2008/9/26 Jhon Thomas <jhon1.tho...@gmail.com>: > 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 <folm...@gmail.com> wrote: >> >> 2008/9/26 Jhon Thomas <jhon1.tho...@gmail.com>: >> > 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------
