why is this strange? 20 mg/ml is fairly high, just dilute the protein
to 10 mg/ml and repeat the screen. Or better yet, repeat the screen
with 1:2 protein:reservoir ratio for precipitated
On Wed, 2010-04-21 at 17:21 -0700, James Holton wrote:
The 0.3% chance of a peak being above 3
sigmas assumes that the histogram of electron density values is
Gaussian. It is not! In fact, it is a funny-looking bimodal
distribution (the peaks are protein and solvent regions).
Indeed!
I second Tim's opinion. In the days of CNS/O, there was a popular rule
to place waters in 3 sigma peaks that make chemical sense, then
re-refine and keep those waters that produce more than 1 sigma in 2fo-fc
map. (With Coot the default cutoff is 5).
There could be a bizarre probabilistic
Couldn't they simply be too thin? After all, unit cell dimensions are
routinely about 0.01um, so if these needles are only fraction of a
micron thick, there is simply not enough material for diffraction.
Nice looking but non-diffracting protein crystals are too disordered
(i.e. while packing is
Use bond command
bond atom1, atom2
once you do that, any subsequent line and stick renderings will connect
the atom1 and atom2 (you can right-click on the corresponding atom to
see their full string representation). I assume you are trying to do
something like this
http://tinyurl.com/y2cdezj
Katherine,
all good questions and all discussed previously on this very discussion
board. My personal opinion did not change much since 2007:
http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19777.html
although I would probably amend couple of minor things. As for riding
hydrogens, take a
Hussain,
http://137.189.50.96/kbwong/teaching/pymol/pymol_tutorial.html
which is the top hit when you google pymol electron density. Using
google (and not to appear biased, other available search engines) is the
most valuable advice (per word) that you may possible get.
On Tue, 2010-04-13 at
It is also possible that mother liquor prevents binding (although often
in such cases you would see some precipitant component in the active
site.
I would generally bet on need for conformational change. And you expect
to see the product complex, right?
Ed.
On Fri, 2010-04-09 at 11:15 +0200,
On Thu, 2010-04-08 at 23:26 +0100, Daniel Bonsor wrote:
both the Rfactor and Rfree get stuck at 30% and 36%
according to
http://xray.bmc.uu.se/gerard/supmat/rfree2000/plotter.html
these are higher than expected. With that said, R/Rfree should not be a
fetish, and your model may be fine (i.e.
On Thu, 2010-03-18 at 12:51 -0500, Jacob Keller wrote:
Does anybody have a good way to understand this?
Sure, it just depends on what would one consider a good way to
understand. For a pure empiricist, it's good enough to see one of those
two-dimensional phase swap pictures. For a
On Fri, 2010-02-26 at 16:50 +0100, Gerard DVD Kleywegt wrote:
But it still won't solve Miri's problem. I think what she is asking
for is a
program that detects which atoms should be matched to which,
irrespective of
their names (i.e., not assuming they are called CA ) and order
(i.e., not
and is
unable to postrefine a value of crystal rotx that is compatible with
all the frames.
It may be possible to turn of post-refinement with POSTREFINE 0
or some such.
Ed
Ed Pozharski wrote:
I want to process bunch of frames with extremely short step - i.e. these
are 0.5degree oscillations
Ethan,
manual handling of the mosaicity seems to help. There are now plenty of
other things to sort out, but at least scalepack does not crash anymore.
I used lower fixed mosaicity setting in denzo and fixed it in scalepack.
Another issue is that there was apparently something funny about first
I want to process bunch of frames with extremely short step - i.e. these
are 0.5degree oscillations but crystal only rotates by 1 degree over
1000 frames (I would have kept it at the same orientation if Rigaku
control software would allow zero step). Denzo can process the frames
all right, but
Nick,
there was a discussion of this three weeks ago. Check this thread
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg14133.html
I still maintain the view that appropriately tight restraints are the
way to go and not the grouped B-factor refinement (at least not the way
it is currently
Pavel,
Simply not true. Think why -:) Hint: in restrained refinement the
weight applies to all terms - bonds, angles, torsions, etc... So if
you choose tight weight in such refinement the torsions will be
restrained as tightly as other terms (at least as it would be in CNS
or phenix.refine).
