Re: [ccp4bb] coot-bones not showing

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

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Subject: Re: Unidentified ligand (electron density) found at active site
From: Gregg Crichlow gregg {- dot -} crichlow {- at -} YALE {- dot -} EDU
Date: 2007-12-01

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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

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

Dear Bernhard,

Bernhard Rupp wrote:
>
> I am trying to make a few high quality shots with Coot.
> There are 2 problems I am stuck with:
> 1) The bones do not show up when I make a screen shot from the draw
> menu to raster3d

Indeed. Also symmetry atoms, atom labels, generic labels and graphics
objects are missing (sad to say).

I'll add in bones and graphics objects to the spec for 0.5.

> 2) The depth cueing of the map grid is too large, i.e. too much
> foging. Can that be reset?

I think that it can be done post-hoc in the raster3d file header.
Perhaps by increasing the ambient light?

http://skuld.bmsc.washington.edu/raster3d/html/render.html

Either that or by adjusting the gamma ramp with the gimp or some such.

Perhaps just widening the clipping planes will reduce the fogging. But
if you mean: can the fogging be decoupled from the clipping in Coot?
then no, you can't do that.

> Batons however, do display.

That I find surprising.

Paul.

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

Previous message:
Subject: Re: Unidentified ligand (electron density) found at active site
From: Gregg Crichlow gregg {- dot -} crichlow {- at -} YALE {- dot -} EDU
Date: 2007-12-01

Next message:
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