From: Robert H. <ha...@st...> - 2010-10-14 22:59:22
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Jmol users interested in protein visualization, I've just released Jmol 12.0.18 and 12.1.15. These both have added features -- specifically DSSP and an assortment of related commands. In addition, there are some bug fixes. There are TWO FEATURE CHANGES: 1) For PDB or mmCIF files that contain no HELIX/SHEET/TURN information, Jmol will now use DSSP instead of the former Ramachandran-angle based calculation (that was written specifically for Jmol) to automatically generate helix, sheet, and turn secondary structures. In the case of alpha-carbon-only chains, Jmol will continue to use the method of Levitt and Greer, Automatic Identification of Secondary Structure in Globular Proteins, J.Mol.Biol.(1977) 114, 181-293. The Ramachandran-angle-based calculation is available still (and has some advantages, perhaps, in certain contexts) as calculate structure RAMACHANDRAN 2) The default for calculate structure is now to use DSSP. As above, the previous default is available, just as RAMACHANDRAN instead of the default. # New feature: Accurate DSSP structure determination should be identical to DSSP calculate structure # default DSSP -- new way calculate structure RAMACHANDRAN # old way calculate HBONDS STRUCTURE # DSSP structure-determining hydrogen bonds only save structure s1 # for example, save the authors' structure assignment restore structure s1 color cartoons STRUCTURE # additional hues for helix310 and helixPI show DSSP -- DSSP report set DEBUG -- verbose DSSP calculation set defaultStructureDSSP --default TRUE --on load, if PDB file has no HELIX/SHEET records, use DSSP to calculate --for calculate structure, with no arguments, use DSSP --setting this FALSE gives previous behavior (Jmol Ramachandran calculation) set dsspCalculateHydrogenAlways --default TRUE -- standard DSSP, ignoring all file backbone amide H atoms --set to FALSE to ensure that file-based NH atoms are used instead of rough approximations select helix310 select helixalpha select helixpi # try this with 2JC9 for a DSSP >>555<< run select substructure = 7 # DSSP "G" -- 3/10 helices select substructure = 8 # DSSP "H" -- alpha helices select substructure = 9 # DSSP "I" -- pi helices label {*.ca} %[substructure] STRUCTURE HELIXALPHA .... STRUCTURE HELIX310 .... STRUCTURE HELIXPI .... PDB and CIF readers now read helix types 1 (alpha), 3 (pi), and 5 (3/10), and color them slightly differently # bug fix: QCHEM reader fails # bug fix: CRYSTAL reader fails to read formico_opt.out # bug fix: CIF reader not reading insertion codes (since forever!) # bug fix: set appendNew FALSE fails # bug fix: getproperty IMAGE (returning JPG64) doubles font size with set antialiasDisplay true # bug fix: "configuration 1" should select all if no alternative locations # bug fix: isosurface "xxxx.jvxl" colorscheme "rwb" does not work (jvxl files specifically) # bug fix: load FILTER does not include %x for PDB files See http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm for examples. To do: documentation Bob -- 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 |
From: Angel H. <ang...@ua...> - 2010-10-16 11:54:30
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Bob, this is a great addition. I am adding this info about the new DSSP method to the Wiki, http://wiki.jmol.org/index.php/Protein_Community > calculate structure # default DSSP -- new way > calculate structure RAMACHANDRAN # old way No way to recover the structure assignment based on the PDB file (authors' spec) ?? Apart from using "save structure" + "restore structure" Maybe calculate structure PDB or better calculate structure FILE > set DEBUG -- verbose DSSP calculation Is that correct? No additional parameters? > select substructure = 7 # DSSP "G" -- 3/10 helices I can find no doc for this "select substructure" command. How new is it? It seems that beta sheets are =2 > label {*.ca} %[substructure] This gives an error in script compiler Maybe select *.ca; label %[substructure]; ?? That works > STRUCTURE HELIXALPHA .... > STRUCTURE HELIX310 .... > STRUCTURE HELIXPI .... What do these do? |
From: Robert H. <ha...@st...> - 2010-10-16 12:40:30
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save/restore is the way to go. 2010/10/16 Angel Herráez <ang...@ua...> > Bob, this is a great addition. > > I am adding this info about the new DSSP method to the Wiki, > http://wiki.jmol.org/index.php/Protein_Community > > > calculate structure # default DSSP -- new way > > calculate structure RAMACHANDRAN # old way > > No way to recover the structure assignment based on the PDB file > (authors' spec) ?? > Apart from using "save structure" + "restore structure" > > Maybe > calculate structure PDB > or better > calculate structure FILE > > > > set DEBUG -- verbose DSSP calculation > > Is that correct? No additional parameters? > > > > select substructure = 7 # DSSP "G" -- 3/10 helices > > I can find no doc for this "select substructure" command. How new is it? > It seems that beta sheets are =2 > > > > label {*.ca} %[substructure] > > This gives an error in script compiler > Maybe > select *.ca; label %[substructure]; > ?? That works > > > > > STRUCTURE HELIXALPHA .... > > STRUCTURE HELIX310 .... > > STRUCTURE HELIXPI .... > > What do these do? > > > > > > ------------------------------------------------------------------------------ > Download new Adobe(R) Flash(R) Builder(TM) 4 > The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly > Flex(R) Builder(TM)) enable the development of rich applications that run > across multiple browsers and platforms. Download your free trials today! > http://p.sf.net/sfu/adobe-dev2dev > _______________________________________________ > 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 |
From: Angel H. <ang...@ua...> - 2010-10-16 18:17:35
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Bob, I see a conflict in coloring of Hbonds In beta sheets, calculate hbonds;color hbonds type renders them in yellow. That was the standard coloring. The new calculate hbonds structure;color hbonds type renders them in cyan or white (parallel/antiparallel strands). That's nice, but these two colors were already reserved in the color scheme. I guess they are not too common, but while testing today I have seen at least the cyan in one occasion. Maybe new unique colors should be chosen to avoid any confusion. |
From: Robert H. <ha...@st...> - 2010-10-17 19:41:21
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We could certainly do that. But it isn't a conflict -- when you create the hbonds using calculate hbonds stucture there are only five types: 3/10 turn (+3), alpha turn (+4), pi turn (+5), parallel bridges, and antiparallel bridges. For those last two, I simply chose to use two unused colors for (+2 and -3), since we already had those colors, and with DSSP those are not possible (in terms of defining structure). I just thought that was simpler. 2010/10/16 Angel Herráez <ang...@ua...> > Bob, I see a conflict in coloring of Hbonds > > In beta sheets, > calculate hbonds;color hbonds type > renders them in yellow. That was the standard coloring. > > The new > calculate hbonds structure;color hbonds type > renders them in cyan or white (parallel/antiparallel strands). That's nice, > but these two colors > were already reserved in the color scheme. I guess they are not too common, > but while > testing today I have seen at least the cyan in one occasion. > Maybe new unique colors should be chosen to avoid any confusion. > > > > > > > > ------------------------------------------------------------------------------ > Download new Adobe(R) Flash(R) Builder(TM) 4 > The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly > Flex(R) Builder(TM)) enable the development of rich applications that run > across multiple browsers and platforms. Download your free trials today! > http://p.sf.net/sfu/adobe-dev2dev > _______________________________________________ > 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 |
From: Angel H. <ang...@ua...> - 2010-10-18 08:27:06
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Oh, I see. I don't have a strong feeling about this. You can leave it as it is. I was mostly thinking on documentation (colors page at website) Any opinions on this from other users? |