Hello, I have a few pdb files of small molecules that I would like to know the dimensions of. Is it possible to use Chimera the measure the minimum x y z lengths - taking into account Van der Waals radii? Or perhaps you could suggest other software for this? Many thanks _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ Do you have a story that started on Hotmail? Tell us now
Yes, something like this: from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): print m.name atoms = m.atoms for dim in range(3): atoms.sort(lambda a1, a2, dim=dim: cmp(a1.coord().data()[dim], a2.coord().data()[dim])) print "minimum %s: %g" % ("xyz"[dim], atoms[0].coord().data()[dim] - atoms[0].radius) print "maximum %s: %g" % ("xyz"[dim], atoms[-1].coord().data()[dim] - atoms[-1].radius) Put the above in a file ending in ".py" and open it in Chimera and it will print the min/max xyz values accounting for radius in the Reply Log. --Eric Eric Pettersen UCSF Computer Graphics Lab On Apr 16, 2010, at 10:46 AM, le monk wrote:
Hello,
I have a few pdb files of small molecules that I would like to know the dimensions of. Is it possible to use Chimera the measure the minimum x y z lengths - taking into account Van der Waals radii? Or perhaps you could suggest other software for this?
Many thanks
Get a free e-mail account with Hotmail. Sign-up now._______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you Eric - this is really helpful. But as these are minimum x y z lengths then the reported dimensions will be different if the molecules coordinates were transformed. Can this script be modified to give the minimum dimensions of the molecule (not just the x y z dimensions)? For example, can a box be drawn around the Van der Waal radii whose volume was the minimum possible for that molecule, and report the lengths of each of its dimensions? This would be really nice to directly compare the size of small molecules. Many thanks CC: chimera-users@cgl.ucsf.edu From: pett@cgl.ucsf.edu To: le_monk@hotmail.com Subject: Re: [Chimera-users] Small molecule dimensions Date: Sun, 18 Apr 2010 07:52:31 -0700 Yes, something like this: from chimera import openModels, Moleculefor m in openModels.list(modelTypes=[Molecule]): print m.name atoms = m.atoms for dim in range(3): atoms.sort(lambda a1, a2, dim=dim: cmp(a1.coord().data()[dim], a2.coord().data()[dim])) print "minimum %s: %g" % ("xyz"[dim], atoms[0].coord().data()[dim] - atoms[0].radius) print "maximum %s: %g" % ("xyz"[dim], atoms[-1].coord().data()[dim] - atoms[-1].radius) Put the above in a file ending in ".py" and open it in Chimera and it will print the min/max xyz values accounting for radius in the Reply Log. --Eric Eric Pettersen UCSF Computer Graphics Lab On Apr 16, 2010, at 10:46 AM, le monk wrote:Hello, I have a few pdb files of small molecules that I would like to know the dimensions of. Is it possible to use Chimera the measure the minimum x y z lengths - taking into account Van der Waals radii? Or perhaps you could suggest other software for this? Many thanks Get a free e-mail account with Hotmail. Sign-up now._______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ Do you have a story that started on Hotmail? Tell us now
On Apr 21, 2010, at 11:20 AM, le monk wrote:
Thank you Eric - this is really helpful. But as these are minimum x y z lengths then the reported dimensions will be different if the molecules coordinates were transformed.
The function used in the script (coord()) uses untransformed coordinates. xformcoord() would use transformed coordinates.
Can this script be modified to give the minimum dimensions of the molecule (not just the x y z dimensions)?
What would be the algorithm for computing that?
For example, can a box be drawn around the Van der Waal radii whose volume was the minimum possible for that molecule, and report the lengths of each of its dimensions?
Again, how? You can get a rough estimate by using the Axes tool to draw an axis along the principal axis of the molecule, with the axis radius equal to the average atom-atom distance from the axis. The axes information can be saved to a file. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc... --Eric
This would be really nice to directly compare the size of small molecules.
