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Re: [ccp4bb] Check the conformation of one important amino acid
 

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CCP4bb <-- 2008 <-- February 2008 <-- 19 February 2008
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Date: 2008-02-19


Subject: Re: Check the conformation of one important amino acid
From: Li Zhijie zhijie {- dot -} li {- at -} UTORONTO {- dot -} CA
Date: 2008-02-19
Sorry, I just figured out how to post to the CCP4bb instead of sending a
private email.

Here are two missed messages that I think should appear on the board:

----- Original Message -----
From: "Miles Pufall"
To: "Zhijie LI"
Sent: Tuesday, February 19, 2008 5:03 PM
Subject: Re: Check the conformation of one important amino acid


> Hi -
>
> I've never tried it! Fast and easy is good...I'll try it out.
>
> I have found both SA-omit and composite omit maps to be very helpful -
> I've found alternate potential alternate builds and flat out wrongheaded
> model building, but I am nowhere neae as experienced as Dr. Rice, so
> maybe I need the check more than she does. I think that computers have
> gotten fast enough that taking too long isn't as big an issue as it once
> was. I calculated a full composite omit map on an older MacBook Pro of a
> 1.7 angstom 32KDa structure and it took about 3 hours. Any desktop will
> do better than that.
>
> Give it a try and see if what you get! Good luck.
>
> Miles
> On Feb 19, 2008, at 12:08 PM, Zhijie LI wrote:
>
>> What about Bhat's omit program included in the CCP4 package? I found it
>> to
>> be very fast and easy to use. Also it allows to manipulate the map
>> coefficients.
>>
>> I had read a summary that Dr. Rice made in 2002 about the omit map
>> calculations: http://www.ysbl.york.ac.uk/ccp4bb/2002/msg01030.html. I
>> wonder
>> if there have been any updates during the last 5 years?
>>
>>
>
> Miles Pufall
> Postdoctoral Scholar
> Yamamoto Lab
> UC San Francisco
> Cellular and Molecular Pharmacology
> Mail Stop 2280
> 600 16th Street, Genentech Hall S-574
> San Francisco, California 94158-2517
> (415)476-4480
>
>
>
>
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