Re: [ccp4bb] MR with electron density model

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

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From: "Deng, Junpeng" junpeng {- dot -} deng {- at -} OKSTATE {- dot -} EDU
Date: 2007-05-29

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Date: 2007-05-29

Subject: Re: MR with electron density model
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-05-29

What have you tried so far for obtaining an MR solution? You have many
options of software, search models, and parameters to use in the MR
search.

Software: Phaser and EPMR should be on your list to try. These two
programs can crack most problems efficiently,
Models: The highest homology models are best, appropriately trimmed
(e.g., CHAINSAW) to match the target. Phaser will do ensemble searches.
Parameters: Do you have a good idea from Matthews Probability analysis
of the ASU content? If you don't nail this down from the start, MR is
pretty much doomed to fail. If the ASU contains more than one molecule,
Phaser or EPMR are especially efficient here. You may have to play with
resolution range and other parameters to find a solution. If you have a
space group with many different permutations of screw axes (e.g., P422)
you may have to search many different space groups and reindex data.
(Phaser and Open-EPMR can do much of this for you automatically.)

Cheers,

___________________________________________
Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowlett@mail.colgate.edu

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of xiuwen zhang
Sent: Sunday, May 27, 2007 9:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] MR with electron density model

Dear all,

I am trying to get a structure using MR. Unfortunately,
it failed to get solution with several model coordinates. Is there any
suggestion for me to how to get the solution with model electron
density?

Thanks all.

Cheers,
Xiuwen

CCP4bb navigation

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

Previous message:
Subject: post-doc position opening
From: "Deng, Junpeng" junpeng {- dot -} deng {- at -} OKSTATE {- dot -} EDU
Date: 2007-05-29

Next message:
Subject: Lectureship in Structural Biology
From: Richard Pickersgill r {- dot -} w {- dot -} pickersgill {- at -} QMUL {- dot -} AC {- dot -} UK
Date: 2007-05-29