Many thanks
CC: chimera-users@cgl.ucsf.edu From: pett@cgl.ucsf.edu To: le_monk@hotmail.com Subject: Re: [Chimera-users] Small molecule dimensions Date: Sun, 18 Apr 2010 07:52:31 -0700
Yes, something like this:
from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): print m.name atoms = m.atoms for dim in range(3): atoms.sort(lambda a1, a2, dim=dim: cmp(a1.coord().data()[dim], a2.coord().data()[dim])) print "minimum %s: %g" % ("xyz"[dim], atoms[0].coord().data()[dim] - atoms[0].radius) print "maximum %s: %g" % ("xyz"[dim], atoms[-1].coord().data() [dim] - atoms[-1].radius)
Put the above in a file ending in ".py" and open it in Chimera and it will print the min/max xyz values accounting for radius in the Reply Log.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 16, 2010, at 10:46 AM, le monk wrote:
Hello,
I have a few pdb files of small molecules that I would like to know the dimensions of. Is it possible to use Chimera the measure the minimum x y z lengths - taking into account Van der Waals radii? Or perhaps you could suggest other software for this?
Many thanks
Get a free e-mail account with Hotmail. Sign-up now._______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Get a free e-mail account with Hotmail. Sign-up now.
Another idea is use the "measure inertia" command http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia which prints the principal axes of inertia of the molecule and their lengths in the Reply Log. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Small molecule dimensions From: Eric Pettersen <pett@cgl.ucsf.edu> To: le monk <le_monk@hotmail.com> Date: 4/21/10 11:37 AM
On Apr 21, 2010, at 11:20 AM, le monk wrote:
Thank you Eric - this is really helpful. But as these are minimum x y z lengths then the reported dimensions will be different if the molecules coordinates were transformed.
The function used in the script (coord()) uses untransformed coordinates. xformcoord() would use transformed coordinates.
Can this script be modified to give the minimum dimensions of the molecule (not just the x y z dimensions)?
What would be the algorithm for computing that?
For example, can a box be drawn around the Van der Waal radii whose volume was the minimum possible for that molecule, and report the lengths of each of its dimensions?
Again, how?
You can get a rough estimate by using the Axes tool to draw an axis along the principal axis of the molecule, with the axis radius equal to the average atom-atom distance from the axis. The axes information can be saved to a file.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
--Eric
This would be really nice to directly compare the size of small molecules.
Many thanks
------------------------------------------------------------------------ CC: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> From: pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu> To: le_monk@hotmail.com <mailto:le_monk@hotmail.com> Subject: Re: [Chimera-users] Small molecule dimensions Date: Sun, 18 Apr 2010 07:52:31 -0700
Yes, something like this:
from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): print m.name atoms = m.atoms for dim in range(3): atoms.sort(lambda a1, a2, dim=dim: cmp(a1.coord().data()[dim], a2.coord().data()[dim])) print "minimum %s: %g" % ("xyz"[dim], atoms[0].coord().data()[dim] - atoms[0].radius) print "maximum %s: %g" % ("xyz"[dim], atoms[-1].coord().data()[dim] - atoms[-1].radius)
Put the above in a file ending in ".py" and open it in Chimera and it will print the min/max xyz values accounting for radius in the Reply Log.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 16, 2010, at 10:46 AM, le monk wrote:
Hello,
I have a few pdb files of small molecules that I would like to know the dimensions of. Is it possible to use Chimera the measure the minimum x y z lengths - taking into account Van der Waals radii? Or perhaps you could suggest other software for this?
Many thanks
------------------------------------------------------------------------ Get a free e-mail account with Hotmail. Sign-up now. <http://clk.atdmt.com/UKM/go/197222280/direct/01/>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
------------------------------------------------------------------------ Get a free e-mail account with Hotmail. Sign-up now. <http://clk.atdmt.com/UKM/go/197222280/direct/01/>
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Eric Pettersen -
le monk -
Tom Goddard