OK, this is in in a much more generally useful way, I think. See
http://chemapps.stolaf.edu/jmol/Jmol-13.zip
___JmolVersion="13.1.12_dev"
new feature: load xxx.pdb filter "TYPE i,n"
-- loads custom text fields into the "atomType" property of an atom upon
customized PDB file loading
where i is the number of the column (starting with 1) and n is the
number of columns
-- text is trimmed
-- e.g. load xxx.pdb filter "TYPE 73,4" loads four characters starting at
column 73 as "atomType" (segID)
-- to convert to a numerical value, convert that to .property_foo:
load xxx.pdb filter "type 22,4"; {*}.property_seqNo = {*}.atomType
new feature: PDB filter "TYPE 73,4=xxx"
-- loads four characters starting at column 73 (1-based) as "atomType"
-- loads only those atoms with atom types starting with "xxx"
Bob
On Tue, Jan 15, 2013 at 5:15 PM, Angel Herráez <[email protected]> wrote:
> **
> Hi
>
> So this is a question of file format.
>
> PDB file format specification has not any hint of columns 72-75 or the
> segID field, either in the current Version 3.3: July, 2011 / Nov. 21, 2012
> http://www.wwpdb.org/documentation/format33/sect9.html#ATOM
> or in the oldest referenced in wwPDB, Version 2.3, July 9, 1998
> http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
>
> So that's really going waaaay far in history :)
>
> You issue is then of a nonstandard format, I'd say.
> Not sure how reasonable it is to implement this, but it can probably be
> easy a new file reader for that (not that I can do it) -- one additional
> problem would be how to differentiate whether files are true pdb or
> "special" pdb. One would have to use the forced syntax,
> load "filetype::filename"
>
>
> If you have someone that can program Java, as an example there is PQR
> format which is an extension of the PDB format and could be used as a guide
>
> http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/adapter/readers/more/PqrReader.java?revision=17863&view=markup
>
> http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java?revision=17863&view=markup
>
>
> > Much application software today incorporates the use of the segid
> keyword
>
> I find that rather odd. Where do the values of segid come from?
> Certainly not from experimental data deposited in PDB.
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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