Cun,
For measuring, also check out the Measurement Wizard. Select
Wizard > Measurement
from the Upper Control Window (the Tcl/Tk window). Then, on the far
right you will see a box with "Distances" in it. This is a menu
option displaying what PyMOL is measuring. If you want to measure
distances leave it as is; if you want to measure angles or dihedrals
click on "Distances" and change it to your desired option. Once
you're done with your measurements, click "Done" to quit the wizard.
As for learning the PyMOL API check out
http://pymolwiki.org/index.php/Category:Commands
which has over 160 commands documented. Most PyMOL API commands
directly mirror their UI counterparts. For example,
save fileName.pdb, objName, state=0
would simply translate to
cmd.save( "fileName.pdb", "objName", state=0 );
Finally, welcome to PyMOL.
-- Jason
Jason Vertrees, PhD
PyMOLWiki -- http://www.pymolwiki.org
On Wed, Nov 25, 2009 at 9:28 PM, Cun Zhang <apzc2...@gmail.com> wrote:
> Hi, pymol users.
> I'm a pymol newbie .I have serval question.
> I have a pdb file which include the information about box size, like
> TITLE God Rules Over Mankind, Animals, Cosmos and Such
> REMARK THIS IS A SIMULATION BOX
> CRYST1 39.000 39.000 56.140 90.00 90.00 90.00 P 1 1
> MODEL 1
> HETATM 1 C UNK 1 25.851 19.500 0.710 1.00 0.00
>
> I run pymol, and load it, then delete some molecules and save it. Now the
> information about box size is losing.
>
> 2. Is there any way to get the information about bonds, angles and
> dihedrals ?
> I found the following command can display the bonds information, but
> can't be assigned to a variable.
> >cmd.select('all')
> >atoms=cmd.get_model('sele')
> >print atoms.list()
> 3. Is there any way to learn these python api commands of pymol ?
>
> Thank you!
>
>
> Blog: http://blog.4message.net
>
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