[ccp4bb] coot CNS maps and looking for blobs

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

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Subject: Research Technician/Associate
From: Nithianantham Stanley nstanley76 {- at -} YAHOO {- dot -} COM
Date: 2007-11-30

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From: Nithianantham Stanley nstanley76 {- at -} YAHOO {- dot -} COM
Date: 2007-11-30

Subject: coot CNS maps and looking for blobs
From: byron delabarre byron {- dot -} ccp4 {- at -} GMAIL {- dot -} COM
Date: 2007-11-30

Hi -

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).

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

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 editting the PDB file but still
saw the problem with the blob search.

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.

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

Some other questions:

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

2) Is this just a 0.4 prerelease problem?

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

Thanks -

Byron

--
Byron DeLaBarre, Ph.D.
byron.delabarre@mpi.com
Structural Biology Group
Millennium Pharmaceuticals

CCP4bb navigation

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

Previous message:
Subject: Research Technician/Associate
From: Nithianantham Stanley nstanley76 {- at -} YAHOO {- dot -} COM
Date: 2007-11-30

Next message:
Subject: Research Technician/Associate Position
From: Nithianantham Stanley nstanley76 {- at -} YAHOO {- dot -} COM
Date: 2007-11-30