Re: [ccp4bb] coot CNS maps and looking for blobs

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CCP4bb <-- 2007 <-- December 2007 <-- 01 December 2007

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Subject: Re: coot-bones not showing
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-12-01

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Subject: Re: coot-bones not showing
From: Ethan A Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-12-01

Subject: Re: coot CNS maps and looking for blobs
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-12-01

byron delabarre wrote:
>
> I'm having troubles with the wonderful 'unmodelled blobs' feature in
> coot when I use a CNS map.
>
> I am using the 0.4 prerelease full prebuilt for unix (running FC5).
>
> The 0.3.3 release didn't seem to be working properly when reading in CNS
> maps (crashed everytime).

Yes, it was a "length of header lines" problem (a clipper issue really).

> The problem is that Coot starts picking density from the symmetry
> related map copies as 'blobs'. This renders the blob searching pretty
> useless.

Hmmm... make sure that your reference molecule is in the place that you
want your blobs to appear. [I sometimes pick the wrong molecule and the
blobs are positioned "in space"]. Perhaps 1 blob in 100 or so may get
wrongly position, but as a rule they should be in and around the
reference molecule.

> I did notice that Coot had some troubles reading the CNS cryst header (C
> 2 as opposed to C 1 2 1). I changed this by editing the PDB file but
> still saw the problem with the blob search.

I suppose the ambiguity of where the 2 fold is needed to be resolved.

> I generated the CNS map using the 'molecule' option - I guess coot does
> some conversion to give the 'everywhere I go there is a map' functionality.

Indeed. EYC-TIED.

> Note that this problem also extends to the water finding routine in Coot.

Hmmm.... I suspect that the map is not in good order - it wouldn't be
the first time that there were infelicities in reading a CNS map into
Coot. I'd rather suggest that you read in the CNS data either directly
using cns->coot or using Joel Bard's cns2coot script.

> Some other questions:
>
> 1) Should the unmodelled blobs function work if you simply read in a
> map (as opposed to auto-open mtz)?

Yes.

> 2) Is this just a 0.4 prerelease problem?

No.

> 3) Is the CNS map format to be blamed for not storing spacegroup info?

"Blame" is too strong a word I think. They have different preconceptions.

HTH,

Paul.

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CCP4bb <-- 2007 <-- December 2007 <-- 01 December 2007

Previous message:
Subject: Re: coot-bones not showing
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-12-01

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Subject: Re: coot-bones not showing
From: Ethan A Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-12-01