On Mon, 2011-04-25 at 09:23 -0400, Michael Murphy wrote:
Hi All,
Does anyone know how to fix the default view mode in Coot, where
things disappear from your view when you zoom in on them?
Have you looked at this
http://www.biop.ox.ac.uk/coot/doc/coot.html#Clipping-Manipulation
--
Coot
On Wed, 2011-04-20 at 14:27 +0800, xinghua qin wrote:
But the protein sequence after partial proteolysis is from 52aa. what
should I do? Are there any reasonable expanation?
The protease cut your protein at position 52 sounds reasonable enough
to me
--
Hurry up before we all come back to our
On Tue, 2011-04-12 at 22:54 -0400, Edward A. Berry wrote:
What about doing the Fourier summation at the precise location
requested,
in order to not calculate the map or interpolate at all?
Input would be the mtz file rather than map file.
eab
One advantage of map interpolation is speed -
Dear Tim,
On Mon, 2011-04-11 at 10:44 +0200, Tim Gruene wrote:
since you pointed it out I wonder if there is any reasonable (i.e.
w.r.t. data
error/ resolution) difference between the interpolated values and the
calculated
value. I actually doubt that
That should depend on the quality of
On Fri, 2011-04-08 at 18:06 -0700, Pavel Afonine wrote:
phenix.map_value_at_point map_coeffs.mtz label=2FOFC point=1 2 3
point=4 5 6
Cool. Afaiu, this is interpolation. A useful extension would be
automatic picking of (x,y,z) from a pdb-file (a la mapman), although a
determined person can
. CHIMERA (Values at Atom Positions) (Eric Pettersen)
On Fri, 2011-04-01 at 11:16 -0400, Ed Pozharski wrote:
I need to calculate the electron density values for a list of spatial
locations (e.g. atom positions in a model) using an mtz-file that
already contains map coefficients. To write my
On Tue, 2011-04-05 at 13:05 +0800, dengzq1987 wrote:
I have a crystal that diffracts to about 4 A. in some direction the
spots overlap. we can't use the data to index .we think it is because
that there is a long unit cell axes. so is there any method to solve
this problem?
With denzo, a
On Sun, 2011-04-03 at 23:17 -0500, Jacob Keller wrote:
While the b cutoff is still be tricky, I assume we could eventually
come to consensus on some reasonable cutoff (2 sigma from the mean?)
Not likely - the distribution of ADPs is not normal, so you can't easily
convert Z-scores to
On Mon, 2011-04-04 at 09:38 -0500, Jacob Keller wrote:
Could it be that they are not normal because of all of the outlier,
huge-b-factor sidechains?
That is part of it
If every exposed sidechain without real
density gets a b-factor of 150, wouldn't that make a sizeable and
illegitimate
Oh, that is where those pesky inhibitors I couldn't find were
hiding...
On Thu, 2011-03-31 at 23:06 -0700, Ethan Merritt wrote:
Given recent discussion and in particular James Holton's suggestion
that
the problem of disordered sidechains is a problem akin to the
difficulty
of describing
I need to calculate the electron density values for a list of spatial
locations (e.g. atom positions in a model) using an mtz-file that
already contains map coefficients. To write my own code may be easier
than I think (if one can manipulate mtz columns, isn't the only problem
left how to
On Thu, 2011-03-31 at 17:04 +0200, herman.schreu...@sanofi-aventis.com
wrote:
Maybe we should really start using cif files, which allow to specify
coordinate uncertainties.
PDB has SIGATM record for that purpose
--
I'd jump in myself, if I weren't so good at whistling.