Pavel,
- In general you are free to decide what you name a domain: it can be
a residue, its part or the whole structure.
- What would be main and side for non-amino acid molecule, like a
whatever ligand?
I don't see how my freedom to explicitly define the terms I use in a
post is relevant.
DISCLAIMER: When I say grouped B-factor refinement I mean CNS-style,
Bmain/Bside refinement. Not to be confused with more general domain
B-factor refinement where single B-factor is assigned to some part of
the structure.
Apart from improving data-to-parameters ratio, another argument for
On Fri, 2010-01-29 at 00:14 -0500, Xun Lu wrote:
So, how can I tell Refmac not to sacrifice the geometry of DNA
to fit my poor density? Or, how to fix the DNA (just like in CNS)?
Anyone could share their experience and tricks about dealing with
DNA?
Xun,
I needed once to restrain
Jose Antonio,
I've seen similar behavior few years ago with grouped B-factor
refinement in CNS. The argument for the grouped refinement is as
follows:
This is better than individual B-factor refinement at low resolution
because you significantly reduce the number of parameters.
There are two
http://hamptonresearch.com/documents/product/hr000175_what_is_tacsimate_new.pdf
turns up once you use google's I'm feeling lucky button.
On Tue, 2010-01-26 at 15:42 +, Zhiyi Wei wrote:
Dear all,
I got a problem with my crystals. I have two total different proteins
that both can be
Phoebe,
my understanding is that power of UV illumination here is not in
salt-vs-protein test (which, imho, can only be finalized by testing
diffraction) but in improved contrast for protein crystal detection. I
haven't used UV microscopes myself, but images provided by manufacturers
are quite
The increase in RFZ is relatively small and not entirely unexpected.
While hydrogens only contribute one electron (as opposed to carbon (6),
nitrogen(7), oxygen(8) and sulfur (16)), there are many hydrogens (in
fact, almost as many as all the other atoms combined). For instance, in
lysozyme you
My knowledge of Fortran is dated, but the ESU_R and ESU_RFREE are
calculated in refmac like this
HESU_CRUIC = SQRT(FLOAT(N_REFINED_ATOMS)/FLOAT(NREFMNPAR))*
+ COMPL**(-0.33)*HD_HIGH*HRFAC_SHELL_WORK(NB1)
HESU_FREE = SQRT(FLOAT(N_REFINED_ATOMS)/FLOAT(NREFA(1,NB1)))*
+
With salt-based conditions sodium malonate is your friend:
Acta Cryst D59: 2356
On Tue, 2009-12-15 at 12:20 +, Natalie Zhao wrote:
-Original Message-
From: owner-c...@dl.ac.uk [mailto:owner-c...@dl.ac.uk] On Behalf Of Rafael
Couñago
Sent: 14 December 2009 20:22
To:
The electron density snapshots I can understand on some level - after
all, picture is sometimes worth thousand words. But it does take a
windows person to post Mb-sized picture instead of a one-line error
message.
flame off
On the substance, you should probably do what the program suggests -
Not to derail the thread, but there is nothing, imho, wrong with I/s=1
cutoff (you expect I/s=2, I assume?). R-factors will get higher, but
there are good reasons to believe that model will actually be better.
This has been discussed many times before and there is probably no
resolution, so why
I would like to point out that this outright fabrication remains an
isolated incident. There are over 50,000 crystal structures in the PDB,
which means that this is only ~0.02% of the total. This is all quite
bad, but let's not overstate the problem.
Maybe such report is not a great idea after
Does anyone know if REFMAC has any SIGFP cutoff? I looked into manual
but perhaps missed it. What I mean is abnormal situation where some
FOBS are 0 or even negative - is there any intrinsic cutoff or
refinement will be done against all the reflections?
Thanks,
Ed.
--
Edwin Pozharski, PhD,
with the cutoff level selected, but it is
the inconsistency of that level with Rmerge and the Rvalues for the
highest shell.
