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@cgl.ucsf.edu wrote:
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Today's Topics:
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)
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Message: 1 Date: Fri, 09 Nov 2007 12:47:12 -0800 From: Tom Goddard <goddard@cgl.ucsf.edu> Subject: Re: [Chimera-users] Z-slice transparency To: Lu <lugan@caltech.edu>, "'Chimera BB'" <chimera-users@cgl.ucsf.edu> Message-ID: <4734C750.5020803@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
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Message: 2 Date: Fri, 9 Nov 2007 15:52:29 -0800 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: [Chimera-users] production release candidate To: chimera BB <chimera-users@cgl.ucsf.edu> Message-ID: <7B31B33A-569C-4808-AD94-EBCD134DEC26@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