The results of the online survey on what to do with disordered side
chains (from total of 240 responses):
Delete the atoms 43%
Let refinement take care of it by inflating B-factors41%
Set occupancy to zero12%
Other
Following an annual (or so) resurrection of the What to do with
disordered side chains argument, this time at the phenix discussion
board, there is a survey set up at google docs to check what is the
consensus on the matter. If willing, please take a second to cast your
vote here:
On Mon, 2011-03-14 at 23:41 -0700, Careina Edgooms wrote:
So I am confused. What am I doing wrong? Please help me with
suggestions
Generally, it may be a good idea to post phaser log-file, etc. when
asking a question. You may be able to get more specific suggestions
then - otherwise, all one
On Tue, 2011-03-15 at 11:20 +, John Chipperfield wrote:
Therefore does anybody know of a quick way to build the remainder of a
residue around its alpha carbon, short of manually building in COOT
Google hit #4 with the keywords building protein from c-alpha trace
points to this
On Wed, 2011-03-09 at 14:14 +0100, Fabien Bergeret wrote:
I would be much grateful for any advice on peptide separation
methods?
How about gel filtration in denaturing conditions? If your protein is
his-tagged, nickel column will do too, again in denaturing conditions.
--
I'd jump in
Also, consider this
http://www.mail-archive.com/coot@jiscmail.ac.uk/msg02024.html
On Mon, 2011-03-07 at 23:57 +0530, Pranjal Mahanta wrote:
Hi,
I just installed CCP4-6.1.13 on my ubuntu (10.10) 64 -bit laptop. I
can run CCP4i successfully. But when i try to run coot, i get error :
No
On Tue, 2011-03-08 at 17:44 -0500, Cale Dakwar wrote:
Amongst other things, I want e.g. generate a histogram from this table
and determine e.g. the shortest HisND1 pair distance observed and the
structure in which this happens.
For this specific question this can be useful
On Fri, 2011-03-04 at 10:39 +, Hough, Michael A wrote:
Could anyone recommend a reasonably priced (i.e. less than £3000)
cooled incubator for crystallisation plates?
Consider wine coolers - many thermoelectric (vibration-free) models are
available. Normally they don't go down to 4 degrees
On Thu, 2011-03-03 at 14:13 +0800, Ting-Wei Jiang wrote:
I'm trying to calculate R-value (and free R) specifically which is
between data and the modified structure(refined by myself without help
from any program).
At long last, someone escaped the tyranny and oppression of the
refinement
On Thu, 2011-03-03 at 12:29 +0100, Roberto Battistutta wrote:
Does anyone know the origin or the theoretical basis of this I/sigmaI
3.0 rule for an appropriate resolution?
There is none. Did editor ask you to follow this suggestion? I
wonder if there is anyone among the subscribers of this bb
On Wed, 2011-03-02 at 19:23 -0500, David Roberts wrote:
What I am really looking for is an answer to a
simple question in that is stereo a nice thing from a pedagogy
standpoint for showing students complex biomolecules.
Of course it is. Exactly how much excitement it generates among the
On Thu, 2011-03-03 at 16:02 +0100, Vellieux Frederic wrote:
For myself, I decide on the high resolution cutoff by looking at the
Rsym vs resolution curve. The curve rises, and for all data sets I
have
processed (so far) there is a break in the curve and the curve shoots
up. To near
On Thu, 2011-03-03 at 08:08 -0700, Bart Hazes wrote:
I don't know what has caused this wave of high I/Sigma threshold use
but
here are some ideas
It may also be related to what I feel is recent revival of the
significance of the R-values in general. Lower resolution cutoffs in
this context
On Thu, 2011-03-03 at 09:34 -0600, Jim Pflugrath wrote:
As mentioned there is no I/sigmaI rule. Also you need to specify (and
correctly calculate) I/sigmaI and not I/sigmaI.
A review of similar articles in the same journal will show what is
typical
for the journal. I think you will find
http://www.ysbl.york.ac.uk/~alexei/molrep.html#stick
On Thu, 2011-02-17 at 19:32 +0100, Christian Roth wrote:
Dear all,
I tried MolRep with a two domain protein. I have cut the two domain as one
domain rotates which prevent a search with the complete model. After I
finished
the first
It was my understanding that Mitegen plastic capillaries only work for
crystal evaluation, since they are permeable enough to cause crystal to
dry up within few hours - hopefully that is enoug time to get a complete
dataset, but one should be concerned about changes in unit cell
parameters as
A quick PDB search reveals that 551 crystal structures were deposited in
2010 that were refined with CNS.