BR
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ed
Pozharski
Sent: Friday, December 11, 2009 12:58 PM
On Sun, 2009-11-22 at 23:33 -0800, Dale Tronrud wrote:
I could be describing my angle as
1.5 radians, 1.5 degrees, or 1.5 cycles (or 1.5 of the mysterious
grad on my calculator).
I thought that use of degrees is based on dividing a circle into 360
parts - roughly one per day (then in
Ian,
On Mon, 2009-11-23 at 17:34 +, Ian Tickle wrote:
Ed,
For instance, if angles are measured in degrees and x1
sin x ~ pi * x / 180
sin x ~ x
Your equations cannot simultaneously be true in fact the 1st one is
obviously wrong, the 2nd is right. In the 1st case I think you
it (but with Emacs).
But I guess the official way would be with Reflection Data Utilities - Edit
MTZ Datasets which will edit the dataset cells. It wraps keywords of CAD.
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Ed Pozharski
Sent: Fri 11/13/2009 9:25 PM
You may be able to open mtz files in a primitive text editor such as
nano (I just did). It's a little awkward, as there are no line breaks.
MTZ header is in the end of the file and it is plain text, so should be
easy to edit manually - just make sure you don't introduce extra space.
There are
Check if you have csh installed in your system. If it still fails, try
installing tcsh.
If I am right, then this is happening because automar-install script is
written for csh but which is not installed by default on your system
(most modern linux distros use bash).
On Mon, 2009-11-02 at 22:06
On Thu, 2009-10-22 at 11:19 -0400, Yuan Cheng wrote:
datasets in scalepack.I am wondering whether there is any way to reindex
these two datasets to make their a/b dimensions match. Any suggestion
will be highly appreciated.
Oh yeah, there is. It's on page 102 of the HKL manual (Scenario 5:
I obviously didn't pay any attention to the specific numbers/space group
(and didn't read the rest of your message). Fred is absolutely right -
the only thing you can do in P21 is to switch a and c (and invert b to
maintain the right hand).
So maybe your crystal can be indexed both ways, but
Both pymol/align and coot/ssm (I presume) do the secondary structure
alignment first followed by structural alignment. So it only works for
proteins. In Pymol, there is fit command that instead matches atoms
with the same names; and super which does sequence alignment first.
You can try to play
*If* you are using WEIGHT AUTO, check the RMSDbonds. You don't say what
your resolution is, but I assume it's in lower 2.0s. I've seen refmac5
in some cases produce somewhat unreasonable geometries (i.e.
RMSDbonds0.025A) at such medium resolution and accordingly, large
R/Rfree gap. If this is
My resolution is 1.6A although I have cut it to 1.8A to bring the
R-factor down. I've been performing restrained refinement in refmac5
using the default settings. The solvent content is 40%
This sounds fundamentally wrong. Even the Rmerge reduction by cutting
resolution practice is
Take a look at this:
Brunger, A., DeLaBarre, B., Davies, J. Weis, W. X-ray structure
determination at low resolution. ACTA CRYSTALLOGRAPHICA SECTION
D-BIOLOGICAL CRYSTALLOGRAPHY 65, 128-133 (2009).
The paper quotes Wayne Hendrickson (says submitted) regarding
determinancy point (i.e. where
I've seen this estimate of the determinancy point for torsion angle
refinement presented by Axel Brunger at ACA meeting this summer. I
don't remember all the details, but no, it did not refer to the approach
described in the paper where higher resolution model is used as a
restraint. It was
On Wed, 2009-09-23 at 16:05 +0200, Dirk Kostrewa wrote:
yes, but this is only in case of torsion angle refinement. For x,y,z
the determinancy point is ~3 A.
True, but to count all the x,y,z,b as parameters is only sensible with
unrestrained refinement. If restraints are properly imposed,
You can use the glass cell disruption pestle
http://www.vwrsp.com/catjpg/mp0/mp0440.jpg
to grind them up. They cost money, of course, and if you plan to buy
something, why not go for seed bead kit? But if you want something very
cheap, then you'll find this amazing discovery interesting:
I suspect that your question is CNS-related. Easy is relative, but what
you need to do is to uncomment the appropriate DIHEDRAL statements
(assuming that used xplo2d, they will be there but mostly commented
out). Just figure out what values you need for particular angles.
