To improve the clashscore you could try increasing the value of the
nonbonded_weight parameter, starting at 1000 (which I understand at one time
was the default in phenix.refine, but recently for me already gives a huge
decrease in clashscore). Since this will be avoiding clashes at the
This old message claims that / = "weighted" by s.
If counting error is significant, s will be larger for stronger reflections, which are likely to
have small I/s, so in general / > unweighted . As Werten points
out.
However this seems to be the opposite of the OP's situation, if both
After using the same reagents for the Lowry assay and seeing the color yield in
the standard curve gradually decreasing year by year, we decided to make new
reagents last year. Sure enough the color yield was restored, but in the next
assay a few weeks later the blank was unusually high. after
upper limit for the molecular weight of this molecule?
David Cobessi solved a structure with heme on a crystallographic 2-fold.
https://www.ncbi.nlm.nih.gov/pubmed/11752777
Heme is almost, but not quite, 2-fold symmetric.
eab
Peer Mittl wrote on 8/27/2021 9:55 AM:
Dear Vaheh,
I agree with
Two suggestions for people sending pictures of electron density to the BB:
1. Reduce the size of the pictures-
The two pictures in yesterday's email appear nice and small in my email client, but still
illustrate what is being described. However they are actually 4032x3024 and 2040x1458
pixels,
>>> Michael Weyand 06/08/20 12:40 PM >>>
Dear CCP4I2 experts,
I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
we use a non standard SSH port.
So far, I'm not able to add any option within the CCP4I2 interface. For
job submission, I need something to do like
'ssh -p
>>> Ian Tickle 05/30/20 7:14 AM >>>
>>(unless of course the completeness calculations were performed on two
different reflection files)?
EDS is in fact using a different dataset compared to the coordinates,
when I submit the output reflections.cif produced by phenix, when the
input I, sigma-I
Apologies for my previous email appearing to put words in Dale's mouth- I'm
using my school's
webmail and it apparently doesn't indicate the quoted text.
The following is what I added:
I think it is not just that the distribution is asymmetric and limited to
positive numbers-
it is due to
>>> Dale Tronrud 04/07/20 12:37 PM >>>
This topic has been discussing on the BB many times and a little
searching should give you some long-winded answers (some written by me).
The short version. If you refine a model with a common B factor for
all atoms, or keep a very narrow
Bear in mind that position of the interferometer mirror or whatever
would have to be constant to within a fraction of an Angstrom- breathe
on the frame and it will warm ever so slightly- the expansion will
change the
phase of the reference beam by a few thousand wavelengths. A real
engineering
CCP4 pdbset is very good for this. Find the symops in $CCP4/lib/data/symop.lib
and use symgen and chain commands to create each with a different chain ID.
The six-fold screw is generated by:
X,Y,Z
-Y,X-Y,2/3+Z
Y-X,-X,1/3+Z
-X,-Y,1/2+Z
Y,Y-X,1/6+Z
X-Y,X,5/6+Z
X,Y,1+Z
but the two-fold
WenHe,
I'm not sure if you want to superimpose a number of structures (as rmsd
would imply) or just compare two structures.
If you want a complete list of the distances between corresponding atoms
in two pdb files of identical sequence,
you can use the fortran program
Thanks, Ian!
I agree it may have to do with being used to computer graphics, where
x,y,z are fixed and the coordinates rotate. But it still doesn't make
sense:
If the axes rotate along with the molecule, in the catenated operators
of the polar angles, after the first two operators the z axis
Edward Berry
03/29/14 5:22 PM
Thanks, Ian!
I agree it may have to do with being used to computer graphics, where
x,y,z are fixed and the coordinates rotate. But it still doesn't make
sense:
-My mistake- in computer graphics x,y,z rotates with the atomic
coordinates relative to screen
I took a look at the first four lessons at the first link, and I think there
must be some mistake-
this site is actually teaching BASIC. All these commands are valid syntax under
say microsoft
GWBasic or QuickBasic. But I think this Zed Shaw has been studying shell
programming also and got
I think the important thing here is that liquid nitrogen in the lab
tends to be exactly at its boiling point, since the temperature is
maintained by continuously boiling off some of the N2.
This means the only mechanism for heat absorption is through vaporization,
depending on the latent heat of
David J. Schuller wrote:
...
even further back, file versioning in VMS might have been relevant and
useful. But I am wandering.
[:)
Problem is both files are version *.*;1.
I keep getting:
-RMS-E-FEX, file already exists, not superseded
%BACKUP-E-OPENOUT, error opening
Dale Tronrud wrote:
In summary, this argument depends on two assertions that you can
argue with me about:
1) When a parameter is being used to fit the signal it was designed
for, the resulting model develops predictive power and can lower
both the working and free R. When a signal is
Dale Tronrud wrote:
In summary, this argument depends on two assertions that you can
argue with me about:
1) When a parameter is being used to fit the signal it was designed
for, the resulting model develops predictive power and can lower
both the working and free R. When a
Dirk Kostrewa wrote:
Dear Ed,
although, I don't think that a comparison of refinement in a higher and
a lower symmetry space group is valid for general NCS cases, I will try
to answer your question. Here are my thoughts for two different cases:
(1) You have data to atomic resolution with
Frank von Delft wrote:
(I'm probably wrong, but I want someone to show me,and not with
hand-waving
arguments or invocation of crystallographic intuition or such)
To convince me, someone needs to show that the expected value of the
change
in |Fo-Fc| at a test reflection upon a change in the
to listen to anyone explain why I am wrong).