On Wed, 2011-02-16 at 13:32 +, REX PALMER wrote:
Does anyone still use CNS ?
Do we expect Rfree from CNS for example to be different from the value
given by Refmac at the end of the
In my experience, the success of molecular replacement depends primarily
on the quality of the model. Thus if your model is good, even P1 will
work. Two extreme cases that I encountered were searching with a
monomer for what turned out to be 4 tetramers (thus first search only
accounted for 1/16
---
pdbset xyzin foo.pdb xyzout foofoo.pdb eof
PICK N O CA C CB
eof
---
should do it
On Fri, 2011-02-11 at 18:03 -0500, crystallogrphy wrote:
Hi,
I am refining a low resolution data (4.7A). I want to cut off all side
chains from my model because they cannot be seen from the density.
measured
but have been added for completeness of the h k l list.
The check is whether the SigF is also 0.00 - in that case they are
genuinely missing..
Eleanor
On 02/09/2011 11:34 PM, Ed Pozharski wrote:
I observe under some conditions that ctruncate sets some reflections
amplitudes to zero
I observe under some conditions that ctruncate sets some reflections
amplitudes to zero. AFAIU, this should not be happening as even
negative intensities (there are none in this particular dataset) should
produce FP0 upon truncation.
66 out of ~23000 reflections are zeros after ctruncate is
Also try lower symmetry space groups. 36% solvent, while not unheard
of, is on a high end.
On Mon, 2011-02-07 at 02:49 -0800, Md. Munan Shaik wrote:
Dear all,
I have a question regarding the refinement and density map.
My protein is 261 amino acids long and crystalize very nicely with
Jonas,
scaling up may be tricky as the increased protein concentration affects
the elution profile. Personally, I tend to think that scaling up may
often be avoided by simply running the protocol that you have developed
several times. Maximum recommended loading capacity of a 1mL monoS is
25
Marcus,
it appears that coot breaks bonds when the distance between atoms
exceeds 1.64A pretty much irrespective of the bond type. Two exceptions
are, of course, sulfurs in MET/CYS. CB-SG bond in cysteine does not
seem to have any cutoff (when you do rotate/translate zone in coot, you
can move
At this resolution it is very much possible to choose a wrong space
group. So try lower symmetry first and see if it helps. Check for
twinning too.
On Sat, 2011-01-08 at 19:08 +, Dimitris Ladakis wrote:
Dear all
I've got a 3A dataset processed with mosflm and scaled. I've
runned MOLREP
On Sun, 2011-01-09 at 13:45 -0600, Kenneth A. Satyshur wrote:
So lets include them in all refinements, regardless of resolution. At
least we
will have given the community a model with the most correct biological
representation.
First of all, the fraction of structures in which the hydrogens
On Thu, 2011-01-06 at 11:30 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote:
how can I obtain a monomer library CIF (_lib.cif) of
a new small molecule that could be recognized by Refmac5?
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Servers_for_ligand_topologies/parameters
--
I'd
On Fri, 2010-12-31 at 17:00 -0600, Nian Huang wrote:
Is there a way that I can make it vertical?
But of course. Edit-Preferences-General-Refinement toolbar
There is also set-model-toolbar-docked-position function which you can
rapidly discover by searching coot manual
--
Coot verendus est
Guess I was too fast, sorry.
On Sat, 2011-01-01 at 20:09 -0500, Ed Pozharski wrote:
On Fri, 2010-12-31 at 17:00 -0600, Nian Huang wrote:
Is there a way that I can make it vertical?
But of course. Edit-Preferences-General-Refinement toolbar
There is also set-model-toolbar-docked-position
On Sun, 2010-12-19 at 18:58 -0500, Hailiang Zhang wrote:
(1). CTLS=a, CC=b
(2). CTLS=a, CC=0; followed by: CTLS=0, CC=b
In (2), you are doing two separate runs, with the second not using TLS.
