Emmanuel Skordalakes, Ph.D.
Assistant Professor
Gene Expression and Regulation Program
The Wistar Institute
3601 Spruce St
Philadelphia, PA 19104
215-495-6884 Office
215-898-2202 Lab
[EMAIL PROTECTED]
Greetings (or in "correct" Swiss German "Grüezi
wohl", with Umlaut=vowel mutation) to all CCP4BB
subscribers,
being a CCP4BB reader (and sometimes writer)
since something like 15 years, I realized today
that the comment of Gerard was the first one I
read since then containing a side-swipe r
I would probably prioritize keeping the same R-free set (thus using
the F^2 output by mtz2various) over
going through the scalepack format and loosing track of it.
You can however use XPREP to transfer the R-free set from the
"inferior" F^2 HKLF4 file output by mtz2various to the proper
int
Dear All,
my reply the other day was, I agree, a bit overly sarcastic and I
should have refrained from sending that mail. I hope Shivesh and you
all will forgive me, as I'm not such an unmissable part of CCP4BB as
Tassos is.
Also, it appears the Gods of CCP4 punish immediately, as today I am
A few years ago I did this by first using the solved structure to
generate a hypothetical (FCALC) data set to some rather optimistic
resolution limit (2A when I was stuck at 2.7), carrying out a random
Rfree selection on this FCALC set, and then dumping the FCALCs while
retaining the Rfree
Risking a potentially trivial question:
Is there a program that will calculate the RMS of distances
between specified (listed) atoms in two different structures?
As far as I could see, LSQMAN will only compute same with same?
lsqman does in fact calculate rmsd valus between arbitrary sets of a
Yes I have always been annoyed by that. I tend to use sftools to trim
and then rename the columns I want followed by mtz2various with
something along the lines of "labin FP=F SIGFP=SIGF FREE=FreeR" and then
finally edit the resulting text file to remove the header and all the
"FREE"'s as you did. I
On Thursday 01 March 2007 10:17, Ian Tickle wrote:
>
> All, I thought this would be a simple task, but for the life of me I
> can't see how to do it! All I want to do is convert an MTZ file to
> Shel-X format for refinement. I thought it would take me 2 secs, but
> it's taken me at least 5 attem
Actually, the merge script will create the superset of both reflection
data sets, so it won't delete reflections from one data set that are
not present in the other data set.
Once you have done the "merge.inp" script, you can use the "make_cv"
script to extend your test set while keeping yo
On Thursday 01 March 2007 10:32, John Bruning wrote:
> Where can I generate the following numbers in CCP4 coming with pdb and mtz
> from Refmac?
>
> Luzzati SigmaA (obs)
> Luzzati ESD (R-free set)
> Luzzati SigmaA (R-free set).
The answer is that you should not be using Luzatti plots to estimate
Where can I generate the following numbers in CCP4 coming with pdb and mtz from
Refmac?
Luzzati SigmaA (obs)
Luzzati ESD (R-free set)
Luzzati SigmaA (R-free set).
If the answer is sfcheck, where exactly are the numbers located, all I can find
is Luzzati ESD overall?
All, I thought this would be a simple task, but for the life of me I
can't see how to do it! All I want to do is convert an MTZ file to
Shel-X format for refinement. I thought it would take me 2 secs, but
it's taken me at least 5 attempts, and it's still not right!
First I tried mtz2various w
1) Convert the CNS protein alone reflection file to an mtz file with
FreeR flags labelled
2) Convert ligand data to myz file - easiest to use the IMPORT scaled
data tool in Data Processing module if you have a *.sca file.
Say you want to import FreeR flag from another mtz file (the
protein-al
LSQKAB will do that - see Coordinate utilities.
You can either match ATOM 7 to 9
MATCH ATOM 17 to 19
etc etc - laborious
Or ask MATCH RESIDUE 22 to 31
to Residue 42 to 51
OUTP RMS XYZ
It makes a huge list to RMSTAB of all distances..
