Re: [PyMOL] Make sure zoom is viewed from surface
Hi Troels, Jason, Edward,
nice little problem and nice layouts by Jason and Edward. Let me
contribute some code, it follows Edwards approach.
See attachment. Requires psico.
Cheers,
Thomas
Edward A. Berry wrote, On 10/08/12 20:57:
Jason Vertrees wrote:
Hi Troels,
I've run into this problem a few times, too, but never took the time
to solve it correctly.
A quick plan might look like:
* cmd.orient on the selection
* store the view vector (http://www.pymolwiki.org/index.php/Get_View)
* let C1 = count the number of atoms behind the view vector, using
something like (http://www.pymolwiki.org/index.php/SelInside)
* invert the view vector
* let C2 = count the number of atoms behind the view vector, using
something like (http://www.pymolwiki.org/index.php/SelInside)
* compare C1 to C2, choosing the
* if C2< C1 then flip the view
You could use other tricks. I'm sure the community has other ideas.
Calculate center of mass or average of all coordinates
calculate vector from that to point of interest
rotate view so that vector points toward front/camera
translate so point of interest is centerd
maybe reverse the last two steps?
Cheers,
-- Jason
On Sun, Oct 7, 2012 at 10:04 AM, Troels Emtekær Linnet
wrote:
Hi pymolers.
I am generating a list of residue ID's from some calculations.
Now I want to make a little script that select the residue and sticks it
and then zoom and make .png file.
How do I make sure that the zoom, is viewed from "outside" the protein for
each residue/.png file?
Best
Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
from pymol import cmd, CmdException
def zoomoutside(selection, ref='', state=-1, operator='byobject',
quiet=1, **kwargs):
'''
DESCRIPTION
Zoom the given selection and orient such that the object center of
mass is behind the selection center of mass.
USAGE
zoomoutside selection [, ref [, state ]]
ARGUMENTS
selection = string: atom selection to zoom on
ref = string: reference selection to orient behind selection
{default: byobject }
SEE ALSO
zoom, orient
'''
from chempy import cpv
from psico.querying import centerofmass
state, quiet = int(state), int(quiet)
if not ref:
ref = '%s (%s)' % (operator, selection)
com_sele = centerofmass(selection, state)
com_ref = centerofmass(ref, state)
view = list(cmd.get_view())
camera_rotation = [view[0:3], view[3:6], view[6:9]]
vec = cpv.sub(com_sele, com_ref)
vec_camera = cpv.transform(camera_rotation, vec)
axis = cpv.cross_product(vec_camera, [0.,0.,1.])
angle = cpv.get_angle(vec_camera, [0.,0.,1.])
rotation = cpv.rotation_matrix(angle, axis)
view[:9] = [x
for row in cpv.multiply(rotation, camera_rotation)
for x in row]
cmd.set_view(view)
cmd.zoom(selection, state=state, **kwargs)
cmd.extend('zoomoutside', zoomoutside)
--
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Re: [PyMOL] Make sure zoom is viewed from surface
Jason Vertrees wrote: > Hi Troels, > > I've run into this problem a few times, too, but never took the time > to solve it correctly. > > A quick plan might look like: >* cmd.orient on the selection >* store the view vector (http://www.pymolwiki.org/index.php/Get_View) >* let C1 = count the number of atoms behind the view vector, using > something like (http://www.pymolwiki.org/index.php/SelInside) >* invert the view vector >* let C2 = count the number of atoms behind the view vector, using > something like (http://www.pymolwiki.org/index.php/SelInside) >* compare C1 to C2, choosing the >* if C2< C1 then flip the view > > You could use other tricks. I'm sure the community has other ideas. > Calculate center of mass or average of all coordinates calculate vector from that to point of interest rotate view so that vector points toward front/camera translate so point of interest is centerd maybe reverse the last two steps? > Cheers, > > -- Jason > > > On Sun, Oct 7, 2012 at 10:04 AM, Troels Emtekær Linnet > wrote: >> Hi pymolers. >> >> I am generating a list of residue ID's from some calculations. >> Now I want to make a little script that select the residue and sticks it >> and then zoom and make .png file. >> >> How do I make sure that the zoom, is viewed from "outside" the protein for >> each residue/.png file? >> >> Best >> >> Troels Emtekær Linnet >> Ved kløvermarken 9, 1.th >> 2300 København S >> Mobil: +45 60210234 >> >> >> -- >> Don't let slow site performance ruin your business. Deploy New Relic APM >> Deploy New Relic app performance management and know exactly >> what is happening inside your Ruby, Python, PHP, Java, and .NET app >> Try New Relic at no cost today and get our sweet Data Nerd shirt too! >> http://p.sf.net/sfu/newrelic-dev2dev >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Make sure zoom is viewed from surface
Hi Troels, I've run into this problem a few times, too, but never took the time to solve it correctly. A quick plan might look like: * cmd.orient on the selection * store the view vector (http://www.pymolwiki.org/index.php/Get_View) * let C1 = count the number of atoms behind the view vector, using something like (http://www.pymolwiki.org/index.php/SelInside) * invert the view vector * let C2 = count the number of atoms behind the view vector, using something like (http://www.pymolwiki.org/index.php/SelInside) * compare C1 to C2, choosing the * if C2 < C1 then flip the view You could use other tricks. I'm sure the community has other ideas. Cheers, -- Jason On Sun, Oct 7, 2012 at 10:04 AM, Troels Emtekær Linnet wrote: > Hi pymolers. > > I am generating a list of residue ID's from some calculations. > Now I want to make a little script that select the residue and sticks it > and then zoom and make .png file. > > How do I make sure that the zoom, is viewed from "outside" the protein for > each residue/.png file? > > Best > > Troels Emtekær Linnet > Ved kløvermarken 9, 1.th > 2300 København S > Mobil: +45 60210234 > > > -- > Don't let slow site performance ruin your business. Deploy New Relic APM > Deploy New Relic app performance management and know exactly > what is happening inside your Ruby, Python, PHP, Java, and .NET app > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > http://p.sf.net/sfu/newrelic-dev2dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