If it is wise to fix
Tassos is absolutely right. While it's unlikely that many subscribers
of the ccp4bb today suffer the indecency of checking their mailbox over
4kbps flaky modem connection (also known as wishful staring at the
progress bar), it still seems pointless to distribute hundreds of
megabytes into
Yes, the problem is with 32-vs-64. At first, I have found an ugly
workaround of getting 32-bit version of libguile-srfi-srfi-1-v-3.so.3
and changing the symbolic link in /usr/lib to fool coot into using it.
Coot will start but will be quite unstable. So to answer your question,
there is no
On Sat, 2009-05-02 at 11:50 +0100, mb1pja wrote:
.. but OSX gives you Unix AND you can run Word /Powerpoint without
rebooting. And you get a user-friendly ergonomic windowing system that
kicks the out of XP/Vista/KDE/Gnome...
best wishes
Pete
I guess you should check some compiz
Should help if you use detergents and, of course, they are cheaper.
On Wed, 2009-04-29 at 15:38 -0400, Sang Hoon Joo wrote:
I sometimes notice people using non-siliconized cover glass and it
makes me wonder what pros and cons we can think about using
siliconized glass... any suggestions?
What is the crystallization condition?
On Fri, 2009-04-24 at 11:46 +0800, Liew Chong Wai wrote:
Hi all,
Good day
I used MPD as a cryoprotectant (20%, 30%) for my crystal. However,
there is no diffraction signal at all. Without the MPD cryo, i still
manage to get 5angstrom, but it has
While CNS manual says that masks can be generated both as cns map and O
mask, the model_mask.inp script does not have an option in define
section to switch the formats. (My guess is that this is because these
scripts were written when one ring still ruled them all - his fingers
instinctively type
Assuming that you did everything else correctly (e.g. placed the new
cr_info file you got from HKL into /usr/local/lib), are you sure you
included un-mar165 in your info file? They have this mar option which
refers to MAR imaging plate detectors (except MAR345) and thus does
not cover CCDs
But wouldn't detwinning be problematic with nearly perfectly twinned
data? I'll post my own question about separately to not hijack the
thread...
On Mon, 2009-03-16 at 11:24 +0100, Clemens Steegborn wrote:
Hi Walter,
You should definitely detwin data for map calculation if you have a
Some time ago, I had a dataset which turned out to be P31 with a dimer
sitting on the three-fold axis. The only way I found to process it was
to run twinned refinement in CNS with (-h,-k,l) and twinning fraction of
0.5. R/Rfree are 20/24% at 2.4A resolution, so the model must be right
at least
I had the same problem. In my case I think it was related to the part
of ccp4 configuration that redefines python path. For some reasons (it
breaks wxPython, at least in Hardy), I had it commented out and then
after starting ccp4i I got these dbccp4i warnings. When I turned python
part of ccp4
And Linux partitions can be accessed from windows:
http://www.howtoforge.com/access-linux-partitions-from-windows
On Mon, 2009-01-19 at 12:49 +, Roger Dodd wrote:
Dear all,
Just to add, linux now has perfectly good read-write stable drivers for
NTFS (the native WinXP filesystem). This
Also I did a 'Google vote' for the two terms. 'Structure amplitude' has
11300 hits. 'Structure factor amplitude' has only 4750. So all round I
would say that 'structure amplitude' wins by a considerable margin.
Results of another Google vote:
Earth is flat:
Jon,
Riding hydrogens are *not* part of your model, they are part of the
algorithm used to predict observations. Thus, the information is
automatically included when you report the software used for refinement.
There are definitely some (many) parameters that are never included in
the deposited
As a follow-up to the question posted by Jon Winger regarding riding
hydrogens, do we all agree that the current PDB format does not allow
complete reconstruction of the final stage refinement? For instance,
the geometry weight factor is never reported.