Eleanor
Jan Lowe wrote:
Risking a potentially trivial
Vineet Gaur wrote:
Hi all
we r trying to solve astructure with two molecules in the asu. we were
initially refining using CNS by applying strict NCS. Now we want to
shift to REFMAC. How can we apply the rotation translation matrices as
determined using CNS, while refining with REFMAC.
Addition
I use a multimeter from Radioshack (catalog number 22-812) that can
record this data on a PC via a serial connection. Presumably by now
there is a similar device with a USB connection. Publishing the
resulting text file on the web would be effortless on a *nix
machine, but I'm not sure how to do
Dear colleagues,
I have a dataset form a protein-ligand complex. I want to use the same
Rfree test set for refinement as used for the protein alone. How can I
extract the test set from the CNS reflection file of the protein-alone
dataset (created with make_cv) to use it with the protein-ligand
We all begin at some point, and should help ourselves before we ask others
for help. Shivesh's question shows he has not even tried looking at
programs, initiate things on his own. I think such e mails should be
discouraged. I found what Mark said quite funny. All my labmates were
laughing..
Ar
Hmm - I think this is a bug..
Garib - what do you think?
Eleanor
Jianghai Zhu wrote:
Dear all,
I have some N-acetyl-glucosamine (NAG) in my structure. When I
searched the monomer library in CCP4 6.0.1, I found out that NAG is
actually N-acetyl-glucose, which is much less common, I believe.
John Bruning wrote:
When using Refmac how does one find/calculate R-free error in the
highest resolution bin?
Look at your loggraph for the final R Rfee - that gives the numbers in
resolution shells.
Eleanor
Attached is an advertisement for a 5 year scientist post in Small Angle
Neutron Scattering at the ILL. It is also posted on the ILL site at
www.ill.fr (Jobs and Careers)
Peter Timmins
VACANCY RESEARCH SCIENTIST (Neutron Small Angle Scattering) (m/f)
The Institut Laue-Langevin (ILL), situated
shivesh kumar wrote:
Dear all,
I have a data set at 2.2A, of the selenomethionene labelled
protein.How should I process the data.Thanx for the help.
Shivesh
I think you should ask your local crystallographer for help. There are
several programs ( MOSFLM in CCP4, DENZO, XDS, D*TREK ) but you
Indeed Strep-II (please note there is also a Strep-I which is not as
good!) tag is a good tag to try if you can. There are a few caveats that
you may want to consider when trying it:
0. if things work out, Strep-II affinity purification can yield
essentially pure protein in one step. The question
What do you know? The NAG-B-D in ccp4 monomer library is actually N-
acetyl-D-glucosamine, even the description says it is N-acetyl-D-
glucose. After I pulled out the structure from the cif file, I found
it is actually the structure I am looking for but with a wrong name.
So I guess if you
Hi,
Yes refmac, use weighting term 0.05
Thanks
On Thu, 1 Mar 2007, Tim Gruene wrote:
How did you do the refinement? Did you use refmac? Did you let the matrix value
at 0.5? That's too high. lower it to, say, 0.1 to start with.
Original-Nachricht
Datum: Thu, 1 Mar 2007 03:
Also MUSTANG (multiple structural alignments) can be configured to output such
data.
http://www.cs.mu.oz.au/~arun/mustang/
J
Ruben Martinez-Buey <[EMAIL PROTECTED]> wrote:>
> Dear Jan,
> I think GROMACS can do that (www.gromacs.org):
> __
Dear Jan,
I think GROMACS can do that (www.gromacs.org):
g_confrms computes the root mean square deviation (RMSD) of two
structures after LSQ fitting the second structure on the first one.
The two structures do NOT need to have t
On 1 Mar 2007, at 10:46, James Whisstock wrote:
Once you have integrated (run in ccp4 for MOSFLM), then you need to
scale the data using, for example, SCALA.
Have a look at the following tutorial for running scala.
http://www.ccp4.ac.uk/courses/ECM2004/runningscala.pdf
An updated versi
HI - try the program contact from the ccp4 suite.
http://www.ccp4.ac.uk/html/contact.html
J
Eleanor Dodson <[EMAIL PROTECTED]> wrote:>
> mathias wrote:
>> Dear all,
>>
>> Can anyone of you guys recommend free software, or any open access
>> internet server, to calculate VDW interactions of smal
Risking a potentially trivial question:
Is there a program that will calculate the RMS of distances
between specified (listed) atoms in two different structures?