If you want to combine TLS and positional refinement, you must have them
included in the same refmac
On Mon, 2010-12-20 at 13:11 -0500, Hailiang Zhang wrote:
Thanks Ian, but I was using the output from 2a for 2b running.
It's not enough to use the pdb output - you have to make the proper tls
input file for refmac to incorporate the tls correction
--
I'd jump in myself, if I weren't so good at
On Thu, 2010-12-16 at 03:53 +0100, Raspudin wrote:
I hope, am not mixing up different things together.
Perhaps you are. Map sharpening (iiuc) is done by applying
B-factor-like correction to amplitudes and has only, according to coot
manual, an educational value. Meaning that it's great if it
By all means 50 is OK. The low end B in the PDB is probably ~10,
whereas the high end is ~100
On Wed, 2010-12-15 at 10:24 -0800, Afshan Fayazi wrote:
Actually i have sioved my structure of the protein but the B factor
(temperature) overall is very high . it sis more than 50 so how can i
On Tue, 2010-12-14 at 08:02 +0100, Charles W. Carter, Jr wrote:
I've run aground trying to find a program to write out individual pdb files
from a long file with multiple (100) models. My file does not contain
separate chain IDs, so I cannot use moleman2 or splitpdb.p. I want to retain
You should have also gotten the .coeff file - try converting it to mtz
and using with coot.
On Tue, 2010-12-14 at 14:01 -0600, Julian Nomme wrote:
Hi all,
I can easily convert my composite omit map from cns to ccp4 format and
open it into coot.
However, how can I make coot use this map to
Jack (?),
On Thu, 2010-12-09 at 21:35 -0800, Jack Russel wrote:
So is it now the time to stop further refining the solution .
R-values are not the only criteria for this. You should be looking for
a) lack of unexplained density
b) good geometry
c) acceptable R-values
This
Assuming that your files are named something_.img what follows must
be one line):
echo | awk '{for(i=361;i721;i++) printf mv something_%d.img something_
%d.img\n,i+720,i;}' | bash -sf
I'd try first without piping it to bash just to make sure that it works
right.
On Fri, 2010-12-10 at 09:51
Ben,
does this assume that the current folder contains only the files to be
renamed? Also, how does one add padding zeros?
While Donghui didn't need zero padding, my one liner can be easily
corrected to do this in the same way Ian's is, by replacing
%d with %0nd, where n is the total number of
On Fri, 2010-12-10 at 19:32 +0100, Petr Kolenko wrote:
But now I have very low RMSDs. And then you read in this
forum quite often, that we should refine against the data and not
against the restraints. :)
Well, at 3.6A you must have low rmsds. And at 3.6A you don't really
have any data to
On Fri, 2010-12-10 at 22:40 +, Ian Tickle wrote:
Application of a symmetry operator to
a point on a special position which is unchanged by the operator
doesn't generate a symmetry copy of the point, because there is no
symmetry copy of such a point!
Why not? Symmetry-related copy may be
On Thu, 2010-12-09 at 01:09 +0900, Keitaro Yamashita wrote:
When I tried to refine using Refmac5, the output told many vdw
repulsions with symmetry mates
What do you mean by that? I had a similar situation recently, and there
are many records in the log file that say something like this
refmac5 to ignore.
K. Yamashita
2010/12/9 Ed Pozharski epozh...@umaryland.edu:
On Thu, 2010-12-09 at 01:09 +0900, Keitaro Yamashita wrote:
When I tried to refine using Refmac5, the output told many vdw
repulsions with symmetry mates
What do you mean by that? I had a similar
If it's on a glass coverslip, another good trick is to (carefully) cut
through the skin around the crystal with a razor blade. With some
practice, one manages not to get the crystal entangled in the skin.
