Dear CCP4ers,
is there a program around that allows to fill an input map or mask with
dummy atoms?
Best regards,
Dirk.
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Can anyone reccomend a free download program that will calculate the energy of
a protein/ligand complex? The ligand has been modelled in.
Thanks
Rex Palmer
Birkeck College
... maybe, to clarifiy my question a little bit: I want to fill an
essentially flat cryo-EM-map with dummy atoms. So, a peak search doesn't
work. I would need a program that fills this map with dummy atoms for a
few things that I want to try with this atomic representation.
Best regards,
Doesnt arp/warp start with doing something like this? If you gave a 0/1
mask I wonder what the first build would look like..
You would have to invent a reflection file for the map ...
E
On 10/13/2010 12:49 PM, Dirk Kostrewa wrote:
... maybe, to clarifiy my question a little bit: I want to
Rex Palmer wrote:
Can anyone reccomend a free download program that will calculate the
energy of a protein/ligand complex? The ligand has been modelled in.
Thanks
Rex Palmer
Birkeck College
Hi Rex,
I think any refinement program such as CNS will do this - problem is,
since these programs
Dear Rex,
Not withstanding Fred's reply just to also mention that in our study:-
G.M. Bradbrook, T. Gleichmann, S.J. Harrop, J. Habash, J. Raftery,
A.J. Kalb (Gilboa), J. Yariv, I H Hillier and J.R. Helliwell “X–ray
and molecular dynamics studies of concanavalin A glucoside and
mannoside
Dear Dirk,
For filling an input map you can try ARP/wARP in an 'old-fashion' way.
The script below should place DUM atoms (1.1 times the requested number)
into the highest density. Prepare your map in the CCP4 format, for
example in P1, extended to cover the asymmetric unit in full (0 1 0 1 0
Flood fills a map with water molecules.
http://xray.bmc.uu.se/usf/flood_man.html
On 10/13/10 6:49 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote:
... maybe, to clarifiy my question a little bit: I want to fill an
essentially flat cryo-EM-map with dummy atoms. So, a peak search doesn't
Lei,
1. Consider making the complex and then purifying the excess peptide
away by dialysis (size exclusion may be tricky since complex may be
diluted in the process).
2. Conventional wisdom would be to try to minimize the amount of excess
peptide as it may interfere with crystallization. But
Would APBS do what you want?
http://www.poissonboltzmann.org/apbs/
It has interfaces with Pymol, VMD and others...
From: Rex Palmer rex.pal...@btinternet.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wed, October 13, 2010 6:43:49 AM
Subject: [ccp4bb] protein ligand
Dear Rex,
It certainly matters what you mean by the energy of a
protein ligand complex. And whether you are comparing a series
of related similar structures or looking for an absolute
energy.
The problem is that there is no such thing as an absolute
energy, it is always relative to something
This is all true. And I think the bottom line is that it is extremely
non-trivial to get a meaningful number.
The Amber MM-PBSA script is the best established one. We have an
equivalent CHARMM-based script at:
http://www.cse.scitech.ac.uk/cbg/software/charmm/
But I guess this is beyond the
Hello All,
I am a graduate student working on my first merohedrally twinned data set. Like
a few, I am a bit intimidated by it. After some trial and error with the help
of some online resources and ccp4bb posts, I seem to have solved the structure.
However, I am still unsure about some of the
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
The image is actually from
http://www.ruppweb.org/Xray/tutorial/vectordiag.htm
but the first image is missing.
There you see that the 'vectors' are actually (general acentric)
structure factors for a single anomalous atom, and each of those
of course has a real and imaginary component.
The
Hi Bill,
the picture does not show Fa (as a vector), but the vector addition Fp+Fa+iFa
(it might be a naming convention of the picture to write Fa instead of iFa,
but that's a matter of taste really).
Furthermore Fa has the same phase as Fa plus the contribution of i, which
corresponds
to the
The Fa vector is always a 90 degree left turn from the Fa vector. For a
centrosymmetric heavy atom substructure such as 1 mercury site in P21,
the Fa vector would point straight up or down.
hope that helps,
Citizen Dan
William Scott wrote:
Hi Citizens:
Try not to laugh.
I have an
Isn't the simplest answer that this is not really an Argand diagram with
real and imaginary axes, but simply a diagram showing the graphical addition
of the component phasors of the atom's scattering components? And aren't
real and imaginary relative terms anyway (in more ways than one, I
Please check the project directory temporary directory is correct or not.
Initially I faced the same problem for not assigning the correct project
directory (I use it Windows, but the problem also occured in Linux system). If
you are running CCP4 in Windows make sure that the folder CCP4
[ ccp4 6.1.13 ]
[ gui 2.0.6 ]
if a data set with merged Bijvoet pairs and a free set is then made anomalous
- i.e. re-scaled with separated Bijvoet pairs - i do not understand how
acentric reflections in the free set are extended by cad or freerflag or
uniqueify.
the easy question : is
Hello:
I am puzzled (probably shows my lack of understanding) by a REFMAC
output using the TWIN option. My data set is in space group 145 (P32),
with a twinning factor (according to the twining server) of ~ 40% along
a*,b*. In this space group there are three possible twinning operators,
Hello
I guess you are using 5.5. In this version in the beginning twin fractions are
just initial values. They need to be refined. This are potential twin
operators. Further down in the log file there should be Rmerge for each twin
operator and estimated twin fractions. What are they? Can you
It is already vertical, relative to the real part of Fa (in red), i.e. the
blue vector is always vertical to the red vector in this picture (and
counter-clockwise).
