Re: [ccp4bb] Archiving Images for PDB Depositions

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: Archiving Images for PDB Depositions
From: James Holton jmholton {- at -} LBL {- dot -} GOV
Date: 2011-11-03

Next message:
Subject: Re: Archiving Images for PDB Depositions
From: Bryan Lepore bryanlepore {- at -} GMAIL {- dot -} COM
Date: 2011-11-03

Subject: Re: Archiving Images for PDB Depositions
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2011-11-03

Hi James,

scary ... I was just looking at exactly the same thing (P21 with
beta~90), using the same tool (POINTLESS).

Currently I'm going through the structures for which images can be
found ... I haven't gone far through that list yet (in fact actually
only the first one), but this first case should indeed be in a higher
spacegroup (P 2 21 21).

As you say (and that's what Graeme looks for): finding 'over-merged'
datasets can be a bit more tricky ... once the damage is done. I have
the hunch that it might happen even more often though: we tend to
look for the highest symmetry that still gives a good indexing score,
right? Otherwise we would all go for P1 ...

Some other interesting groups for under-merging:

* orthorhombic with a==b or a==c or b==c (maybe tetragonal?)

* trigonal (P 3 etc) when it should be P 6

* monoclinic with beta==120

A few cases for each of those too ... all easy to check in
ftp://ftp.wwpdb.org/pub/pdb/derived_data/index/crystal.idx and then
(if structure factors are deposited) running POINTLESS on it (great
program Phil!).

Cheers

Clemens

On Thu, Nov 03, 2011 at 12:00:33PM -0700, James Holton wrote:
> I tried looking for such "evil symmetry problem" examples some time
> ago, only to find that primitive monoclinic with a 90-degree beta
> angle is much more rare than one might think by looking at the PDB.
> About 1/3 of them are in the wrong space group.
>
> Indeed, there are at least 366 PDB entries that claim "P2-ish", but
> POINTLESS thinks the space group of the deposited data is higher
> (PG222, C2, P6, etc.). Now, POINTLESS can be fooled by twinned
> data, but at least 286 of these entries do not mention twinning. Of
> these, 40 explicitly list NCS operators (not sure if the others used
> NCS?), and 35 of those were both solved by molecular replacement an
> explicitly say the free-R set was picked at random. These are:
>
> Now, I'm sure there is an explanation for each and every one of
> these. But in the hands of a novice, such cases could easily result
> in a completely wrong structure giving a perfectly reasonable Rfree.
> This would happen if you started with, say, a wrong MR solution, but
> picked your random Rfree set in PG2 and then applied "NCS". Then
> each of your "free" hkls would actually be NCS-restrained to be the
> same as a member of the working set. However, I'm sure everyone who
> reads the CCP4BB already knew that. Perhaps because a discerning
> peer-reviewer, PDB annotator or some clever feature in our modern
> bullet-proof crystallographic software caught such a mistake for
> them. (Ahem)
>
> Of course, what Graeme is asking for is the opposite of this: data
> that would appear as "nearly" PG222, but was actually lower
> symmetry. Unfortunately, there is no way to identify such cases
> from deposited Fs alone, as they will have been overmerged. In
> fact, I did once see a talk where someone managed to hammer an NCS
> 7-fold into a crystallographic 2-fold by doing some aggressive
> "outlier rejection" in scaling. Can't remember if that ever got
> published...
>
> -James Holton
> MAD Scientist
>
> On 11/2/2011 1:33 AM, Graeme Winter wrote:
> >Hi Ed,
> >
> >Ok, I'll bite: I would be very interested to see any data sets which
> >initially were thought to be e.g. PG222 and scale OK ish with that but
> >turn out in hindsight to be say PG2. Trying to automatically spot this
> >or at least warn inside xia2 would be really handy. Any
> >pseudosymmetric examples interesting.
> >
> >Also any which are pseudocentred - index OK in C2 (say) but should
> >really be P2 (with the same cell) as the "missing" reflections are in
> >fact present but are just rather weaker due to NCS.
> >
> >I have one example of each from the JCSG but more would be great,
> >especially in cases where the structure was solved& deposited.
> >
> >There we go.
> >
> >Now the matter of actually getting these here is slightly harder but
> >if anyone has an example I will work something out. Please get in
> >touch off-list... I will respond to the BB in a week or so to feed
> >back on how responses to this go :o)
> >
> >Best wishes,
> >
> >Graeme

--

***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************

CCP4bb navigation

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

Previous message:
Subject: Re: Archiving Images for PDB Depositions
From: James Holton jmholton {- at -} LBL {- dot -} GOV
Date: 2011-11-03

Next message:
Subject: Re: Archiving Images for PDB Depositions
From: Bryan Lepore bryanlepore {- at -} GMAIL {- dot -} COM
Date: 2011-11-03