Ligandfit_SigmaF_obs

张怀东

1 Nov 2012 1 Nov '12

4:36 a.m.

Hello, I am a newcomer. I need help. I have done phenix.ligandfit, and the result contained a mtz file named resolve.mtz. While sigma_F_obs in the file are all 1.0. Is there something wrong with the file? Is this a bug? Could I do phenix.refine with the resolve.mtz added R_flag, next? sincerely, Huaidong Zhang

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Terwilliger, Thomas C

1 Nov 1 Nov

12:23 p.m.

Hi Huaidong, The resolve.mtz from ligandfit is just a map file, so you won't want to use it for anything other than looking at a map. The sigma values are not useful, and are just set to 1.0 in that file. For running phenix.refine you would want to use an original data file with original freeR flags. If you have not previously refined this model but got the model from another crystal with the same space group and cell parameters, you can use the reflection editor in the GUI to transfer the test set from the previous datafile to this one. I hope that helps! All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of 张怀东 [[email protected]] Sent: Thursday, November 01, 2012 12:36 AM To: [email protected] Subject: [phenixbb] Ligandfit_SigmaF_obs Hello, I am a newcomer. I need help. I have done phenix.ligandfit, and the result contained a mtz file named resolve.mtz. While sigma_F_obs in the file are all 1.0. Is there something wrong with the file? Is this a bug? Could I do phenix.refine with the resolve.mtz added R_flag, next? sincerely, Huaidong Zhang

Ed Pozharski

1:44 p.m.

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

Terwilliger, Thomas C

1:48 p.m.

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.

张怀东

2 Nov 2 Nov

12:11 a.m.

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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Ed Pozharski
Terwilliger, Thomas C
张怀东