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
