[Chimera-users] IDLE for listing selected residues.
Jean-Didier Maréchal
jeandidier.marechal at uab.es
Mon Nov 12 11:19:22 PST 2007
Hi everyone,
I'd like to use chimera to generate the list of the oxygen atoms of the
water molecules located at less than 5.0 A of a ligand.
Selecting the water molecules have been the easiest part...
select :HOH & :301.a zr < 5.0
with :301.a my ligand.
Then in the IDLE, I tried a series of alternative to generate the list.
I use the different tips that were posted in the digest recently and
arrived to this:
for i in range(1,len(chimera.selection.currentResidues()):
print chimera.selection.currentResidues()[i]
Right, this gives me the list of residues, unfortunately, that would be
a LOOOT better for me is to have the Serial number of the oxygen
atoms...
currentSerialNum and currentSerialNumber do not see to be a correct
selection type. If there is any way that can do this?
Thanks a lot
JD
On Sat, 2007-11-10 at 12:00 -0800, chimera-users-request at cgl.ucsf.edu
wrote:
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> Today's Topics:
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> 1. Re: Z-slice transparency (Tom Goddard)
> 2. production release candidate (Eric Pettersen)
> 3. pipes and planks (Dougherty, Matthew T.)
> 4. Re: pipes and planks (Eric Pettersen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 09 Nov 2007 12:47:12 -0800
> From: Tom Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Z-slice transparency
> To: Lu <lugan at caltech.edu>, "'Chimera BB'"
> <chimera-users at cgl.ucsf.edu>
> Message-ID: <4734C750.5020803 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Lu,
>
> I think I know why the volume planes are slightly transparent for
> you. You are using Chimera version 1.2422 and I changed the volume
> solid rendering transparency behavior in the later Chimera version
> 1.2434 (August 3, 2007). You can either get the most recent Chimera
> from the daily builds web page:
>
> http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
>
> Or in older Chimera versions use volume menu entry Features / Brightness
> and Transparency and change transparency to 0. You'll have to type this
> in the entry field and press return because the slider does not go all
> the way down to zero. This transparency value modulates the
> transparencies given by the height of the brightness / transparency
> yellow curve on the histogram. Newer Chimera changed the modulation
> behavior to keep completely opaque voxels still completely opaque while
> older Chimera did not.
>
> Tom
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 9 Nov 2007 15:52:29 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: [Chimera-users] production release candidate
> To: chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <7B31B33A-569C-4808-AD94-EBCD134DEC26 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi all,
> We have put a production release candidate up for download (http://
> www.cgl.ucsf.edu/chimera/download.html). It would help us out if
> people would try it out and see if it all works okay. Major changes
> from the 1.2422 release include: incorporation of what were
> previously "experimental features", such as morphing between volume
> data sets; major revamp of the Volume Viewer interface; display of
> dendrograms in Multalign Viewer; use of rotamer libraries in swapping
> residue side chains and the ability evaluate possible swaps based on
> clashing, fit into density maps, or hydrogen-bond formation. A more
> exhaustive list of features is here: http://www.cgl.ucsf.edu/chimera/
> docs/relnotes/snapshot.html
>
> --Eric
>
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
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> ------------------------------
>
> Message: 3
> Date: Fri, 9 Nov 2007 18:11:40 -0600
> From: "Dougherty, Matthew T." <matthewd at bcm.tmc.edu>
> Subject: [Chimera-users] pipes and planks
> To: <chimera-users at cgl.ucsf.edu>
> Message-ID:
> <41F968EBC39129469A28E53880F2DFCA013679B0 at BCMEVS6.ad.bcm.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I have about 80 pdb datasets, each corresponding to a single helix.
> I know I can do one at a time using the gui.
> What is the method for scripting?
>
> thanks, Matt
>
>
> Matthew Dougherty
> 713-433-3849
> National Center for Macromolecular Imaging
> Baylor College of Medicine/Houston Texas USA
> =========================================================================
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> ------------------------------
>
> Message: 4
> Date: Fri, 9 Nov 2007 16:39:47 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] pipes and planks
> To: "Dougherty, Matthew T." <matthewd at bcm.tmc.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <64B83061-86FD-4ED4-A0BE-B7FD2DFAAEE2 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> On Nov 9, 2007, at 4:11 PM, Dougherty, Matthew T. wrote:
> > I have about 80 pdb datasets, each corresponding to a single helix.
> > I know I can do one at a time using the gui.
> > What is the method for scripting?
> >
> > thanks, Matt
>
> Well, looking at the Apply method in choose.py of the PipesAndPlanks
> extension, it looks like the code would be something like:
>
> from PipesAndPlanks.base import displayHelices, initialize, deinitialize
> from chimera import openModels, Molecule
> from CGLutil import vrml
> from chimera.misc import getColorByName
>
> red = getColorByName("red")
> for m in openModels.list(modelTypes=[Molecule]):
> initialize()
> wrl = vrml.Transform()
> helices = displayHelices(mol, red, False, 2.5, False, 2.5)
> for node in helices:
> wrl.addChild(node)
> openModels.open(vrml.vrml(wrl), type="VRML", sameAs=m, identify="%s
> - P&P script" % m.name)
> deinitialize()
>
> If haven't tested the above, so it may take a few swift kicks to get
> it to start up and run. Alternatively, I have been working on an
> extension to measure helix axes that can give you a helix-only
> display like Pipes and Plank and can do multiple models at once. I
> could send it to you if you want to try it out.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
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