[phenixbb] ligand fitting, density and refinement

Hi Huaidong, I'm not quite sure exactly what you did...could you possibly elaborate a little? My confusion comes from two things. First, this phrase: "did the refinement with the output files from ligandfit", is confusing to me because I would not think that you would want to use any output files from ligandfit except for the ligand PDB file. Second, I agree, I can't see why ligandfit would find good density for your ligand if it is not present in a difference map calculated from the original data. All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of 张怀东 [[email protected]] Sent: Thursday, November 01, 2012 8:11 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Ligandfit_SigmaF_obs Hi,Tom T We followed the instruction after the ligandfit, and did the refinement with the output files from ligandfit. The electron density for the ligand is clear, but in the refinement with the original mtz file, the density is not there. So how to explain the difference? Is this a bug? Thanks! Huaidong

-----原始邮件----- 发件人: "Terwilliger, Thomas C" 发送时间: 2012年11月1日 星期四 收件人: "PHENIX user mailing list" 抄送: 主题: Re: [phenixbb] Ligandfit_SigmaF_obs

Hi Ed,

Yes, good point. I will be changing the way the wizards read in and store reflection data (sometime soon I hope!) and at that point this should be moot because the wizards won't write out dummy intermediate files.

All the best, Tom T

________________________________________ From: [email protected] [[email protected]] on behalf of Ed Pozharski [[email protected]] Sent: Thursday, November 01, 2012 9:44 AM To: PHENIX user mailing list Subject: Re: [phenixbb] Ligandfit_SigmaF_obs

On Thu, 2012-11-01 at 14:23 +0000, Terwilliger, Thomas C wrote:

...

The sigma values are not useful, and are just set to 1.0 in that file.

Tom,

I've seen this issue before, and I am just wondering what could be the rationale to reset sigmas to 1.0? Seems like one would have to code for this to happen, and even if the sigma values are not used for map generation, why isn't the column simply omitted but instead replaced with obviously incorrect values?

Ed.

-- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs

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