Second question: is it important to make
Riding hydrogens are *not* part of your model,
The fact that you don't see H in your fo-fc map due to limited
resolution and high level of noise does not mean that H atoms are not
present in actual real structure -:)
Let me ask you this - are bond length restraints part of the *model*?
- bond length restraints do not contribute to the scattering and
hence do not affect the R-factors, while H atoms do contribute to
scattering and therefore R-factors computed from the model with or
without hydrogens can be different (I spent a couple of months
implementing it in PHENIX and I
On Thu, 2008-12-18 at 10:15 -0800, Ethan A Merritt wrote:
The riding-hydrogen treatment is definitely part of the model.
But the number of parameters associated with it is not derived from the
number of individual hydrogen atoms and their coordinates, it is
limited to the number of parameters
On Tue, 2008-12-09 at 09:31 +0100, Tim Gruene wrote:
...you must set the occupancy of those residues to
zero...
I think this approach (which Tim is not supporting) makes no sense.
When I place an ATOM record into a pdb-file, what I am really saying is
based on the data, this atom's
Thanks to all who answered (so quickly). To summarize, the premise
fails because NMR/FRET and crystallography are based on different
phenomena, and the energy-distance relationship is only valid for the
latter. One has to wonder why they need to build bigger and bigger
accelerators instead of
You may also consider HYDRO suite:
http://leonardo.fcu.um.es/macromol/programs/programs.htm
It does calculate the radius of gyration, but also stokes radius,
diffusion coefficients, etc.
On Wed, 2008-10-29 at 23:39 -0400, David M Shechner wrote:
Hallo, one and all,
I was wondering if anyone
May I also suggest that the more traditional avenue - requesting the
reprint from the corresponding author - is always tried first? I used
to do this back in time when I was a poor russian grad student with zero
access to full-text articles. Also handy if you collect stamps :)
On Tue,
] On Behalf Of Ed Pozharski
Sent: Thursday, July 10, 2008 2:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] pdbset bug - seqres record
There is a bug in pdbset: when you output a sequence (using SEQU PDB), the
residue names are shifted to the left by one position. Here is how it looks
like
for processing in hydropro. Don't know if it's important
anywhere else, but hydropro can't read the sequence if it's shifted.
--
Ed Pozharski [EMAIL PROTECTED]
University of Maryland - Baltimore
GROMACS binaries are available for Macs
http://www.gromacs.org/content/view/32/100/
Afaic, GROMACS is user-friendly. There are good tutorials, and there is
even third-party GUI:
http://resal.atspace.com/grogui.htm
IMHO, the GUI is not much better than running Gromacs jobs from command
line,
The word weak is, of course, relative. Free energy of crystallization
is roughly 1-2 kcal/mole of crystal contacts (I think I carried this
number from Sir Blundell's book, but quick look at papers by Peter
Vekilov's group seems to confirm it - am I wrong on this?). I think
that crystal contacts
.
On Thu, 2008-05-15 at 10:08 -0700, William Scott wrote:
On May 15, 2008, at 10:01 AM, Ed Pozharski wrote:
1.2A (not surprisingly since this is about the length of covalent
bond).
A carbon-carbon single bond is about 1.55 Å.
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland
resolution. I think anything better than ~3
Å should allow unambiguous definition of nucleotide and amino acid
positions.
On May 15, 2008, at 11:28 AM, Ed Pozharski wrote:
Of course. However, C=0 bond is ~1.2A, and bonds made by those pesky
hydrogens are ~1A. And I would think
02
[EMAIL PROTECTED]
-Message d'origine-
De : Ed Pozharski [mailto:[EMAIL PROTECTED]
Envoyé : Tuesday, April 08, 2008 3:56 PM
À : Philippe DUMAS
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
RMS deviation refers to the variance of a random
On Mon, 2008-03-17 at 10:51 +, Partha Chakrabarti wrote:
Not just one of them. If you are pushing it too far, you will see the
effect in later refinement step..
And the effect in later refinement step will be the slight increase in
R-factor? IMHO, this does not justify throwing away data
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