Peter, Based on what you provided, it doesn't look like you're loading a structure site about which to carve. Does:
load test_file.xplor isomesh mesh1, test_file, 1.0 work to show you the whole map? Cheers, Warren ________________________________________ From: peter hudson [mailto:peter.hudson.pe...@gmail.com] Sent: Thursday, April 02, 2009 2:12 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] problem in showing the electron density map Hello all I am trying to upload the ED map on pymol. but, it is not visible on the screen. Although i checked at pymol wiki and i did as it is given on the wiki. For example. I took ccp4 format map and coverted it into xplor format with mapman.(beacuse i tried with ccp4 format map with test_file.map as well as test_file.ccp4 maps, but pymol showed this kind of error. I begin like this- load test_file.xplor, test_file isomesh map, test_file, 2.0, site, carve=1.6 But, it doesnot show up on the screen. I am writing the pymol taskbar reponse. 1) loading of the map file It has been loaded sucessfully, and shows this kind of information on task bar. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- mdException Exception in Tk callback Function: <bound method Normal.file_open of <pmg_tk.skins.normal.Normal instance at 0xb7833a2c>> (type: <type 'instancemethod'>) Args: () Traceback (innermost last): File "/home/soft/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/home/soft/pymol/modules/pmg_tk/skins/normal/__init__.py", line 438, in file_open self.cmd.load(ofile,quiet=0) File "/home/soft/pymol/modules/pymol/importing.py", line 496, in load raise pymol.CmdException CmdException: <pymol.CmdException instance at 0x985dc8c> Crystal: Unit Cell 54.064 84.618 101.215 Crystal: Alpha Beta Gamma 90.000 90.000 90.000 Crystal: RealToFrac Matrix Crystal: 0.0185 -0.0000 -0.0000 Crystal: 0.0000 0.0118 -0.0000 Crystal: 0.0000 0.0000 0.0099 Crystal: FracToReal Matrix Crystal: 54.0640 0.0000 0.0000 Crystal: 0.0000 84.6180 0.0000 Crystal: 0.0000 0.0000 101.2150 Crystal: Unit Cell Volume 463037. ExecutiveLoad: "/home/peter/test_file.xplor" loaded as "test_file", through state 0. -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 2. generation of map-- isomesh map, test_file, 2.0, site, carve=1.6 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PyMOL>load test_file.xplor, test_file Crystal: Unit Cell 54.064 84.618 101.215 Crystal: Alpha Beta Gamma 90.000 90.000 90.000 Crystal: RealToFrac Matrix Crystal: 0.0185 -0.0000 -0.0000 Crystal: 0.0000 0.0118 -0.0000 Crystal: 0.0000 0.0000 0.0099 Crystal: FracToReal Matrix Crystal: 54.0640 0.0000 0.0000 Crystal: 0.0000 84.6180 0.0000 Crystal: 0.0000 0.0000 101.2150 Crystal: Unit Cell Volume 463037. ExecutiveLoad: "test_file.xplor" loaded as "test_file", through state 0. PyMOL>isomesh map, test_file, 2.0, site, carve=1.6 Selector-Error: Invalid Selection Name. ( site )<-- Executive: object "map" created. Isomesh: created "map", setting level to 2.000 ObjectMesh: updating "map". ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- But, finally map doesnot show up. What could be the problem. Suggestions would be appereciated. Thanks in advance Peter