On Thu, 2010-11-25 at 16:03 +, Frederic VELLIEUX wrote:
Hi,
In our hands, the
On Wed, 2010-11-24 at 09:54 -0800, Huiying Li wrote:
I have two structures of the same protein superposed with the LSQ
Superpose in Coot by matching the first ~100 residues of the
N-terminal
domain. Now I'd like to calculate the pair-wise RMSD for the entire
pre-superposed structures
Not sure if all the sirs will concur (and it might be a good idea to ask
madams also), but the answer is probably no. As far as protonation
state goes (guess that is what you are after, not oxidation), a better
strategy may be to look into the bond lengths between the appropriate
heavy atoms that
model_phase.inp
On Wed, 2010-11-10 at 21:31 -0800, Matt Colins wrote:
Hi,
I am trying to calculate phases and FOM from a model map. However, CNS 1.2
model_map.inp does not output map phases and FOM. Instead, it only gives map
coefficients. My question is how to convert these map
You need to define the environmental variable PYMOL_PATH first, which
for example in Ubuntu with pymol installed from repositories should
point at /usr/lib/pymodules/python2.6/pymol. Try this from python
prompt to verify
from imp import find_module
print find_module('pymol')[1]
You may also
I am trying to read Bruker's Smart 6000 images with mosflm and it fails.
Based on some limited googlearch I feel that NPIXELB:1 is a relevant
information and when these files were processed in HKL (not by me), the
relevant detector line says format ccd bruker smart6000 binned. I see
from mosflm
That depends on what you are trying to do. Maybe the best strategy is
to use fuzzy logic, whereby a residue which has 30% of it's Gly-X-Gly
ASA buried has the surfaceness of 0.7.
On Wed, 2010-11-03 at 09:55 -0400, Buz Barstow wrote:
Dear All,
Thanks for your suggestions! I ended up using
ctruncate outputs the table with Mn(F/sd) (which will be twice Mn(I/sd))
when it does anisotropy analysis
On Mon, 2010-11-01 at 15:18 -0500, Radisky, Evette S., Ph.D. wrote:
Dear all,
I have previously used SCALA for data reduction, and in publications
and pdb depositions, reported the
-39-22582
On Wed, 27 Oct 2010, Ed Pozharski wrote:
On Tue, 2010-10-26 at 21:16 +0100, Frank von Delft wrote:
the errors in our measurements apparently have no
bearing whatsoever on the errors in our models
This would mean there is no point trying to get better crystals, right
On Tue, 2010-10-26 at 21:16 +0100, Frank von Delft wrote:
the errors in our measurements apparently have no
bearing whatsoever on the errors in our models
This would mean there is no point trying to get better crystals, right?
Or am I also wrong to assume that the dataset with higher I/sigma
One can also release structure in the PDB prior to submission - I
believe the HPUB option is rarely (if ever) justified.
Ed.
On Wed, 2010-10-27 at 22:56 +0200, VAN RAAIJ , MARK JOHAN wrote:
perhaps we should campaign for it to be obligatory to provide the pdb
and structure factor file to the
Jackie,
please note that (at least imho) the desire to obtain better R-factors
does not justify excluding data from analysis. Weak reflections that
you suggest should be rejected contain information, and excluding them
will indeed artificially lower the R-factors while reducing the accuracy
of
I must note that it is also interesting to know why the sfcheck produced
the R-factor that is twice as high. Of course, the R/Rfree are not
supposed to match precisely (as I recall, sfcheck uses Babinet bulk
solvent correction which is presumably inferior to the mask-based
approach), but 28.6
Ethan pointed out to me that Babinet-principle based solvent correction
is not always inferior to mask-based approach. My belief was based on
some old observations which were in fact made prior to mask
implementation in refmac and thus not exactly side-by-side comparisons.
I hereby recant my
There is nothing fundamentally wrong with refining in P1 even if the
P21212 symmetry is present. An effective way to reduce the number of
parameters wold be to introduce tight restraints. If you decide to
lower the symmetry, go with P21 as it still keeps your ligand off
symmetry axes. You can
Because refining in the (right) higher symmetry space group leads to a
better model.
On Thu, 2010-10-21 at 11:34 -0500, Jacob Keller wrote:
I have heard many times that it is a black eye to refine in a
lower-symmetry spacegroup, but I could never really understand why.
