Re: [ccp4bb] arp/warp in p22121

- 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: arp/warp in p22121
From: Florian Schmitzberger Florian {- dot -} Schmitzberger {- at -} KI {- dot -} SE
Date: 2007-09-18

Next message:
Subject: Re: arp/warp in p22121
From: Victor Lamzin victor {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-09-18

Subject: Re: arp/warp in p22121
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2007-09-18

Hi -

ARP/wARP only likes standard space groups, like P21212,
P22121 is not-standard ... oh well ...
(Eleanor is complaining about it for about 13 years ... but never
mind that she is right)

Just re-index your sg to be P21212 (refl. utilities, reindex, in ccp4i).
Choose 'Entering reflection transformation'
P22121 to become P21212 you need

h=l
k=k
l=-h

set SG to p21212

if you are too lazy redo the Molrep or a nice brain teaser is to
apply the correct transformation to your PDB
(PDBSET will do that for you) and you are ready to go with ARP/wARP

A.

PS. depending on cell axes length, and given that convention wants
the smaller 21 axis first,
the formally correct transformation above might be

h=k
k=l
l=h

(in other words if your CURRENT b axis is smaller than your current c
axis its the one above.
if the CURRENT c axis is smaller than b, the use the one on top)

PS2 I think i got the - right, you need to be sure you do not invert
the hand - reindex will complain if I was wrong,
in which case get rid/add a the '-' sign ;-)

On Sep 18, 2007, at 12:28, Florian Schmitzberger wrote:

> Dear All,
>
> I am trying to build a molecular replacement model in arp/warp in
> space group P22121.
> Refmac alone seems to be fine with refining the model in P22121;
> but arp/warp fails, as far
> as I can see at the first Refmac refinement stage. In the log-file
> it says "this space group is
> not supported".
>
> I am wondering whether arp/warp needs the Hermann-Mauguin
> convention space group
> P21212. I suppose I will need to reindex in P21212 in order to use
> arp/warp? (the diffraction
> data were indexed in XDS, scaled in SCALA, and then run through CAD
> to change the space
> group from P222 to P22121). I am using arp/warp via the ccp4i
> interface.
>
> Also, arp/warp gives the following message when I load the mtz file
> "cannot extract
> arp/warp asymmetric unit limits, the job will fail if run." (i did
> run arp/warp successfully with
> other mtz-files).
>
> Thank you in advance for any comments!
>
> Florian

CCP4bb navigation

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

Previous message:
Subject: arp/warp in p22121
From: Florian Schmitzberger Florian {- dot -} Schmitzberger {- at -} KI {- dot -} SE
Date: 2007-09-18

Next message:
Subject: Re: arp/warp in p22121
From: Victor Lamzin victor {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-09-18