I'm a big fan of choice and suggest we have multiple options: 1) only show biopolymers with standard 1-letter codes, O for water, X for others. 2) mix known abbreviations and full 3-letter codes with visual cues. 3) full residue names (up to 4 letters allowed) 4) chains 5) segments [rarely used now, but needed for big/symmetric structures] 6) states 7) atoms
An orthogonal setting will control what we show, and that could be any and all of: 1) ATOMs 2) HETATMs 3) polymers 4) ligands 5) ions 6) waters Any other dimensions to consider? 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 1:50 PM > To: Warren DeLano ; pymol-users-ad...@lists.sourceforge.net; > pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] Linux Beta Version with Sequence Viewer > > > > 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 > > > > ------------------------------------------------------- > 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 >
