so then for segID, it might look like:
load xxx.pdb filter "type 73,4"
display atomtype="PROA"
Var proagroups = {atomtype="PROA"}
select *.ca and atomtype="PROA"
*for example
*
On Wed, Jan 16, 2013 at 7:21 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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 <angel.herr...@uah.es>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.
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS
>> and more. Get SQL Server skills now (including 2012) with LearnDevNow -
>> 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts.
>> SALE $99.99 this month only - learn more at:
>> http://p.sf.net/sfu/learnmore_122512
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery
and much more. Keep your Java skills current with LearnJavaNow -
200+ hours of step-by-step video tutorials by Java experts.
SALE $49.99 this month only -- learn more at:
http://p.sf.net/sfu/learnmore_122612
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
