From: Eric M. <mar...@ya...> - 2010-01-18 14:00:58
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Dear Bob, You've made FANTASTIC progress! Really exciting! For 11.9.20_dev Jan 16 18:11 It appears to me that the map is slightly offset from the atoms, in the negative X direction -- look at the red oxygens sticking up and down in this snapshot (axes are visible): http://www.umass.edu/molvis/tests/jmol-edm-test3/3hyd_jmol.png Compare with same in PyMOL: http://www.umass.edu/molvis/tests/jmol-edm-test3/3hyd_pymol.png Secondly, the PyMOL map is contoured at 1.0 sigma. The Jmol map appears similar -- is the default 1.0 sigma? Is the "cutoff" reported as 1.48 the sigma value? How do I set the sigma? (Please remember, the script manual is unavailable at the moment.) By the way, I've made every map I've mentioned on this list downloadable at the URL I gave in the email -- download links are in a big pink box. No matter now, we can all use the easily available ccp4 maps from http://eds.bmc.uu.se/eds/ (just wanted you to know I tried to make it easy for you to get the files). -Eric > From: Robert Hanson <ha...@st...> > Subject: [Jmol-users] Electron density in X-PLOR format and CCP4 format SUCCESS! > To: jmo...@li... > Date: Sunday, January 17, 2010, 7:58 PM > OK, Eric, I found a couple of map files. > Everything looks perfect to me, but of course it needs > testing. See http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip. > Jmol 11.9.20_dev > > > WOW, I have to say, this is exciting. I want to learn more > about electron density maps! Jmol loads this one > instantly: > > isosurface color yellow within 2.0 {*} > "c:/temp/3hyd_map.ccp4" mesh nofill; > > reading isosurface data from c:/temp/3hyd_map.ccp4 > FileManager opening c:\temp\3hyd_map.ccp4 > data file type was determined to be MRC > > FileManager opening c:\temp\3hyd_map.ccp4 > MRC header: mode: 2 > MRC header: dmin,dmax,dmean: > -1.1890318,4.998787,-0.014114891 > > MRC header: ispg,nsymbt: 5,0 > MRC header: rms: 0.74718976 > MRC header: labels: 1 > Created by MAPMAN V. 080625/7.8.5 at Fri Jan 15 04:34:50 > 2010 for A. Nonymous > MRC header: bytes read: 1024 > > > MRC/Jmol interpretation: > > MRC/Jmol cutoff set to (dmean + 2*rms) = 1.4802647 > grid parameters: nx,ny,nz: 38,90,55 > grid parameters: nxStart,nyStart,nzStart: -11,-6,-11 > grid parameters: mx,my,mz: 144,16,56 > > grid parameters: a,b,c,alpha,beta,gamma: > 49.475,4.8375,19.4375,90.0,96.65,90.0 > grid parameters: mapc,mapr,maps: 2,1,3 > grid parameters: originX,Y,Z: 0.0,0.0,0.0 > grid header: a,b,c,alpha,beta,gamma: > 49.475,4.8375,19.4375,90.0,96.65,90.0 > > Jmol unit cell vectors: > a: (0.34357637, 0.0, 0.0) > b: (-1.3215866E-8, 0.30234376, 0.0) > c: (-0.040195342, -1.692914E-8, 0.34476298) > Jmol origin in unit cell coordinates: (-3.3371913, > -1.8140624, -3.7923927) > > Jmol use isosurface OFFSET {x y z} if you want to > shift it. > Jmol origin in slow-to-fast system: (-1.8140624, > -3.3371913, -3.7923927) > > voxel grid origin:(-1.8140624, -3.3371913, -3.7923927) > voxel grid count/vector:55 -0.040195342 -1.692914E-8 > 0.34476298 > > voxel grid count/vector:90 0.34357637 0.0 0.0 > voxel grid count/vector:38 -1.3215866E-8 0.30234376 0.0 > JVXL read: 55 x 90 x 38 data points > VolumeFileReader reading data progressively > boundbox corners {-0.7172928 -0.3137546 -1.3790519} > {25.194487 5.128433 12.066704} > > VolumeFileReader closing file: data min/max/mean = > -1.1890318, 4.998787, -0.01760154 > isosurface1 created with cutoff = 1.4802647 ; number of > isosurfaces = 1 > > > On Sun, Jan 17, 2010 at 12:26 PM, Robert Hanson <ha...@st...> > wrote: > > I'll need the xplor file. Not > finding that... > > > On Sun, Jan 17, 2010 at 11:50 AM, Eric Martz <mar...@ya...> > wrote: > > I > found instructions here > > http://www.ucl.ac.uk/~rmhasek/pymol.html > > > > for using a program called mapman to convert ccp4 electron > density maps to x-plor format. I think I did that, but my > results in Jmol 11.9.19 were unsatisfactory. You can see > snapshots and download the map and other files here: > > > > > > http://www.umass.edu/molvis/tests/jmol-edm-test2/ > > > > Comments? Help? > > > > -Eric > > > > > > > > > > > > ------------------------------------------------------------------------------ > > Throughout its 18-year history, RSA Conference consistently > attracts the > > world's best and brightest in the field, creating > opportunities for Conference > > attendees to learn about information security's most > important issues through > > interactions with peers, luminaries and emerging and > established companies. > > http://p.sf.net/sfu/rsaconf-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 > > > > > -- > 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 > > > -----Inline Attachment Follows----- > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently > attracts the > world's best and brightest in the field, creating > opportunities for Conference > attendees to learn about information security's most > important issues through > interactions with peers, luminaries and emerging and > established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > -----Inline Attachment Follows----- > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |