That seems the right procedure.
I presume the two crystals have similar cell, etc?
What is the Riso plot from scaleit look like - if it is 55% + then there
is no isomorphism, but if it is < 30% then the map should be reasonable.
which phase did you use for the map calculation?
Eleanor
intekh
Hi Intekhab Alam,
an Fobs-Fobs' map usually works only if the two crystals are
isomorphous, which means that there are neither large cell constant
changes nor any other larger structural changes (like overall rotations,
domain movements, other rearrangements) than the bound compound (ligand,
Hi Folks
I have a query regarding the difference map between the two structures
ligand bound data (2.5A) and native (2.8A).
I tried to calculate the fourier difference map between two data sets ligand
bound- native.
The protocol in CCP4 that i used is as:
1.merge the mtz file of native nad ligand b
in board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim
Gruene
Sent: Wednesday, June 17, 2009 4:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Difference Map images
I know that sometimes Fo(complex)-Fo(apo) cannot be done because of
nonisomorphism. We've had a lot of success with this with the d
map (from
first F's) is cleaner.
Doug
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim
Gruene
Sent: Wednesday, June 17, 2009 4:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Difference Map images
> I know that sometimes Fo(complex)
I know that sometimes Fo(complex)-Fo(apo) cannot be done because of
nonisomorphism. We've had a lot of success with this with the dioxygenases
because there is no large scale alteration in the active site. As for the
technique itself, Brian Matthews drilled this into me when I was a postdoc
in his
a
Lab web site:
http://biosci.cbs.umn.edu/bmbb/ohlen_lab/index.html
-Original Message-
From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com]
Sent: Wednesday, June 17, 2009 12:08 PM
To: Doug Ohlendorf
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] Difference Map images
Hi Douglas
Do
te the beam to
reduce radiation damage to an acceptable level.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Doug Ohlendorf
> Sent: 17 June 2009 16:41
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: RE
Wow, you can read too! Impressive.
Indeed, it seems Larson et al did use Pymol, as have I. The question
to the board was what they use, so that I might experiment with other
methods.
Any other helpful suggestions, please don't hesitate Jon.
Thanks to all for their responses.
A
2009/6/17 Jo
Andy,
on the practical point of view, you can create such images using Pymol
and the command 'carve'.
load composite_omit-ccp4.map, map-to-display, format=ccp4
isomesh mesh, map-to-display, 1.5, resi 45, carve=3
color blue, mesh
this will display the map at 1.5 sigma, at 3 angstroms around the
r
s.umn.edu/bmbb/ohlen_lab/index.html
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of ANDY
DODDS
Sent: Wednesday, June 17, 2009 8:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Difference Map images
Hello,
I was wondering what people used to generate
There seems to be a clue in the text?
"Models were displayed and figures were produced with PyMOL (Delano,
2002)", which you can read at the end of section 2 "Materials and Methods".
ANDY DODDS wrote:
Hello,
I was wondering what people used to generate difference map images of,
say, a ligan
Dear Andy,
before answering your question, I dare say that since the rise
of sigma-A-weighted maps, simple Fo-Fc or 2Fo-Fc maps are deprecated and
one ought to use the appropriate sigma-A-weighted map instead.
Refmac5 produces data columns required both for sigma-A-weighted data
columns and a
Hello,
I was wondering what people used to generate difference map images of,
say, a ligand in their structures?
e.g. Figure 2a here
http://journals.iucr.org/f/issues/2009/05/00/tt5012/tt5012.pdf
Cheers,
Andy
On Fri, 28 Dec 2007 15:55:39 +
Brenda Patterson <[EMAIL PROTECTED]> wrote:
Hello,
I am fairly new to this lark
No problem. With a name like Patterson, your future is guaranteed (unless of
course you see everything in the world with intensity but no phase).
I have a d
There is another possibility that your ligand is not fully occupied,
if the binding site of protein endures an apparent change when bound
by ligand. Lijun
On Dec 28, 2007, at 7:55 AM, Brenda Patterson wrote:
Hello,
I am fairly new to this lark so please forgive me if this question
is un
t?
A picture would help!
Artem
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Brenda
Patterson
Sent: Friday, December 28, 2007 10:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Difference Map in COOT - Possible lignad but clash with
structure?
Hell
Covalent modification?? Bias in 2fo-fc map?
Can you show us a pic of offending density?
Dave
On 28/12/2007, Brenda Patterson <[EMAIL PROTECTED]> wrote:
>
> Hello,
>
> I am fairly new to this lark so please forgive me if this question is
> unclear,
> but it is really puzzling me.
>
> I have used
Hello,
I am fairly new to this lark so please forgive me if this question is unclear,
but it is really puzzling me.
I have used phaser to generate a molecular replacement structure of my target
(which has 100% identity to my template) and this particular crystal I had
soaked with a ligand.
I ha
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