date:20140124

[PyMOL] Is it Possible to Redirect PyMOL Output?

2014-01-24 Thread Wilson Omesiete

I am using...

import __main__, os
os.environ['PYMOL_PATH'] = "C:\Python27\PyMOL"
 __main__.pymol_argv=["pymol","-qx"]
 import pymol
pymol.finish_launching()

... to launch PyMOL from another Python based program that has it's own GUI.

Is it possible for me to reroute the output from PyMOL to a file or string
to avoid a command prompt spawning along with the PyMOL viewer?
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Re: [PyMOL] Roving maps from scripting level?

2014-01-24 Thread Nat Echols

On Fri, Jan 24, 2014 at 11:55 AM, Schubert, Carsten [JRDUS] <
cschu...@its.jnj.com> wrote:

> I am trying to get the roving density features to work from a scripting
> level w/o invoking the Density Wizard. Setting up the following script
> loads fine, but does not enable roving. Is there anything else I need to
> define in the settings or am I stuck with using the Density  Wizard?
>

Try this:

cmd.load("test.pdb","MyProt")
cmd.zoom("polymer and chain A and resi 1")

cmd.load("2fofc.ccp4",object="2FoFc_map")
cmd.load("fofc.ccp4",object="FoFc_map")

cmd.set("suspend_updates", 1)
cmd.set("roving_detail", 10)
cmd.set("roving_origin", 1)
cmd.set("roving_map1_name","2FoFc_map")
cmd.set("roving_map2_name","FoFc_map")
cmd.set("roving_map3_name","FoFc_map")

cmd.set("roving_map1_level",1.0)
cmd.set("roving_map2_level",3.0)
cmd.set("roving_map3_level",-3.0)

cmd.isomesh(name="rov_m1",map="2FoFc_map",level="1.0", selection="polymer
and chain A and resi 1")
cmd.color("skyblue","rov_m1")
cmd.isomesh(name="rov_m2", map="FoFc_map", level="3.0", selection="polymer
and chain A and resi 1")
cmd.color("green","rov_m2")
cmd.isomesh(name="rov_m3", map="FoFc_map", level="-3.0", selection="polymer
and chain A and resi 1")
cmd.color("red","rov_m3")

cmd.set("suspend_updates", 0)

-Nat
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Re: [PyMOL] quiet copy

2014-01-24 Thread Osvaldo Martin

Thank you Thomas!


On Fri, Jan 24, 2014 at 1:06 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Osvaldo,
>
> http://pymolwiki.org/index.php/Feedback
>
> PyMOL> feedback disable, executive, actions
>
> Cheers,
>   Thomas
>
> On 24 Jan 2014, at 13:33, Osvaldo Martin  wrote:
> > When I run a script, like this
> >
> > import __main__
> > __main__.pymol_argv = ['pymol','-qc']
> > import pymol
> > from pymol import cmd
> > pymol.finish_launching()
> >
> > cmd.copy('mol_copy','mol_ori')
> >
> > I get the message "Executive: object mol_copy created." in the terminal.
> It is posible to keep the copy comand quiet?
> >
> > Thanks.
>
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
>
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[PyMOL] Roving maps from scripting level?

2014-01-24 Thread Schubert, Carsten [JRDUS]

Dear All,

I am trying to get the roving density features to work from a scripting level 
w/o invoking the Density Wizard. Setting up the following script loads fine, 
but does not enable roving. Is there anything else I need to define in the 
settings or am I stuck with using the Density  Wizard?

Many thanks for any pointers

Carsten


# Roving_test.py

cmd.load("test.pdb","MyProt")
cmd.zoom("polymer and chain A and resi 1")

cmd.load("2fofc.ccp4",object="2FoFc_map")
cmd.load("fofc.ccp4",object="FoFc_map")

cmd.isomesh(name="2fofc",map="2FoFc_map",level="1.0", selection="polymer and 
chain A and resi 1")
cmd.color("skyblue","2fofc")
cmd.isomesh(name="fofc", map="FoFc_map", level="3.0", selection="polymer and 
chain A and resi 1")
cmd.color("green","fofc")
cmd.isomesh(name="neg-fofc", map="FoFc_map", level="-3.0", selection="polymer 
and chain A and resi 1")
cmd.color("red","neg-fofc")

cmd.set("roving_map1_name","2fofc")
cmd.set("roving_map2_name","fofc")
cmd.set("roving_map3_name","neg-fofc")

cmd.set("roving_map1_level",1.0)
cmd.set("roving_map2_level",3.0)
cmd.set("roving_map3_level",-3.0)

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Re: [PyMOL] quiet copy

2014-01-24 Thread Thomas Holder

Hi Osvaldo,

http://pymolwiki.org/index.php/Feedback

PyMOL> feedback disable, executive, actions

Cheers,
  Thomas

On 24 Jan 2014, at 13:33, Osvaldo Martin  wrote:
> When I run a script, like this
> 
> import __main__
> __main__.pymol_argv = ['pymol','-qc']
> import pymol
> from pymol import cmd
> pymol.finish_launching()
> 
> cmd.copy('mol_copy','mol_ori')
> 
> I get the message "Executive: object mol_copy created." in the terminal. It 
> is posible to keep the copy comand quiet?
> 
> Thanks.


-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


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[PyMOL] quiet copy

2014-01-24 Thread Osvaldo Martin

When I run a script, like this

import __main__
__main__.pymol_argv = ['pymol','-qc']
import pymol
from pymol import cmd
pymol.finish_launching()

cmd.copy('mol_copy','mol_ori')

I get the message "Executive: object mol_copy created." in the terminal. It
is posible to keep the copy comand quiet?

Thanks.
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[PyMOL] Is it Possible to Redirect PyMOL Output?

Re: [PyMOL] Roving maps from scripting level?

Re: [PyMOL] quiet copy

[PyMOL] Roving maps from scripting level?

Re: [PyMOL] quiet copy

[PyMOL] quiet copy

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