I think it would make sense to include everything (ions, waters etc.) in the 3-letter residue view. This is straightforward, as the codes can be taken directly from the PDB file, so PyMOL does not need to recognize them. It may be necessary to allow for 4-letter codes also?
But in the 1-letter view, it would probably be a good idea to stick to the 20 standard residues (omit heteroatoms and put "X" for unknown residues). As it is now, some of the ions are kept as 3-letter codes (eg,. SO4) and shown in the one-letter sequence pane, which I think is a bit confusing. We showed the sequence feature to some of our web-lab colleagues (who use win-PyMOL for creating pictures). They can't wait to get the Windows version ;-) Cheers, Esben -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net To: EPF (Esben Peter Friis); pymol-users@lists.sourceforge.net Sent: 19-05-04 18:32 Subject: RE: [PyMOL] Linux Beta Version with Sequence Viewer Thanks for the input. > * sequence colors could (optionally?) match atom (C-alpha) > colors in the 3D view. Good idea. > * When a 3D-alignment is done, there is a sequence alignment behind. > Having this transferred to the sequence window would be > extremely useful. Planned -- but this is nontrivial. > * The heteroatoms should not appear in the sequence windows > - at least not in "residue" modes. Hmm. Some heteroatoms you definitely want, like S-met and modified bases. Others like water aren't quite so useful. What we may need in PyMOL is a set of categories/selection keywords such as the following: "polymers": all natural bases/amino acids and any hetatms connected through main chain chemistry "waters": all recognized waters (HOH, WAT, TIP, etc.) "ions": isolated atomic cations, anions, metals, etc. "ligands": anything not contains in the above By default, polymers and ligands make sense in the sequence view and waters can probably be omitted. Ions we should also probably keep in by default since they often play important roles in coordinating ligands. Does this sound like a useful addition? Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > EPF (Esben Peter Friis) > Sent: Wednesday, May 19, 2004 4:58 AM > To: Warren DeLano; pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] Linux Beta Version with Sequence Viewer > > > Hi Warren > > This is GREAT! > I was going to suggest this for the future development, but (as usual > :-) you're ahead. > > > Very good points: > * possible to chose between atoms/1-letter > residues/3-letter residues etc. > * The background color of the scrollbar area shows a > complete overview of the selections. > > Proposals: > * sequence colors could (optionally?) match atom (C-alpha) > colors in the 3D view. > * When a 3D-alignment is done, there is a sequence alignment behind. > Having this transferred to the sequence window would be > extremely useful. > * The heteroatoms should not appear in the sequence windows > - at least not in "residue" modes. > > > How are the sequences represented in the data structure? It > could be fun to interface with an extrenal modelling program, > such as Nest. That goal seems relatively close with this new feature. > > > Cheers, > > Esben > > > > -----Original Message----- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf > Of Warren > > DeLano > > Sent: 18. maj 2004 10:22 > > To: pymol-users@lists.sourceforge.net > > Subject: [PyMOL] Linux Beta Version with Sequence Viewer > > > > > > PyMOLers, > > > > I just finished the first beta version of PyMOL with a built-in > > sequence viewer (96beta6) and am looking for some experienced LINUX > > PyMOL users who are willing to poke around with this new stuff and > > provide feedback or suggestions. > > > > Screenshot & download at: > > > http://delsci.com/beta > > NOTE: don't install this over your main version -- try this > in a separate directory instead. > > Load your favorite structure, click on the "S" on the lower > right hand corner to enable the sequence viewer, and then see > what you can do with it. Try various button combinations on > the sequence, and try mixing in shift and/or control with the > left & middle buttons. Please let me know what you think... > > Cheers, > Warren > > -- > mailto:war...@delanoscientific.com > Warren L. DeLano, Ph.D. > Principal Scientist > DeLano Scientific LLC > Voice (650)-346-1154 > Fax (650)-593-4020 > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: SourceForge.net Broadband > Sign-up now for SourceForge Broadband and get the fastest > 6.0/768 connection for only $19.95/mo for the first 3 months! > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > ------------------------------------------------------- > This SF.Net email is sponsored by: SourceForge.net Broadband > Sign-up now for SourceForge Broadband and get the fastest > 6.0/768 connection for only $19.95/mo for the first 3 months! > http://ads.osdn.com/?ad_id%62&alloc_ida84&op=ick > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > ------------------------------------------------------- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
