[PyMOL] Electron density map in pymol
Hello all pymol users I am new to pymol and trying to open a .xplor map file in pymol to get the electron density map of publication grade. The command i write for pymol to open the file and show electron density map is - 1) I convert ccp4 .map file into the .xplor file through mapman. # mymap.xplor loaded as " mymap" loaded as state 0. 2) Then i load the .xplor map file into pymol and write the following commands- *isomesh map, mymap.xplor, 2.0, site, carve=1.6 * isomesh: map or brick object "*mymap.xplor*" not found. What could be the problem? can any one give suggestion to solve it? Thanks in advance Jhon
Re: [PyMOL] Electron density map in pymol
2008/9/26 Jhon Thomas : > Hello all pymol users > > I am new to pymol and trying to open a .xplor map file in pymol to get the > electron density map of publication grade. > The command i write for pymol to open the file and show electron density > map is - > > 1) I convert ccp4 .map file into the .xplor file through mapman. > > # mymap.xplor loaded as " mymap" loaded as state 0. > 2) Then i load the .xplor map file into pymol and write the following > commands- > > isomesh map, mymap.xplor, 2.0, site, carve=1.6 > > isomesh: map or brick object "mymap.xplor" not found. > I have to "load" the map first! Example: load mymap.xplor, themap isomesh themapobject, themap, 2.0, site, carve=1.6 > > What could be the problem? can any one give suggestion to solve it? > > Thanks in advance > > Jhon > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Folmer Fredslund Kantatgatan 84 21570 Malmö Sverige Tlf.: (+46) 40 66 72 194 Mobil: (+45) 61 468 009 Mail: folm...@gmail.com MSN: folm...@gmail.com Skype: folmerfredslund -BEGIN GEEK CODE BLOCK- Version: 3.1 GS/MU$ d>++$ s:>+++:+++ a->? C> UL P+ L++ E++@ W+ N? o? K?(+) w-- O- M-->+++$ V? PS+ PE-- Y? PGP- t+++>--- 5 X+ R*>$ tv++>! b+(+++) DI++(-) !D? G e+++()>* h---()>* r+++ y+++@>$ --END GEEK CODE BLOCK--
Re: [PyMOL] Electron density map in pymol
2008/9/26 Jhon Thomas : > hello Mr. Fredslund > > I tried the way you have written but it is not working-- > > map file name - test_map.xplor > load test_map.xplor > > isomeah map, test_map.xplor, 2.0, site, carve=1.6 > > Is this is the correct of writing the command Dear Mr. Thomas Ok, some basic PyMOL knowledge: whenever you "load" something to PyMOL it is given a name. load test_map.xplor, test_map Now PyMOL knows that the map is henceforth called "test_map" Therefore you should write isomesh mapobject, test_map, 2.0, site, carve=1.6 btw it is also possible to use a ccp4 map; simply rename the file to end with ccp4 instead of map example: mv test_map.map test_map.ccp4 use test_map.ccp4 instead of the xplor map. (this might prove to be slower though) furthermore I would suggest you read the pymol wiki (http://www.pymolwiki.org/index.php/Load) or when using PyMOL try the help function: help load help isomesh help color hope this helps > On Fri, Sep 26, 2008 at 5:42 PM, Folmer Fredslund wrote: >> >> 2008/9/26 Jhon Thomas : >> > Hello all pymol users >> > >> > I am new to pymol and trying to open a .xplor map file in pymol to get >> > the >> > electron density map of publication grade. >> > The command i write for pymol to open the file and show electron density >> > map is - >> > >> > 1) I convert ccp4 .map file into the .xplor file through mapman. >> > >> > # mymap.xplor loaded as " mymap" loaded as state 0. >> > 2) Then i load the .xplor map file into pymol and write the following >> > commands- >> > >> > isomesh map, mymap.xplor, 2.0, site, carve=1.6 >> > >> > isomesh: map or brick object "mymap.xplor" not found. >> > >> >> I have to "load" the map first! >> >> Example: >> >> load mymap.xplor, themap >> isomesh themapobject, themap, 2.0, site, carve=1.6 >> >> >> >> >> >> >> > >> > What could be the problem? can any one give suggestion to solve it? >> > >> > Thanks in advance >> > >> > Jhon >> > >> > >> > - >> > This SF.Net email is sponsored by the Moblin Your Move Developer's >> > challenge >> > Build the coolest Linux based applications with Moblin SDK & win great >> > prizes >> > Grand prize is a trip for two to an Open Source event anywhere in the >> > world >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> > ___ >> > PyMOL-users mailing list >> > PyMOL-users@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/pymol-users >> > >> > >> >> >> >> -- >> Folmer Fredslund >> Kantatgatan 84 >> 21570 Malmö >> Sverige >> Tlf.: (+46) 40 66 72 194 >> Mobil: (+45) 61 468 009 >> Mail: folm...@gmail.com >> MSN: folm...@gmail.com >> Skype: folmerfredslund >> -BEGIN GEEK CODE BLOCK- >> Version: 3.1 >> GS/MU$ d>++$ s:>+++:+++ a->? C> UL P+ L++ E++@ W+ N? o? >> K?(+) w-- O- M-->+++$ V? PS+ PE-- Y? PGP- t+++>--- 5 X+ R*>$ >> tv++>! b+(+++) DI++(-) !D? G e+++()>* h---()>* r+++ y+++@>$ >> --END GEEK CODE BLOCK-- > > -- Folmer Fredslund Kantatgatan 84 21570 Malmö Sverige Tlf.: (+46) 40 66 72 194 Mobil: (+45) 61 468 009 Mail: folm...@gmail.com MSN: folm...@gmail.com Skype: folmerfredslund -BEGIN GEEK CODE BLOCK- Version: 3.1 GS/MU$ d>++$ s:>+++:+++ a->? C> UL P+ L++ E++@ W+ N? o? K?(+) w-- O- M-->+++$ V? PS+ PE-- Y? PGP- t+++>--- 5 X+ R*>$ tv++>! b+(+++) DI++(-) !D? G e+++()>* h---()>* r+++ y+++@>$ --END GEEK CODE BLOCK--
Re: [PyMOL] Electron density map in pymol
Jhon, all the newer builds of PyMol are able to read ccp4 maps, no need to convert to xplor format. As far as your commands are concerned, you are almost there. Try this: load mymap.ccp4, format=ccp4, mymap isomesh map, mymap, 2.0, site, carve=1.6 were map is the name of the map graphical object you want to create, mymap is the name of the object that holds the actual map as defined by the load command. HTH Carsten -Original Message- From: Jhon Thomas [mailto:jhon1.tho...@gmail.com] Sent: Friday, September 26, 2008 7:15 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Electron density map in pymol Hello all pymol users I am new to pymol and trying to open a .xplor map file in pymol to get the electron density map of publication grade. The command i write for pymol to open the file and show electron density map is - 1) I convert ccp4 .map file into the .xplor file through mapman. # mymap.xplor loaded as " mymap" loaded as state 0. 2) Then i load the .xplor map file into pymol and write the following commands- isomesh map, mymap.xplor, 2.0, site, carve=1.6 isomesh: map or brick object "mymap.xplor" not found. What could be the problem? can any one give suggestion to solve it? Thanks in advance Jhon
