Rex Palmer wrote:
What seems to be a possible sulphate has been identified in our electron
density.
What steps could/should be taken to confirm or consolidate this assignment that
would satisfy referees?
Rex Palmer
Birkbeck College
If you place a sulphate and it refines in a sensible way
You can feed the SHELX sites into phaser_er or CRANK both of which will
give this sort of information.
Or mlphare if you know how to set it up..
Eleanor
Harmer, Nicholas wrote:
Dear CCP4ers,
I've been asked by a referee to provide the phasing statistics for a SAD
dataset that I used to
A thought - are these molecules related by a non-crystallographic
translation involving 0.5 along any axes. In such a case it is easy to
get the space group wrong, and assign a 1 axis when it is really only a
pseudo 21. if that happends your refinement will stick..
I think that at that
I thought truncate applied the scale but not the B value.
you can use CAD to apply a scale
- see the documentattion..
And yo can rerun truncate to check that you now have a fle with B =0, nd
scale = 1..
but why do you want to do that?
All refinement will rescale your output Fs to the
Hi -
A year or so ago, I have asked as a referee somebody to provide for a
paper the statistics for their heavy atom derivative dataset,
and for the phasing statistics. For some good reasons, they were
unable to do that, and they (politely) asked me
'what would it change if you knew these,
I fully agree, for high quality data.
What though if the data are not impeccable and the structure necessarily
ropey? E.g. 4A phases and anisotropic diffraction. By what metrics do
we then judge the results?
(I don't know the answer, btw, but our membranous colleagues surely
spend quite a
Hi Tassos,
my personal opinion is, that I would like to see the usual phasing
statistics. At least to me, they provide hints how well the structure
was determined, analogous to the R-factor/Free-R-factor providing hints
how well the structure was refined.
It would be good if SHELXE would
Hiya Frank
Well my take on it would be that they did a certain experiment - which includes
phasing datasets - and we have an expectation to see all the steps reported.
Good structures are not the 'be all' and 'end all'. Reporting data is not
merely to convince readers that this is not a 'made
With OCA your program/script can, for example,
- GET PDB ON-HOLD structures related to tuberculosis
http://oca.weizmann.ac.il/oca-bin/ocaids?hl=TUBERCULOSIS
- GET structures that contain ligand BTN and that belong to Author Freitag
As Tassos correctly says, the 'usual phasing statistics' are utterly
irrelevant to phasing a structure with SHELXE. SHELXC/D/E adopt a
minimalist approach, and input and calculate only what is needed to get a
map that is good enough to interpret. For example, in order to calculate
RCullis one
Dear ccp4 users,
I have found contadictory classifications in side-chain dihedral chi1,
namely for gauche(+) and gauche(-), and I would like to know the actual
convention.
It seems that in general for polymers G- (gauche(-) ?) and G+ (gauche(+)
?) correspond to dihedral angles -60 and +60
Please bring this position to the attention of anyone in your lab who might
be interested.
Thanks,
Kendall
The Scripps Research Institute
Palm Beach Co, Florida
Post-doctoral Position:
Nuclear Receptor Signaling and Structure-Based Drug Design
The Scripps Research Institute has established
Hi Dirk -
I am afraid I still don't agree and will try to defend my thesis a bit
further.
First, as eorge explained why in SHELXE these things are meaningless
anyway, so the answer to that referee is simple:
SHELXE that was used for calculating phase probabilities; that
precludes
Frank-
Are you referring to our colleagues personal qualities, or the projects
on which they work? :)
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Frank von Delft
(I don't know the answer, btw, but our membranous colleagues surely
Hi Tassos,
On Mon, Apr 12, 2010 at 04:10:57PM +0200, Anastassis Perrakis wrote:
As for Frank's argument, I fully agree low resolution cases are a
different ball game
(talking about ball games, I usually agree with Frank, he is much
bigger than me, and its healthier to agree with him,
Well, Frank, your membranous by their science (not very frequently)
colleagues will say - first of all look on the properly calculated electron
density maps first of all - good map will be manifested by continuity, shape,
accordance to the secondary structure elements etc.
For us/them
I like the ideal of calling SHARP 'vintage'. ;-)
Indeed, it gets better by the time, but at the same time i like having
a sip or two all the time, and not wait for it to really mature!
Maybe Gerard can hint if major releases of SHARP are always coinciding
with good years in the valley of
Dear all,
we recently purchased a couple of Zalman monitors. While on machines with an
NVIDIA Quadro FX580 (Debian Stable), installation was simply plug-and-play, one
machine with a NVIDIA Quadro FX1700 (Debian Testing) the sense of rotation by
dragging the mouse is inverted: while moving the
Please direct applications to the email address below.
Thanks,
Andrew
Protein Expression Scientist
Starting Salary: £22,100 to £37,100 depending on experience
The Beatson Institute Drug Discovery Programme will become established as an
Industry Standard Unit, exploiting world
Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download
Now! http://messenger.yahoo.com/download.php
Dear all
i'm trying to show ligand which is in the pdb of my protein as sticks, but it
is showing the folowing message in the pymol Tcl/Tk GUI.
You clicked /1204//X/TL1`0/C10
Selector: selection sele defined with 45 atoms.
but it not responding to that command.
can any one help..??
thank
Hussain,
You can do a couple things.
(1) At the PyMOL command line type:
as sticks, organic
(2) Create an organic selection using the mouse via the object menu, A
Generate Selection Organic. PyMOL makes a new selection for you (if
there is at least one organic small molecule). Then,
--- On Mon, 12/4/10, Jason Vertrees jason.vertr...@schrodinger.com wrote:
From: Jason Vertrees jason.vertr...@schrodinger.com
Subject: Re: [ccp4bb] How to show the ligand in my protein as sticks???
To: Hussain Bhukyagps hsn...@yahoo.com
Cc: CCP4BB@jiscmail.ac.uk
Date: Monday, 12 April,
Dear Jason Vertrees,
My ligand is a metal complex.
i followed the way u suggested to me, but still i'm not able to solve it.
it is working for spheres, dots, nb_spheres etc.. But not sticks and lines.
By the way i'm able to generate
thank U...
Send free SMS to your Friends on Mobile from
Hussain,
Spheres, dots, non-bonded spheres are for atoms. Sticks and lines show
bonds. This indicates that your metal isn't bound to anything. If you
like, feel free to send me the file or a snippet of it and I'll take a
look. PyMOL does have some weirdness when it comes to figuring out
Dear all,
I am getting protein crystals in clusters. How can I achieve isolated
crystals.
Thanks
Amit Sharma
One way to separate crystal cluster is to poke
them with a tiny probe, e.g. Hampton Research HR-217. Then scoop up a
single crystal or large fragment for screening/data collection.
Cheers.
On 4/12/2010 3:31 PM, Amit Sharma wrote:
Dear all,
I am getting protein crystals in clusters. How
Have you tried anything, yet? The list of answers can be quite long.
A couple of keywords:
- micro-seeding
- macro-seeding
- cross-seeding
- additive screens
- extend to purification protocol
- change temperature, pH, etc.
- have you search around the current conditions
...
if you describe a
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