Re: [ccp4bb] Density modification

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

Previous message:
Subject: Re: Problem with different map when ligand refinement
From: Christine Gee chrgee {- at -} GMAIL {- dot -} COM
Date: 2009-07-26

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Subject: Re: ccp4i, OS X 10.5.7, & security enforcement
From: Martyn Winn martyn {- dot -} winn {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-07-27

Subject: Re: Density modification
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-07-27

This message means that the starting electron density map is completely
flat, which makes any density modification impossible. There are several
possible reasons for this:

1. No FOM specified on LABIN.

2. FOM specified, but all FOMs are equal to zero.

3. All F's equal to zero.

4. Input map coefficients (FDM) specified and equal to zero.

5. Some sort of filter applied (either resolution of Free-flag) which is
removing all of the reflections from use.

If you send your full log file and an mtzdump of your mtz file, than I
can be more specific.

Kevin

kumar wrote:
> Dear CCP4’ers, I’m trying to run DM for after Refmac on an MR solution
> but it crashes. I do have the FOM’s listed in my log file. I get a
> similar error when I use the mtz file from Phaser’s SAD + MR. I’d
> appreciate any help. Thanks! Kumar
>
> *After Refmac …………………………..
> *
> HISTLIB opened:
> Number of histograms = 18
> Number of entries per histogram = 100
> RESL 10.0 8.0 7.0 6.0 5.0 4.5 4.0 3.6 3.3 3.0 2.8 2.6 2.4
> 2.2 2.0 1.8 1.6 1.5
>
>
>

Initial Solvent Mask

> dm: (WFO) No density in map! Check input FOM present and nonzero
> Times: User: 0.2s System: 0.0s Elapsed: 0:01
>
>
> ***************************************************************************
> * Information from CCP4Interface script
> ***************************************************************************
> The program run with command: dm HKLIN
> "/home/elias/kumar/7_20/K15/reprocess/ccp4/cns/round2/round3/round4/round4_refmac1.mtz"
> HKLOUT
> "/home/elias/kumar/7_20/K15/reprocess/ccp4/cns/round2/round3/round4/round4_dm2.mtz"
> SOLOUT
> "/home/elias/kumar/7_20/K15/reprocess/ccp4/cns/round2/round3/round4/round4_dm1.msk"
>
> has failed with error message
> dm: (WFO) No density in map! Check input FOM present and nonzero
> ***************************************************************************
>
>
> #CCP4I TERMINATION STATUS 0 " dm: (WFO) No density in map! Check input
> FOM present and nonzero"
>
> ***********************************************
> *After Phaser (SAD+MR)……………..
> *
>

Initial Solvent Mask

> dm: (WFO) No density in map! Check input FOM present and nonzero
> Times: User: 0.2s System: 0.0s Elapsed: 0:00
>
>
> ***************************************************************************
> * Information from CCP4Interface script
> ***************************************************************************
> The program run with command: dm HKLIN
> "/home/elias/kumar/7_20/K15/reprocess/ccp4/cns/round2/round3/round4/round4_9.mtz"
> HKLOUT
> "/home/elias/kumar/7_20/K15/reprocess/ccp4/cns/round2/round3/round4/round4_9_dm1.mtz"
> SOLOUT
> "/home/elias/kumar/7_20/K15/reprocess/ccp4/cns/round2/round3/round4/round4_9_dm1.msk"
>
> has failed with error message
> dm: (WFO) No density in map! Check input FOM present and nonzero
> ***************************************************************************
>
>
> #CCP4I TERMINATION STATUS 0 " dm: (WFO) No density in map! Check input
> FOM present and nonzero"
> ************************************
>
>

CCP4bb navigation

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

Previous message:
Subject: Re: Problem with different map when ligand refinement
From: Christine Gee chrgee {- at -} GMAIL {- dot -} COM
Date: 2009-07-26

Next message:
Subject: Re: ccp4i, OS X 10.5.7, & security enforcement
From: Martyn Winn martyn {- dot -} winn {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-07-27