Re: [PyMOL] why losing information about simulation box size in pdb file after edit it?

[Jason V. <jas...@gm...>]

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 <apz...@gm...> 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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