From: Daniel C. <dan...@gm...> - 2012-06-11 17:09:38
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Or just load append 3NUR.pdb filter ":A, protein"; probably? 2012/6/11 Daniel Carbajo <dan...@gm...> > Thanks Rolf! > So how would it be when loading the structure (if I want to load it > excluding those "hetero not protein")? > load append 3NUR.pdb filter ":A, !hetero and not protein"; > Like that? > Thanks > > 2012/6/11 Rolf Huehne <rh...@fl...> > >> On 06/11/2012 03:40 PM, Daniel Carbajo wrote: >> > Any idea anyone? >> > >> > 2012/6/11 Daniel Carbajo<dan...@gm...> >> > >> >> Hello everyone, >> >> I am wondering whether I could filter filter HETATMS so I get only >> those >> >> which are peptide-linking and not others, like waters, etc. >> surrounding or >> >> interacting the protein (I only want those part of the protein). I want >> >> those embedded in the normal ATOM records, and not after the TER line >> in >> >> the PDB file. >> >> For example http://www.rcsb.org/pdb/files/3NUR.pdb Here I want the >> MSE to >> >> appear, but not the CA and HOH; as I load many structures I never know >> >> which are the ones I need to filter. >> >> Is there a general way I can say "filter only those HETATMS after the >> TER >> >> line in the PDB file"? Or should I provide a list of non-peptide >> linking >> >> HETATMS that should be filtered? I already have my own list >> (associative >> >> array in php) of peptide linking HETATMS in the PDB... how could I say >> >> "filter all those HETATMS except the ones on such list"? >> >> Thanks a lot! >> >> Daniel >> >> >> With these atom expressions you should be able to discriminate them in >> Jmol (tested for 3NUR): >> >> "hetero and protein" >> "hetero and not protein" >> >> Example command: >> hide hetero and not protein >> >> Regards, >> Rolf >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > |