From: Ananya C. <ana...@ya...> - 2013-09-10 15:22:15
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Dear all, I have aligned two structures (one the initial structure and another one is the final structure after MD simulation) in pymol, now I want to measure the C-alpha- C-alpha distances of each residue between the initial and the final structure of the MD simulation. Is it possible to do it by pymol, if yes then how to do it. Please help me in this regard I am very new to this field. Thank u in advance, Ananya |
From: Jason V. <jas...@sc...> - 2013-09-10 18:21:43
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Hi Ananya, This is easily doable in PyMOL. If you've already aligned the two structures and, let's stay they're called protein1 and protein2, then use "rms_cur": rms_cur protein1 and guide, protein2 and guide If the initial and final structures are in the same object loaded from disk then you can easily copy the last state to a new object using "create" then use "rms_cur": # extract state 20 from my_trajectory and make it state 1 # in "final_copy". Here I use 20, but you use whichever # state is your final state. create final_copy, my_trajectory, 20, 1 # do the RMS calculation rms_cur initial, final_copy Cheers, -- Jason On Tue, Sep 10, 2013 at 10:21 AM, Ananya Chatterjee <ana...@ya...> wrote: > Dear all, > > I have aligned two structures (one the initial structure and another one is > the final structure after MD simulation) in pymol, now I want to measure the > C-alpha- C-alpha distances of each residue between the initial and the final > structure of the MD simulation. Is it possible to do it by pymol, if yes > then how to do it. Please help me in this regard I am very new to this > field. > > Thank u in advance, > > Ananya > > ------------------------------------------------------------------------------ > How ServiceNow helps IT people transform IT departments: > 1. Consolidate legacy IT systems to a single system of record for IT > 2. Standardize and globalize service processes across IT > 3. Implement zero-touch automation to replace manual, redundant tasks > http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk > _______________________________________________ > 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 |
From: Thomas H. <tho...@sc...> - 2013-09-11 09:14:06
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Hi Ananya, if you really want CA-CA distances of *each residue*, it will be a few lines of scripting: xyz_initial = cmd.get_model('initial & guide').get_coord_list() xyz_final = cmd.get_model('final_copy & guide').get_coord_list() from chempy import cpv for xyz_pair in zip(xyz_initial, xyz_final):\ print cpv.distance(*xyz_pair) Hope that helps. Cheers, Thomas Jason Vertrees wrote, On 09/10/13 20:21: > Hi Ananya, > > This is easily doable in PyMOL. > > If you've already aligned the two structures and, let's stay they're > called protein1 and protein2, then use "rms_cur": > > rms_cur protein1 and guide, protein2 and guide > > > If the initial and final structures are in the same object loaded from > disk then you can easily copy the last state to a new object using > "create" then use "rms_cur": > > # extract state 20 from my_trajectory and make it state 1 > # in "final_copy". Here I use 20, but you use whichever > # state is your final state. > > create final_copy, my_trajectory, 20, 1 > > # do the RMS calculation > > rms_cur initial, final_copy > > > Cheers, > > -- Jason > > On Tue, Sep 10, 2013 at 10:21 AM, Ananya Chatterjee <ana...@ya...> wrote: >> Dear all, >> >> I have aligned two structures (one the initial structure and another one is >> the final structure after MD simulation) in pymol, now I want to measure the >> C-alpha- C-alpha distances of each residue between the initial and the final >> structure of the MD simulation. Is it possible to do it by pymol, if yes >> then how to do it. Please help me in this regard I am very new to this >> field. >> >> Thank u in advance, >> >> Ananya -- Thomas Holder PyMOL Developer Schrödinger Contractor |