Modification of Eleanor's suggestion-
It is fairly trivial to write a program (e.g.
https://www.cytbc1.com/berry/for/pdbdist3w.for) which;
reads coordinates from one pdb file into memory
reads a second pdb file, and for each atom/hetatm
checks whether it is within threshold distance of th
I think you are right, in the final equilibrium all the moisture would condense
on the (evaporator?) coils, and there should be provision for them to drip into
a reservoir outside. However each time the door opens and humid air is
admitted, there will be condensation everywhere. If you leave th
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 expense
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 measur
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 you
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 XXX
>>> 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 fro
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 distribu
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 defines
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
http://www.cytbc1.net/berry/fo
>>> 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
coordin
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 would
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 mix
>>> Jacob Keller 10/13/10 2:50 PM >>>
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 any
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 DISK$USER1:[00.AC
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 per
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
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 hig
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 m
Dirk Kostrewa wrote:
Dear Dean and others,
Peter Zwart gave me a similar reply. This is very interesting
discussion, and I would like to have a somewhat closer look to this to
maybe make things a little bit clearer (please, excuse the general
explanations - this might be interesting for begin
are asymmetric and there is no reason 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 a
"R_merge" percent, eg; about 2-5% . Observed and
calculated 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 in
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 limitin
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
If the structures are from not-perfectly-isomorphous crystals
or different ncs-related molecules in the same crystal,
you want to do this in two steps:
First find an operator that superposes one domain, and move a
copy of the structure to that position. Then find the operator
taking the second dom
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 wa
void checking those interactions, but I
think
at one point we were turning off the NBONDS messages but not the vdw
interaction,
so there may be two separate things needed here. I would be glad for any
clarification.
Ed
On Dec 17, 2007 2:24 PM, Edward Berry <[EMAIL PROTECTED]
<mailto:
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 occuanc
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 amo
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 ga
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 t
molecules apart and preventing real crystal
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]&g
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
We've grown crystals of the cytochrome bc1 complex in the
presence of glycerol.
I think as high as 25% in the initial droplet (protein in 50%
glycerol mixed with equal volume of precipitant),
but that was diluted somewhat by reverse vapor diffusion.
Glycerol tends to increase the solubility in ou
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),
bu
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 super
Oh- let me try!!
Given two structures each containing the domains A and B,
the angle in question is the further angle through which
domain B of the second structure must be rotated to
superimpose it on domain B of the first structure,
after structure 2 has already been rotated to optimally
superp
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]<
think about your old chemical kinetics courses.
what counts is concentration and not amount.
M
Dear Marius and others,
here I would like t
What about giving the correctly positioned partial solution,
and fixed angles/translation of 0,0,0,0,0,0 for that part?
Jay Thompson wrote:
Hi,
I have a question with molecular replacement using Phaser. I'm trying
to solve a complex and I have a partial molecular replacement solution
solved
Bart Hazes wrote:
I must admit that I've never understood the rationale for including dFc
for missing terms, although it has been discussed "lively" on a few
occassions. Yes, dFc is a better estimate for the true structure factor
than leaving out the term (equivalent to setting the amplitude
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:
h
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.lbl.gov/cytbc1/sfcheck-1ppj.pdf ).
I suspect there is also a log file with the numeric
values.
Ed
Charles W. Carter Jr
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