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Re: [Jmol-users] frozen Jmol Applet on hBonds calculation
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From: Thomas S. <tho...@gm...> - 2009-05-12 04:57:20
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AFAIK OT/OT1/OT2 are no longer "standard" but are still freqently generated by legacy software (XPLOR comes to mind as a primary source of OTs versus O/OXT). So, you shouldn't be finding any in the PDB, but you're still apt to run into them in "local" .pdb files... -Tom On May 11, 2009, at 8:28 PM, Robert Hanson <ha...@st...> wrote: > Jaime, this is fixed now in the sense that the OT1/OT2 oxygens are > ignored for hydrogen bond calculation purposes. I don't think that's > a perfect solution, but until we find out whether these are official > RCSB designations, I think we will leave it that way. > > On Mon, May 11, 2009 at 12:57 PM, Robert Hanson <ha...@st...> > wrote: > This is a problem arising from using OT1 and OT2 instead of O and > OXT. Are these now standard names for oxygen atoms in PDB files? > > Bob > > > On Mon, May 11, 2009 at 12:46 PM, Robert Hanson <ha...@st...> > wrote: > Thanks, that's a bug. I will fix it. > > On Mon, May 11, 2009 at 12:37 AM, <lsp...@we...> wrote: > Dear Jmol, > > On the attached sample structure file, 'calculate hbonds', freezes > the Jmol Applet. Does the calculation for hydrogen bonds get lost? > > To reproduce the problem, open a browser page with a Jmol applet, > get the Console from the Jmol menu and type these lines, with Execute > or enter at the end of each line: > > load 0123.pdb > spin on > color structure > calculate hbonds > > Executing the last command, freezes the applet. The first few lines > are > there only to see that the applet works at the beginning. > > Suggestions? What's special about this structure? > > Thanks in advance, > Jaim > -- > Dr Jaime Prilusky | > Jai...@we... > Head Bioinformatics | > R&D Bioinformatics and Data Management | > Department of Biological Services | > Weizmann Institute of Science | fax: 972-8-9344113 > 76100 Rehovot - Israel | tel: 972-8-9344959 > > OCA, http://oca.weizmann.ac.il (the protein structure/function > database) > Proteopedia, http://proteopedia.org (because life has more than 2D) > > --- > --------------------------------------------------------------------- > > --- > --- > --- > --------------------------------------------------------------------- > The NEW KODAK i700 Series Scanners deliver under ANY circumstances! > Your > production scanning environment may not be a perfect world - but > thanks to > Kodak, there's a perfect scanner to get the job done! With the NEW > KODAK i700 > Series Scanner you'll get full speed at 300 dpi even with all image > processing features enabled. http://p.sf.net/sfu/kodak-com > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > --- > --- > --- > --------------------------------------------------------------------- > The NEW KODAK i700 Series Scanners deliver under ANY circumstances! > Your > production scanning environment may not be a perfect world - but > thanks to > Kodak, there's a perfect scanner to get the job done! With the NEW > KODAK i700 > Series Scanner you'll get full speed at 300 dpi even with all image > processing features enabled. http://p.sf.net/sfu/kodak-com > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |