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,
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
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)-Fo(apo) cannot be done
...@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 dioxygenases
because
Andy,
One important thing if your complex crystals are isomorphous with apo is to
use nFo(complex) - Fo(apo). These maps give the maximum information as the
uninterpretable 'stuff' in the Fo-Fc map is likely quite similar in both
crystal forms so the difference signal should be cleaner.
Douglas
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
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
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: [ccp4bb] Difference Map images
Andy
:
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 you have
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
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 phaser to
What's the resolution? At low res it is possible to miss a subtle movement
of e.g. some sidechains which are being replaced by the ligand. What quality
parameters did the MR have? Can you omit the entire ligand binding site,
refine, and re-generate the map - what does it look like after that?
A
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
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
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