Re: [PyMOL] problem in showing the electron density map
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. -0. Crystal: 0. 0.0118 -0. Crystal: 0. 0. 0.0099 Crystal: FracToReal Matrix Crystal: 54.0640 0. 0. Crystal: 0. 84.6180 0. Crystal: 0. 0. 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 -- PyMOLload 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. -0. Crystal: 0. 0.0118 -0. Crystal: 0. 0. 0.0099 Crystal: FracToReal Matrix Crystal: 54.0640 0. 0. Crystal: 0. 84.6180 0. Crystal: 0. 0. 101.2150 Crystal: Unit Cell Volume 463037. ExecutiveLoad: test_file.xplor loaded as test_file, through state 0. PyMOLisomesh 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
Re: [PyMOL] Visualizing symmetry
Mark, No, unfortunately PyMOL doesn't have a way of isolating those atoms which strictly lie within a single unit cell. That is a longstanding request. As for the second case, what you're describing should work, provided that the segment identifiers are different. The segi option to symexp will assign a unique segment identifier to each of the newly created chains. For example: fetch 1re1, async=1 symexp sym, 1re1, 1re1, 4.0, segi=1 create dimer, 1re1 or sym0300 delete 1re1 sym* Cheers, Warren -Original Message- From: Mark Nance [mailto:mrna...@lsi.umich.edu] Sent: Thursday, April 02, 2009 2:52 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Visualizing symmetry I have a pair of questions about displaying symmetry. First, I would like to recreate the packing of my protein within a single, distinct unit cell. I'd also like to show the lines of the unit cell around it. I can do it with multiple iterations of the symexp command, but is there a more elegant way? Second, if I use symexp to generate the second chain of my dimer I end up with two objects that I would like to merge. If I create dimer, monomer or sym_monomer the resulting object contains half of the atoms from each chain rather than all of the atoms from both chains. I assume the problem is having two atoms with the same name in one object; is there a way around this? Thanks, Mark Nance Life Sciences Institute University of Michigan -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] problem in showing the electron density map
Hi Peter, On Fri, 03 Apr 2009 02:38:03 +0530, peter hudson peter.hudson.pe...@gmail.com wrote: 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- Warren answered the later problem regarding the site selection or object. You should be able to load a ccp4 map either directly as a .ccp4 file, or to force it to load as a ccp4 format with: load test_file.ccp4, map, format=ccp4 Does PyMOL complain that it doesn't know the format with an error like: PyMOLload test_ccp4.map Error: .map is ambiguous. Please add format or use another extension: Error: For example, load fofc.map, format=ccp4 or load 2fofc.xplor. or was the error that you couldn't display the map on the molecule (as in the error that Warren commented on about using site as a selection when site has not been defined? Also be aware that PyMOL needs to have a map that is calculated to cover the molecule that you are showing since it does not automatically extend the map using symmetry. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