The higher symmetry
On Thu, 2010-10-21 at 12:58 -0500, Jacob Keller wrote:
On the other hand, if somehow a few sidechains became systematically
different between molecules in the p1 cell, it *would* make sense to
refine
in p1
And sometimes (but rarely) such differences become detectable at high
resolution
On Thu, 2010-10-21 at 18:59 +0100, Clemens Vonrhein wrote:
I think I understand what you're getting at: you have a lower symmetry
with a NCS axis that is basically perfectly aligned with the
corresponding crystallographic axis in the higher symmetry
spacegroup. And the only part of the model
(type 0 means
dictionary values will be overwritten and type 2 is external restraints for
non-covalent bonds)
I hope it helps
regards
Garib
On 14 Oct 2010, at 21:51, Ed Pozharski wrote:
It appears that external restraints are included in bond_rmsd
calculation. When
Thanks, Ian, this is excellent. It appears that depending on the
sequence the ideal target rmsd may vary from 0.018 for a poly-H to
0.024 for a poly-P. Except for some really short sequences, in PDB the
variation is generally between 0.021-0.022, indeed undetectable.
On Fri, 2010-10-15 at 10:26
To upgrade the Refmac version that I am running from inside the CCP4i, I
did the following
mv $CCP4/bin/refmac5 $CCP4/bin/refmac5.5
cp refmacgfortran $CCP4/bin/refmac5.6
ln -s $CCP4/bin/refmac5.6 $CCP4/bin/refmac5
It seems to have worked fine. Is there more intelligent way of doing
this?
--
A couple of twinning-related questions.
I have a protein-DNA complex in P65. Protein binds DNA as a dimer, DNA
itself is not palindromic and has sticky ends located asymmetrically
with respect to the protein (dimer).
DNA contains a single fluoro-uracil which is flipped into the active
site.
The definition game is on! :)
Vectors are supposed to have direction and amplitude, unlike scalars.
Curiously, one can take a position that real numbers are vectors too, if
you consider negative and positive numbers having opposite directions
(and thus subtraction is simply a case of addition of
On Thu, 2010-10-14 at 08:41 +0200, Tim Gruene wrote:
This sounds as though you are saying that a single photon interacts
with several
electrons to give rise to a reflection.
Not only with several - it shouldn't be much of an exaggeration to say
that the photon senses all the electrons in the
into the new one by using exactly
the same operator. This is the correct definition of a vector.
G.
On Thu, 14 Oct 2010 10:22:59 -0400, Ed Pozharski
epozh...@umaryland.edu wrote:
The definition game is on! :)
Vectors are supposed to have direction and amplitude, unlike scalars
On Thu, 2010-10-14 at 09:11 -0700, James Holton wrote:
I wonder if anyone on this
thread can explain to me the difference between a matrix and a
tensor?
Matrix is a 2nd order tensor. Tensors may have any number of
dimensions, including zero. Tensor is just a fancy name for a
It appears that external restraints are included in bond_rmsd
calculation. When they are used to restrain the hydrogen bonds to
maintain the Watson-Crick pairing in a 3A resolution structure of a
protein-DNA complex, the bond_rmsd is inflated about 5 times. To verify
this, the refmac run was
On Thu, 2010-10-14 at 23:31 +0200, Tim Gruene wrote:
you observe that each photon decides on exactly one slit
that it goes through.
That is if you observe which slit it goes through.
--
I'd jump in myself, if I weren't so good at whistling.
Julian, King of
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
You don't need twinning to invalidate the Rmerge as a criterion for the
resolution cutoff, there are other reasons why you should use I/sigma
instead. If you process data all the way to 3A, what's the I/sigma in
the highest resolution shell?