As far as I could see, LSQMAN will only compute same with same?
Calculate RMSD of M1 A20 A30 A40 A50
And M2 A20 A30 A4
Dear Shivesh
Below I've tried to give you some broad ideas about where to look / read and
some packages / approaches to try.
For a start there is a very comprehensive tutorial on the ccp4 site together
with the experiemental phasing roadmaps.
http://www.ccp4.ac.uk/dist/examples/tutorial/html/h
I have found in my usenet adventures that usenet mavens often point
to this link before trying to sort out among themselves exactly what
level of humor to take with dubious posts:
http://www.catb.org/~esr/faqs/smart-questions.html
Of course usenet mavens also complain a little too m
mathias wrote:
Dear all,
Can anyone of you guys recommend free software, or any open access
internet server, to calculate VDW interactions of small molecules
binding to protein. The only information I need is an output file
which lists all amino acids of the target protein which make VDW
int
Such a "twinning operator" can also indicate that you spacegroup has an
extra symmetry operator (h,-h-k,-l)
That is in fact one of the symmetry operators for P3i21 H32 P6i22
Have you solved the structure in the lower symmetry and is that missing
density properly generated by this operator?
Dear Sankar,
One thing to consider is that the Oxford Xcalibur system has been on the
market and in users hands for quite some time (even though this does not
strictly apply to the NOVA source). I'm not sure how many of the MM002
Rigaku has sold, and the Bruker instrument is very recent.
Apart f
Goede dag Gerard,
interesting that you think my last e-mail was addressed to you ;-)!
Yes, this was my first moralizing posting on this board after some 16
years. A bit sense of humor is fine, but the last posting was simply too
much. We shouldn't attack people personally or discriminate agains
gruzi dirk,
come on - lighten up a little! your reply wasn't funny or helpful either -
just moralising. (by the way - 't is a strange fact that whenever i get any
negative reactions to my own postings they stem *exclusively* from any or all
of these three countries: the us, germany and switzer
hi ...
there is very likely a correlation between quality of the vacuum and
filament lifetime.
it had been recommended to us to monitor the vacuum continuously on the
rigaku ru300 (?) generators we had at the time. this was fairly easy by
just plugging a left over plotter from an old chromatograp
Dear all,
two days ago I asked the ccp4 and 3DEM lists how one could prevent carbon
films from being destroyed by detergent. At least that's what I meant to
ask. Thanks for the many responses I got in no time (summarized below).
Thanks to all who responded and apologies to those I don't mention
Dear all,
I wholeheartedly agree with Dirk. I was quite speechless yesterday when
seeing one sarcastic reply after another being sent to this correspondent,
who has probably been put off using this BB ever again. Its purpose is to
help people who need to ask such questions, rather than to ser
Hi all
we r trying to solve astructure with two molecules in the asu. we were
initially refining using CNS by applying strict NCS. Now we want to shift to
REFMAC. How can we apply the rotation translation matrices as determined
using CNS, while refining with REFMAC.
Additionaly how do we mentain t
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Dear ccp4bbers,
I agree with Dirk. I have also noticed that much due to the way X-ray
crystallography is evolving, a lot of students/early-postdocs find
themselves "doing crystallography" in labs without a tradition in
crystallography, even without "r
Dear all,
I am sorry to trouble you again because I am facing a very weird
situation:
Three copies from Phaser are the right solutions based upon:
1, Rfree 42% R 39%
2, No packing clash
3, The packing within the 3 makes good sense
4, Density evenly distributed among the 3 copies even without N
Hi,
We got some good experiences using the IBA streptag for baculo-expressed
proteins. You'll have to redo the cloning, but it will be worth your while when
you see the first purification step,
cheers
Joost
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTE
Hi Mark,
although Shivesh's question was not very specific, and he should have
clearly given some more informations about what he would like to know,
he is probably a beginner in crystallography and simply asked for help
on this board. Not everyone has always time or is always in the mood to
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