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Hi Rhys,
Just to add onto Herman's suggestions: filling space with waters/atoms is actually what Arp-wArp is doing in the process of building the model. Perhaps you could also try that?
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of herman.schreu...@sanofi.com [herman.schreu...@sanofi.com]
Sent: Monday, July 06, 2015 2:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: [ccp4bb] Improving MR map contrast Dear Rhys,
what you are trying to do is at the edge of what is possible and you may, or may not succeed. It will also depend on the percentage solvent in your crystals. The more solvent, the better the chances. What I would do is to automatically add a lot of water, to fill features of the unknown parts of your structure and see if refinement gets more stable. Then I would look around the part which has been built for recognizable densities and build in those, refine and build more. In general the map close to parts which have been built will have the best quality and you may be able to extend the chains only a few residues at a time. You may also try solvent flattening, but so far it did not work for me.
Of course, trying to get direct phase information (SAD, MAD) will be the best way to go.
Best, Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
Im Auftrag von Rhys Grinter
Hi All,
I recently obtained a molecular replacement solution for a 100kDa protein I'm working on, using an ensemble of low sequence identity models for around 1/4 of the protein into 2.6A data. I got initial Tfz scores of around 8.2 (LLG of 100 or so), which I improved to 14 (LLG 350) which manual rebuilding of the placed fragment. There were enough local features in the map to rebuild the sequence on my protein for this fragment. However, I now have the problem that there is very little contrast in the rest of the map to build into, and the flexibility of the rest of the protein makes it uncertain where the rest of the domains will go. Refinement of my model so far doesn't seem stable and so far attempts at autobuilding have unsurprisingly failed. I was wondering if someone had an idea of how to improve the contrast of my map so I can place the other domains and build the rest of my protein? The solvent content of the crystal is around 55%.
Cheers,
-- Dr Rhys Grinter Sir Henry Wellcome Fellow Monash University +61 (0)3 9902 9213 +61 (0)403 896 767
Dr Rhys Grinter Sir Henry Wellcome Fellow Monash University +61 (0)3 9902 9213 +61 (0)403 896 767
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- [ccp4bb] Improving MR map contrast Rhys Grinter
- [ccp4bb] AW: [ccp4bb] Improving MR map contrast Herman . Schreuder
- Re: [ccp4bb] Improving MR map contrast Boaz Shaanan
