Try the program DIBER to evaluate the likelihood your crystal contained ordered
nucleic acid in addition to protein. See Acta Cryst. (2010). D66, 643-653
“DIBER: protein, DNA, or both?” by G. Chojnowski & M. Bochtler.
Good luck, Pete
From: CCP4 bulletin
Does anyone have the dictionary file for BrU, as in the brominated
ribonucleotide?
The distributed files include the deoxy version,
5-bromo-2'-deoxyuridine-5'-monophosphate.
Best wishes, Pete
Frank,
Don't you already get a plot of SigmaA versus resolution from refmac,
where the free set of reflections has been used to estimate SigmaA?
Have a look at some of your log files.
Pete
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Fra
I like the species icon for 2cbr, human crabp in your list
http://xray.bmc.uu.se/gerard/structures_pdbprints.html.
Is it something from Greek mythology?
From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Gerard DVD
Kleywegt [ger...@xray.bmc.uu.
Regarding backsoaking [2],
This is one of those nice exercises for the reader!
Try raddose calculations with versus without 1 mM heavy-atom compound
in the solvent channels.
Pete
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Francis E
Reyes
Se
If you publish the paper a year from now, with no hold,
will everyone be happy?
-Original Message-
From: CCP4 bulletin board on behalf of [EMAIL PROTECTED]
Sent: Fri 2/16/2007 6:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] journals with on-hold policy
Dear CCP4ers,
This is a new qu
And just to be complete . . .
Solve will calculate data with the anomalous component for you,
although you can't stop it from adding some "experimental" error.
Phenix.refine is another option.
Pete
A few thoughts following on Richard Baxter and George Sheldrick . . .
Re: gaps in the lattice see the tyr-tRNA synthase structures (1tya for
example). Fersht has written a whole book full of insights from these
structures.
Re: Phaser Z scores. For some MR work with two xtal forms of a str
Here's one - FOM > 0.5 after shelxe, SAD phases, not traceable
Lots of weak data, as truncate shows . . .
Analysis of mean intensity by parity for reflection classes
For each class, Mn(I/sig(I)) is given for even and odd parity with respect to
the condition,
eg group 1: h even & odd; group
And how will you know if they are the calcium citrate xtals Sam asked about,
and not
sodium citrate xtals? Sodium citrate in the Hampton Crystal Screen condition
will
crystallize out at 4 degrees. It's solubiility is pH and temperature dependent.
You'll need to go to your friendly neighborhood
Is this just a consequence of old/new conventions for the SEQRES records?
If so, send a feature request to ccp4, asking for an option to be added to
pdbset.
Pete
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ed Pozharski
Sent: Thursday, July 10, 200
Look at the "reject fraction" keyword and increase the value,
as described on pp 39-40 of the manual
Pete
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mona Rahman
Sent: Tuesday, July 15, 2008 7:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb
May be old fashioned, but what about cut with ClaI, fill in,
and then you have a blunt end to work with.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Artem Evdokimov
Sent: Sunday, July 20, 2008 12:02 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb]
Bill, You still lose a point for missing
the fourth pKa in ammonium citrate, the
ammonium ion.
Kind regards, Pete
-Original Message-
From: CCP4 bulletin board on behalf of William G. Scott
Sent: Sat 8/9/2008 12:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ammonium citrate triba
I hadn't realized phenix.refine handles this differently.
If I start with an mtz file from truncate, with F, SIGF, IMEAN, SIGIMEAN all
available,
the default for phenix.refine seems to be to work with IMEAN, SIGIMEAN.
>From the log file . . .
Intensities converted to amplitudes for use in refi
I mentioned previously phenix.refine tosses your weak data if IMEAN, SIGIMEAN
are chosen during refinement.
I'm wondering if this omission of weak Fobs from the Fobs-Fcalc difference map
explains why the difference maps out of refmac seem to be more helpful in
showing where to move atoms.
Hi Eleanor,
Are you sure about the application of twinning tests to look for
lattice-translocation defects? In twins the intensities sum, but in
lattice translocation cases, the domains can be so small that you can't
simply sum intensities . . . at least that's how I interpret
http://www.am
But see Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):227-38. Epub
2006 Feb 22.
on why thin shells aren't necessarily the answer.
And note neither program mentioned, dataman nor sftools, will allow you to
extend the set
of shells to higher resolution if you want to follow the practice o
18 matches
Mail list logo
