Hi David, You have a rotate command in that script. Did you mean to 'turn' the camera rather than 'rotate' the atomic coordinates?
Cheers, Warren > -----Original Message----- > From: David Garboczi [mailto:dgarbo...@niaid.nih.gov] > Sent: Thursday, October 22, 2009 7:00 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] not getting a simple translation > > I have a 5 similar domains (struct.pdb) aligned on another > one (rcsb.pdb). I made a copy of one of them and translated > it 37 angstroms to the right. translate [37, 0, 0 ]. > But I did not get a simple translation. The two molecules > end up having a rotation between them. > Here's the script. I need an "origin" command or other...? > thanks, > Dave > > #macpymol-1_1r1.tgz > reinitialize > bg_color white > set antialias , 1 > set ray_trace_fog=0 > set depth_cue=0 > set direct, 0.7 > > set ribbon_smooth, 1 > set ribbon_width, 3 > > set_view (\ > -0.342648655, 0.901220083, -0.265300900,\ > 0.939403236, 0.325558662, -0.107372068,\ > -0.010394786, -0.286019355, -0.958166420,\ > 0.000000000, 0.000000000, -128.319412231,\ > 22.162364960, 43.079395294, 12.406776428,\ > 101.167999268, 155.470825195, 0.000000000 ) > > load rcsb.pdb, rcsb2 > load rcsb.pdb, a33alone > > #1kcg:A > load struct(2).pdb, 22 > #1e8i:A > load struct(3).pdb, 33 > #1ypo:A > load struct(4).pdb, 44 > #1B6E_dimer.pdb:A > load struct(5).pdb, 55 > #1qo3:C > load struct(6).pdb, 66 > > hide lines, /rcsb2//* > hide nonbonded, /rcsb2//* > hide lines, /a33alone//* > hide nonbonded, /a33alone//* > hide lines, /22//* > hide nonbonded, /22//* > hide lines, /33//* > hide nonbonded, /33//* > hide lines, /44//* > hide nonbonded, /44//* > hide lines, /55//* > hide nonbonded, /55//* > hide lines, /66//* > hide nonbonded, /66//* > > color red, /a33alone//* > show ribbon, /a33alone//* and (name ca or name c or name n) > > color red, /rcsb2//* > show ribbon, /rcsb2//* and (name ca or name c or name n) > > color yelloworange, /22//* > color blue, /22//A/98-134/* > color blue, /22//A/190-215/* > show ribbon, /22//* and (name ca or name c or name n) > > color yelloworange, /33//* > color blue, /33//A/83-121/* > color blue, /33//A/174-199/* > show ribbon, /33//* and (name ca or name c or name n) > > color yelloworange, /44//* > color blue, /44//A/142-180/* > color blue, /44//A/244-269/* > show ribbon, /44//* and (name ca or name c or name n) > > color yelloworange, /55//* > color blue, /55//A/60-97/* > color blue, /55//A/153-179/* > show ribbon, /55//* and (name ca or name c or name n) > > color yelloworange, /66//* > color blue, /66//C/144-175/* > color blue, /66//C/233-258/* > show ribbon, /66//* and (name ca or name c or name n) hide > ribbon, /66//C/140-143/* > > rotate y, 30 > > set_view (\ > -0.287066191, 0.957891881, 0.004756007,\ > 0.607159078, 0.178112596, 0.774357498,\ > 0.740909398, 0.225178465, -0.632728696,\ > 0.000000000, 0.000000000, -191.885284424,\ > 24.745697021, 46.720252991, 14.490940094,\ > 151.283813477, 232.486755371, 0.000000000 ) > > translate [37, 0, 0 ], a33alone > zoom complete=1 > > #ray 4800,4800 > #png /Users/dgarboczi/Documents/A_on_A/A_on_A_2_newview_4.png, dpi=600 > > > -- > > -------------------------------------------------------------- > ---------------- > Come build with us! The BlackBerry(R) Developer Conference in > SF, CA is the only developer event you need to attend this > year. Jumpstart your developing skills, take BlackBerry > mobile applications to market and stay ahead of the curve. > Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