Ed
Edward Berry wrote:
Dean Madden wrote:
Hi Dirk,
I disagree with your final sentence. Even if you don't apply NCS
restraints/constraints during refinement, there is a serious risk of
NCS contaminating your Rfree. Consider the limiting case in which
Dean Madden wrote:
Hi Dirk,
I disagree with your final sentence. Even if you don't apply NCS
restraints/constraints during refinement, there is a serious risk of NCS
contaminating your Rfree. Consider the limiting case in which the
NCS is produced simply by working in an artificially low
reflections agree within R_Factor of each other, so about
20-30%. The experimental errors are pretty much negligible and
overfitting is not a question about error bars; it is about how hard to
push a round peg into a square hole?
Cheers,
Jon
Edward Berry wrote:
Actually the bottom lines below were my
to
believe Fc will move in the same direction, even in this artificial
case. So Dirk's assertion still stands, I believe.
Dean
Edward Berry wrote:
Actually the bottom lines below were my argument in the case
that you DO apply strict NCS (although the argument runs into
some questionable points
Sampath Natarajan wrote:
Dear all,
I solved a structure with four molecules in the assymetric unit which
form a dodecameric oligomeric structure in the biological process. I
need to create the symmetrical molecules to find out the cavity size of
the entire molecule. I tried in coot, but I
17, 2007 2:24 PM, Edward Berry [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED] wrote:
I think the correlation between occupancy and B-factor depends
also on the size of the ligand (relative to resolution).
Bob Stroud, I think, has estimated occupancy by comparing
the integrated
I think the correlation between occupancy and B-factor depends
also on the size of the ligand (relative to resolution).
Bob Stroud, I think, has estimated occupancy by comparing
the integrated electron density of the ligand with that of
a well-defined, isolated water (assumed to be at unit
In case you end up compiling your own list, here is one entry:
von Jagow and co-workers (Biochim Biophys Acta. 1977 462(3):549-58.)
used tritiated Triton X-100 to measure the binding to Complex III
5. In accordance with the high polarity the amount of bound
detergent is relatively low, it
This is not such a problem when using the old Map-cover command
in O, because the cut-offs are flat planes, you would get cubic
density around each atom which would raise the suspicion of even
the most gullible reader.
But a better solution would be to not contour the carved surface-
leave a
Das, Debanu wrote:
Hi,
There are at least 4 methods to try to estimate amount of detergent in a membrane protein crystal
.
In summary, someone wanting to estimate amount of detergent in their
crystals and have sufficiently large and numerous crystals, could try out
any of
contacts. This was the rationale behind Michel's use of small
amphiphiles to replace the bulky micelle, and antibody fragments to
bridge the gap and provide hydrophilic areas for contact.
Savvas
Quoting Edward Berry [EMAIL PROTECTED]:
I would use a very general definition for solvent,
including
I would use a very general definition for solvent,
including disordered detergent and lipids.
As you know in many cases ordered detergents and lipids
have been modeled in the coordinates, so they are part of
the model not the solvent. In some cases I think waters
should be included in the model
Someone should design a device like a compass gimbal with an extra ring
for teaching euler's angles, patent it (Gnu hardware license- world demand
is probably 100 pieces), and persuade Hampton research or MitEGen to
manufacture it.
The device (picture at (http://sb20.lbl.gov/berry/Euler2.gif),
Since Jie Liu is talking about coiled coils and heptad
repeat, I think what may be needed is the displacement
along the bundle axis. So an expression for the best
bundle axis line, and then the projection of different
C-a's onto that line to measure the difference between
them?
Ed
Eleanor Dodson
Procheck puts out such a correlation (% most favorable
vs resolution) in the _04.ps file. For example look at
page 7, first panel of the sample procheck output at:
http://sb20.lbl.gov/SQR/procheck-2H88.pdf
It appears that 83.5% would be well above average
for a 3 A structure according to procheck
[EMAIL PROTECTED] wrote:
Hello Mona,
I am guessing you have the atom name,number and coordinates in your file.
I did something like that and Openbabel will convert it to the pdb file
you desire but as far as I know, you will have to assign a residue name to
the atom yourself. I did this by
In those old chemical kinetics courses it was explicitly or
implicitly clear that [I] refers to I(free), not I(total).
The way assays are usually run, [E]K(I), so to a good
approximation the amount of bound ligand is negligible.
The way we set up crystallization, [E] is often mM
while K(I) is uM
Sorry, I didn't read the question.
sfcheck wouldn't calculate CC between exp and MR map.
Ed
Edward Berry wrote:
Also sfcheck calculates correlation coefficient for
main chain and side chain of each residue, presented
graphically in row 2 of the figure starting page 3
(example:
http://sb20
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