From: Jacob P. <Jac...@ei...> - 2013-05-30 19:08:48
|
Hi all, can anyone suggest a straightforward way of collecting the cealign output in bulk, (RMS, #atoms compared), using alignto doesn't even print this to screen (I tried adjusting quiet=, to no avail). thanks in advance jacob <https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgAAAADDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlAAAASCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWInAAAA&s=Draft&pspid=_1369930182703_402002554#> <https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgAAAADDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlAAAASCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWInAAAA&s=Draft&pspid=_1369930182703_402002554#> |
From: Jason V. <jas...@sc...> - 2013-05-30 21:28:25
|
Hi Jacob, Use the result from cmd.cealign and an "alignment object". Here's an example: # fetch two proteins fetch 1cll 1ggz, async=0 # use a python block python # cealign the two structures and create a corresponding "alignment" object result = cmd.cealign("1cll", "1ggz", object="aln") # print out the values from the result print result.keys() for key in result: print "%s: %s" % (key, result[key]) # end the python block python end # now access those atoms in the alignment select 1cll and aln # or count the atoms in 1ggz and aln print cmd.count_atoms("1ggz and aln") Cheers, -- Jason On Thu, May 30, 2013 at 2:07 PM, Jacob Pessin <Jac...@ei...>wrote: > Hi all, > > can anyone suggest a straightforward way of collecting the cealign output > in bulk, (RMS, #atoms compared), using alignto doesn't even print this to > screen (I tried adjusting quiet=, to no avail). > > > thanks in advance > > jacob > > <https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgAAAADDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlAAAASCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWInAAAA&s=Draft&pspid=_1369930182703_402002554#> > <https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgAAAADDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlAAAASCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWInAAAA&s=Draft&pspid=_1369930182703_402002554#> > > > ------------------------------------------------------------------------------ > Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET > Get 100% visibility into your production application - at no cost. > Code-level diagnostics for performance bottlenecks with <2% overhead > Download for free and get started troubleshooting in minutes. > http://p.sf.net/sfu/appdyn_d2d_ap1 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) Jas...@sc... (o) +1 (603) 374-7120 |