Hi,
I would go even further down SG ladder, i.e. all the way to P1, reprocess the data in P1 (you won't lose reflections with special indices that way, the only thing to worry here is completeness, but hopefully you recorded highly redundant data) and do the MR. It worked for me and for others.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: [log in to unmask]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Eleanor Dodson [[log in to unmask]]
Sent: Sunday, March 25, 2012 9:55 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Refinement with pseudo-translation
You don't say how many molecules you are looking for?
I would try to first work in SG C2 pretending that the pseudo translation
is 100% of the origin.
Reindex the data as k,l,h, change the SG to C2 and then redo the scaling
and merging. You will lose all the reflections k+l =2n+1 in your indexing -
h+k = 2n+1 after reindexing, but the MR should be simpler.
Once you have a C2 solution you can convert it back to the orthorhombic one
with a certain amount of intellectual struggle! The C2 origin along your b
axis is free, so you will have to
Or you can use ZANUDU from the ysbl software web site which will maybe help.
Eleannor
On Mar 22 2012, Shiva Kumar wrote:
>Dear CCP4bb members
>
> I have a 3.0 Å dataset which has an off-origin peak of height 36% in
> patterson map. The peak is at fractional co-ordinates 0, 0.5, 0.5. Data
> has been indexed in P2(1)22(1) SG using HKL2000. I have located all the
> molecules in asu (as far as I know) using Molrep with the 'locked
> rotation' and 'Use' PST feature. After 1 round (20 cycles) of rigid body
> and 1 round (10 cycles) of restrained refinement (Refmac), the R and
> Rfree are 49 and 53 %. Although the R factors are very high, I feel the
> solution might be correct because the electron density follows c-alpha
> trace in almost all places. To be sure, I deleted a beta strand from the
> structure's core and repeated the refinement and found that the electron
> density for the strand was still present (I have no experimental phases).
> I have the following questions:
>
> 1) Are the final R factors never expected to reduce to acceptable values
> given the 36% off-origin peak?
>
> 2) What is the best way to settle the SG? I was considering
> P2(1)2(1)2(1), P2(1)22, P2(1)2(1)2 and P2(1)22(1), considering the
> off-origin peak is at 0,0.5,0.5. I found all the molecules in asu only
> using the P2(1)22(1) data in Molrep. Is this the best way to settle my
> SG?
>
> 3) Some CCP4bb archives advise either refining against weak and strong
> reflections alternatively
> (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1010&L=ccp4bb&D=0&1=ccp4bb&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=204490)
> or refining against medium intensity reflections. Should I also be doing
> these things? If yes, then what is the best way of doing it?
>
> Your suggestions and corrections to my interpretation of our data would
> be appreciated.
>
>Regards
>Shiva
>
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
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