Yong
William Scott wgsc...@chemistry.ucsc.edu
Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK
10/13/2010 01:48 PM
Please
As a general rule intensity based refinement gives higher R-factor especially
when intensities are weak. Truncate smoothes out data and Rfactors become lower
(it is not necessary that model becomes better)
In your case it may happen that your space group is higher. To check that you
can do
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
Dear Dirk
You might find one of the programs mentioned by Andreas below useful
for your purpose.
Cheers
Alex
Am 28.07.2010 um 18:26 schrieb Andreas Förster docandr...@gmail.com:
Here's a preliminary summary of the suggestions I got from the ccp4
community regarding the problem stated
Dear Bill,
The discussion is becoming complicated because of the mixing of notations.
There is a theory or model which describes the atomic scattering factor as
f = f0 + f' +if
from which the structure factor is calculated. That right angle that you see in
the picture you sent us with that
Bill,
If I understand you correctly, the problem turns to be understanding
coordinate system.
The coordinate system in the plot in your original email is not a
complex one but a polar coordinate system [|F| and phase (polar
angle)]. In order to add the contribution of an atom with
Hello Garib,
Thank you for the reply helpful insight.
I ran the refinement of structure factor amplitudes without the TWIN command,
and obtained much higher R and Rfree (32% and 36%). Also, in the process, I
found out that I made a mistake earlier in that the amplitudes were refined as
Hello Fred,
Thank you for the response.
I have made a mistake in the twin refinement settings (see the other email) and
the best R Rfree values I obtained were from the twin refinement of structure
factor amplitudes, which is about 1% less than the twin refinement of
intensities.
I have
I see. Thank you for the reassuring and helpful pointers.
Best,
Peter
Subject: Re: [ccp4bb] Twin - Data reduction and refinement in Refmac
From: ga...@ysbl.york.ac.uk
Date: Wed, 13 Oct 2010 23:55:56 +0100
CC: CCP4BB@JISCMAIL.AC.UK
To: pc...@hotmail.com
It seems that evidence is convincing:
It seems that evidence is convincing: twin is present. All evidences indicate
that space group is P6(5) and twin is present.
Theoretically that is what you would expect at the end of refinement if twin is
present: Huge drop in Rfactor and marginal improvement if any in electron
density.
While we are on embarrassingly simple questions, I have wondered for a long
time what is the reference phase for reflections? I.e. a given phase of say
45deg is 45deg relative to what? Is it the centrosymmetric phases? Or a
theoretical wave from the origin?
Jacob Keller
- Original
On Oct 13, 2010, at 4:21 PM, Jacob Keller wrote:
While we are on embarrassingly simple questions, I have wondered for a long
time what is the reference phase for reflections? I.e. a given phase of say
45deg is 45deg relative to what? Is it the centrosymmetric phases? Or a
theoretical wave
It is relative to a single point electron at the origin.
-James Holton
MAD Scientist
On Wed, Oct 13, 2010 at 4:21 PM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
While we are on embarrassingly simple questions, I have wondered for a long
time what is the reference phase for
When talking about the reflection phase:
While we are on embarrassingly simple questions, I have wondered for
a long
time what is the reference phase for reflections? I.e. a given phase
of say
45deg is 45deg relative to what?
=
Relative to a defined 0.
Is it the centrosymmetric
Hi all,
I found some microcrystals the other day in some trays grown at 4C. Strangely
enough, they disappeared the next day after putting them back in the fridge
overnight, but after letting the tray sit at RT for 5-10 min, the microcrystals
reappeared. Leaving them at RT for 2-3 hrs, and then
On Oct 13, 2010, at 3:09 PM, Tim Gruene wrote:
Dear Bill,
The discussion is becoming complicated because of the mixing of notations.
There is a theory or model which describes the atomic scattering factor as
f = f0 + f' +if
from which the structure factor is calculated. That right angle
So let's say I am back in the good old days before computers,
hand-calculating the MIR phase of my first reflection--would I just
set that phase to zero, and go from there, i.e. that wave will
define/emanate from the origin? And why should I choose f000 over f010
or whatever else? Since I have no
Does f000 mean the direct beam? Having a hard time imagining such a miller
index or the corresponding planes...
No, F000 is NOT the direct beam. I may not have made that clear enough in
some of my drawings and captions, and it will be emphasized in the second
printing/ebook. There is in fact
I used NaF in the precipitant thrice for three different proteins to be
crystallized each time I got crystals and they were all salt crystals ! I
thought low solubility of NaF causes this quick crystallization of salt.
Recently I got crystals of a protein at 20 degree grown in gradient
So let's say I am back in the good old days before computers,
hand-calculating the MIR phase of my first reflection--would I just
set that phase to zero, and go from there, i.e. that wave will
define/emanate from the origin?
I do not think this could be done to get the origin correctly
An interesting guide to doing phasing by hand is to look at direct
methods (I recommend Stout Jensen's chapter on this). In general
there are several choices for the origin in any given space group, so
for the first reflection you set about trying to phase you get to
resolve the phase
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