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The RCSB PDB website's choice of model structure for biological units is annoying to many people. The equivalent files served by the Protein Data Bank in Europe (http://www.ebi.ac.uk/pdbe/) are structured as a single "model" with unique chain names. This can result in a lot of chain names and it is hard to predict what those names will be, but the file will be displayed by most programs. Perhaps you could download your assemblies from there. Dale Tronrud On 6/19/2014 10:14 AM, Rolf Huehne wrote: > On 06/19/2014 05:25 PM, Andreas Truszkowski wrote: >> Hi, >> >> hiding protein chains with display *:chain or *:chain\modelnr is >> no problem. But how can I hide a specific chain within a >> bilogical assembly? The problem is that in biological assemblies >> the unit cell (assymetric unit) is transformed n-times as >> described in the PDB REMARK 350 section i.e. if I take the >> protein 4ins with two chains in the assymetric unit and I apply >> the filter BIOMOLECULE 5 to it, the resulting hexamere consists >> of three times chain A and B. Using something like display >> *:Aleads to that every chain A is hidden. >> >> Is there a way to only show or hide a specific chain e.g. chain A >> in the second unit cell? >> > I don't know about any simple way to achieve this (but I might be > wrong). > > Unfortunately the BIOMOLECULE filter of Jmol was implemented > different than what the PDB does with the biological unit files > they provide. In these files each copy is placed into a new model > so selecting each chain individually is rather easy. So maybe > switching to use these biological unit files might be the easiest > way to solve your problem. > > If that is not an option you might be able to solve the problem by > using the 'atomindex' property (see > http://jena3d.fli-leibniz.de/doc/jmol_scripting/index.htm#atomproperties) > in combination with the atom selector function 'within(POLYMER, > atomindex=n' (see > http://jena3d.fli-leibniz.de/doc/jmol_scripting/index.htm#atomexpressions). > > If you would only need to do this for a small set of predefined > PDB entries you might collect the necessary data rather easily. If > you would need it for any PDB structure it might require quite some > Jmol script programming. > > The general idea is like this: > > 1) Each atom has an individual index number assigned, starting with > zero. It can be used for atom selection by using for example > 'atomindex=0'. > > 2) You should be able to select all atoms belonging to the same > chain by using the atom expression 'within(POLYMER, > atomindex=0)'. > > 3) Identify the atomindex for the first atom of each chain > (manually or programmatically) and build the proper atom expression > from 2). > > I don't know if 2) will work in all cases. I just tried it for PDB > entry 4INS and it worked. > > The order of the chains you will get by 'atomindex' might not be > the same as you might expect. It will depend on the way how the > atoms for the copies are created. To solve this programmatically > might be difficult. > > One way to achieve 3) might be to go like this: a) Use atomindex=0 > to identify the atoms of the first chain. b) Select the first chain > and determine the maximum atomindex. c) Add one to the maximum > atomindex and use it in a) to find the next chain. d) Repeat this > until the maximum atomindex of the whole structure is reached. This > will of course not work, if the atomindex numbers within each chain > are not sequential. You would have to check this first. > > Good luck, Rolf > -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlOjILwACgkQU5C0gGfAG10HYACeOlJkgLlrckTutDgZkV6Yi5Vl NkcAn0r2+nrZv0MwWZUkukELuXit8PZg =v3Oy -----END PGP SIGNATURE----- ------------------------------------------------------------------------------ HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