On Wed, 2010-10-06 at 11:28 +0200, fulvio saccoccia
It's best to have dedicated NVIDIA (don't have much experience with ATI,
but it is my understanding that they may be more difficult to configire
sometimes). However, Intel on-board graphics has gotten much better
recently (in fact, Intel releases drivers as open source (guess because
they are not
On Wed, 2010-09-15 at 07:57 -0700, Pavel Afonine wrote:
if you refined your structure with H, then you should deposit it with
H
sure. But the structure is not *refined with hydrogens* when they are
in predicted positions. Following the same logic one could suggest that
electron density
On Wed, 2010-09-15 at 09:14 -0700, Dale Tronrud wrote:
I know that in my refinements I manually move the hydrogen
from one nitrogen to the other in a couple Histidine side chains,
and have created my own rules for hydrogen generation in co-factors.
Excellent point. And I believe in this
On Wed, 2010-09-15 at 10:50 -0700, Pavel Afonine wrote:
I wouldn't dare calling a model manipulation that typically changes
the
R-factor by 0.5 ... ~2% as nothing. Although, you are may be right
-
who cares?
It's not a manipulation because no parameters were manipulated in the
model.
On Wed, 2010-09-15 at 13:13 -0700, Pavel Afonine wrote:
I can't agree with this, sorry. A change to a model content
(especially
the one that changes Fcalc) is a model manipulation.
That is not what I asked. Do you agree that using the riding model does
not add additional refinable
On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote:
So the riding hydrogen model is imperfect. At least with
phenix.refine
you can measure it, unlike the default behavior of REFMAC. (But you
can
tell it to write hydrogens out, I believe).
My impression is that default behavior of
Sure. But if I start with model that has no hydrogens, they will be
generated but not passed to the output, right. just like refmac.
On Wed, 2010-09-15 at 14:52 -0700, Pavel Afonine wrote:
Dear Ed,
On 9/15/10 2:47 PM, Ed Pozharski wrote:
On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey
Mark,
On Tue, 2010-09-14 at 13:34 -0400, Dr. Mark Mayer wrote:
Where does the crystallographic community stand
on deposition of coordinates with riding
hydrogens?
Surely community is divided on this. There could be arguments made both
ways. Personally, I think that riding hydrogens can be
On Mon, 2010-09-13 at 15:52 +0100, Paul Holland wrote:
that has very high sequence similarity to the search model
How high exactly?
--
I'd jump in myself, if I weren't so good at whistling.
Julian, King of Lemurs
David is absolutely right. There is no design, Jacob, we just
instinctively look for it everywhere because seeking purpose instead of
understanding mechanism conveys advantage to our species. Your
rationale is flawed - just because it is imaginable (with caveats) does
not mean that it must exist
Ian is, as always, absolutely right. The only comment/correction I have
is that Hailang was apparently referring to severely incomplete model,
for which the poor phases will dominate the mFo map. Under such
circumstances, even 2fo-fc map will not correctly reflect the actual
relative
the maximum likelihood estimate of the best approximation
of the true map in the following form
DFc + k*(mFo-DFc)
Ed.
On Wed, 2010-09-01 at 10:49 +0100, Ian Tickle wrote:
On Wed, Sep 1, 2010 at 4:26 AM, Ed Pozharski epozh...@umaryland.edu wrote:
The
reason you see the missing region in (2mFo-DFc
Unfortunately, some crystals don't diffract at all. You may want to try
to 100% verify that it's protein either by SDS-PAGE or mass-spec
(100x100x100 micron crystal could contain ~0.5mcg of protein, so you my
need to use silver staining). If it is, I'd consider trying to get
diffracting crystals
Well said. I've seen three cases by now when switching to a homologue
from a different organism led to solving a structure (and way too many
cases when crystals just did not diffract, either at all or well
enough :).
On Tue, 2010-08-31 at 18:48 +0300, Tommi Kajander wrote:
Or might be worth
On Tue, 2010-08-31 at 11:57 -0500, Jacob Keller wrote:
I just don't want this guy to get misled into perhaps wasting
months/years on something not particularly promising.
Trouble is, of course, that one never knows if a particular trick will
work this time. We routinely get PEG/fluoride salt
On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote:
Is the difference
between mFo and Fo maps supposed to be very small?
For an essentially correct model, yes. The major advantage of (2mFo-DFc)
maps is suppression of model bias, so if you don't see much difference
then your model is very
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