RasMol/Raster 3D question

Bernard Murray bernard at elsie.nci.nih.gov
Fri Mar 15 17:47:58 EST 1996


In article 
<Pine.LNX.3.91.960311095856.18757B-100000 at repressor.pharmacy.wisc.edu>, 
ross at repressor.pharmacy.wisc.edu says...
>
>On Mon, 11 Mar 1996, Bernard Murray wrote:
>
>> Hello all,
>> 
>>       I'm using RasMol 2.5 under Windows 3.1 and am hoping to colour
>> parts of molecules by manipulation of PDB format files.  One possible
><deleted>
>
>Bernard - 
>The COLO fields are an extension to PDB format orginially invented by
>David Bacon for Raster3D. They documented in the Raster3D docs somewhere,
>but also in the RasMol 2.5 docs you have right there - I believe it's an
>MS-Write file called manual.doc.  - Here's an excerpt:
>
>PDB Colour Scheme Specification

First of all, thanks very much for pointing out what I should already
have read about (blush).  I have since done some experimentation with
adding COLO records to PDB files for viewing with RasMol and have found
the following (which is not evident from the documentation);

1) RasMol allows a maximum of only 40 COLO records in the file
	(I had hoped that I could have one per residue or per atom)
2) RasMol will only implement a limited number of these user shades
	(under DOS/Win these are the 16 DOS colours)
3) RasMol does not read the "mask" as documented
	It should take columns 7 - 30 of the COLO record as significant
but actually only those forming valid PDB fields are checked.  I had
hoped that I could add a colour flag at column 29 (currently unused
by PDB files) but RasMol ignores this.  So, the only way to trigger the
use of a COLO record is to set it to;
atom serial number, atom name, alternate location, residue name,
alternate location, residue number or insertion code (or any combination
of these).  I haven't actually tested all these fields but hopefully
I can use the alternate location or insertion fields for my purposes.
	The RasMenu program is very nice but it will still not permit
me to do what I want to do (colour non-contiguous residues in the same
shade).  I had some luck adding fake B values and scaling for temperature
but RasMol's autoscaling feature makes this a guessing game.
	Ah well....
		Thanks once again for all your help,
			Bernard

Bernard Murray, Ph.D.
bernard at elsie.nci.nih.gov  (National Cancer Institute, NIH, Bethesda MD, USA)





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