Re: [ccp4bb] solvent mask with refmac

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: solvent mask with refmac
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-06-02

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Subject: Re: solvent mask with refmac
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-06-02

Sorry found it:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1853337

... and it's Brian Matthews not Mathews.

-- Ian

> -----Original Message-----
> From: owner-ccp4bb@jiscmail.ac.uk [mailto:owner-ccp4bb@jiscmail.ac.uk]
On
> Behalf Of Ian Tickle
> Sent: 02 June 2009 10:35
> To: Ana-Maria Goncalves
> Cc: Dirk Kostrewa; CCP4BB
> Subject: RE: [ccp4bb] solvent mask with refmac
>
> The other possibility of course is that the data is good, that this is
> an accurate experimental result and there really is a void, or at
least
> a cavity where the mean bulk density is lower than in bulk water. One
> way to test the void theory would be to fill the cavity with O atoms
of
> zero (or very small, say 0.01) occupancy. Hopefully (!) that will
> prevent Refmac filling the cavity with bulk solvent. One could then
try
> giving these O atoms large B factors, say 200, to smear them out, and
> then increase the occupancies to titrate the actual bulk density.
>
> There was a paper by Brian Mathews group (sorry I don't have the
> reference) on a high pressure form of lysozyme where they found a
large
> hydrophobic void (I think sufficient to contain something like 5
> waters). Bulk water could only be compelled to enter the void by
> application of very high external pressure.
>
> Interesting!
>
> Cheers
>
> -- Ian
>
> > -----Original Message-----
> > From: owner-ccp4bb@jiscmail.ac.uk
[mailto:owner-ccp4bb@jiscmail.ac.uk]
> On
> > Behalf Of Dirk Kostrewa
> > Sent: 02 June 2009 10:13
> > To: CCP4BB
> > Subject: Re: [ccp4bb] solvent mask with refmac
> >
> > Dear Ana-Maria,
> >
> > in my experience, mask bulk solvent artifacts can only occur at
narrow
> > channels, where the mask radius is too big to define the channel as
> > belonging to the bulk solvent region, leaving it "empty" and thus
> > resulting in positive (!) difference density. Changing from simple
> scaling
> > to Babinet scaling is an important check to exclude mask bulk
solvent
> > artifacts, but there, you have to uncheck the "calculate
contribution
> from
> > the solvent region", because this is done by the Babinet scaling,
> already.
> > However, in your case, you have negative difference density in a, as
> you
> > say, big cavity. This will be certainly filled with bulk solvent
> density.
> > One possible reason for a negative difference density are
> underestimated
> > magnitudes of
Fobs
at very low resolution, either because they are
> > weakened by the beam-stop (half-)shadow, or because they are
overloads
> > that have been poorly extrapolated. A simple check for wrongly
> determined
> > low-resolution
Fobs
is to cut your low resolution data during
> refinement
> > at a somewhat higher resolution, say 20 A instead of 80 A, and see
> whether
> > the negative difference density disappears. If, yes, you should
check
> your
> > data processing again.
> >
> > Best regards,
> >
> > Dirk.
> >
> > Am 02.06.2009 um 10:43 schrieb Ana-Maria Goncalves:
> >
> >
> > Dear BB,
> >
> > I'm refining a structure which presents a big hydrophobic cavity
> > where a strong residual difference negative density can be seen. I
> presume
> > that this is an effect of not having a proper solvent mask
determined
> and
> > I was wondering if there is a way to provide a better mask
description
> to
> > REFMAC. The resolution of the data is 1.6 A and I have already tried
> > changing from simple to Babinet scaling, without any improvement.
Any
> > advice/suggestion would be very welcome.
> >
> > Many thanks,
> > Ana-Maria
> >
> >
> >
> > --
> > Ana-Maria Goncalves
> > Macromolecular Crystallography Group
> > European Synchrotron Radiation Facility
> > B.P. 220, 6 rue Jules Horowitz
> > F-38043 GRENOBLE CEDEX
> > FRANCE
> >
> > Tel: +33 (0) 4.76.88.19.12
> > Fax: +33 (0) 4.76.88.29.04
> >
> >
> >
> >
> > *******************************************************
> > Dirk Kostrewa
> > Gene Center, A 5.07
> > Ludwig-Maximilians-University
> > Feodor-Lynen-Str. 25
> > 81377 Munich
> > Germany
> > Phone: +49-89-2180-76845
> > Fax: +49-89-2180-76999
> > E-mail: kostrewa@lmb.uni-muenchen.de
> > *******************************************************
> >
>
>
>
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Disclaimer
This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing I.Tickle@astex-therapeutics.com and destroy all copies of the message and any attached documents.
Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: solvent mask with refmac
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2009-06-02

Next message:
Subject: postdoc position available
From: Peijun Zhang pzhang {- at -} STRUCTBIO {- dot -} PITT {- dot -} EDU
Date: 2009-06-02