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[PyMOL] Help Download structural alignment
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From: Clarisa A. <cla...@gm...> - 2016-06-24 13:02:57
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Hi everyone: I am writing asking help to download the structural aligment performed in pymol. Thanks in advance. Regards, Clarisa. 2016-06-14 11:01 GMT-03:00 <pym...@li...>: > Send PyMOL-users mailing list submissions to > pym...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pym...@li... > > You can reach the person managing the list at > pym...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. Analysis of docking poses from 2 nmr-ensembles (James Starlight) > 2. Re: Analysis of docking poses from 2 nmr-ensembles > (Sampson, Jared M.) > 3. Selective valency on bond (McIntyre, Patrick) > 4. Re: Selective valency on bond (Andreas Warnecke) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Jun 2016 15:41:58 +0200 > From: James Starlight <jms...@gm...> > Subject: [PyMOL] Analysis of docking poses from 2 nmr-ensembles > To: pymol-users <pym...@li...> > Message-ID: > < > CAA...@ma...> > Content-Type: text/plain; charset=UTF-8 > > Dear Pymol users! > > I am studying protein-protein assosiation using 2 different proteins > as test case by means of variety of computational methods. > For my particular caseI need to compare binding poses emerged as the > result of protein-protein docking (ensemble 1: which consists of 20 > snapshots according to docking ranking) as well as MD simulation > (ensemble 2: which consists of 10 snapshots each of which represents > binding pose which has been established during long MD run). > Loading those two ensembles in pymol as 2 different models (in > NMR-like model format) I need to performs some analysis to find some > shared trends in each of them e.g RMSD of the distances between common > residues-pairs found in contact map analysis > or something else. What are most trivial suggestions might be in that > particular case? > > > Thanks for the suggestions! > > > James > > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Jun 2016 16:08:31 +0000 > From: "Sampson, Jared M." <jm...@cu...> > Subject: Re: [PyMOL] Analysis of docking poses from 2 nmr-ensembles > To: James Starlight <jms...@gm...> > Cc: pymol-users <pym...@li...> > Message-ID: <FDA...@co...> > Content-Type: text/plain; charset="us-ascii" > > Hi James - > > First, it will be useful to split the states< > http://www.pymolwiki.org/index.php/Split_states>. > > split_states ensemble1 > split_states ensemble2 > delete ensemble1 > delete ensemble2 > > Then, superimpose<http://pymolwiki.org/index.php/Super> all structures > onto a reference structure for easier visualization. This won't affect > your distance measurements, but will make it easier to see the changes from > one object to the next. > > python > ref = 'ensemble1_0001' # your reference object > for obj in cmd.get_names(): > if obj != ref: > cmd.super(obj, ref) > python end > > For your residue pair analysis, you have to decide what kind of distance > you want to measure (e.g. CA-CA; average position of all atoms in the > residue; closest atoms, which would require looping through all atom pairs > in each residue pair and keeping only the shortest distance). Then create > selection strings based on those criteria, use them in distance< > http://pymolwiki.org/index.php/Get_Distance> measurement, and print them > or add them to a variable to be output. If you want to create and > visualize distance objects, use `distance` instead of `get_distance` and > pass a distance object name as the first parameter before the selections. > > python > sel1 = "resi 100 and name CA" > sel2 = "resi 200 and name CA" > sel3 = "resi 300 and name CA" > for obj in cmd.get_names(): > d12 = cmd.get_distance("{} and {}".format(obj, sel1), "{} and > {}".format(obj, sel2)) > d23 = cmd.get_distance("{} and {}".format(obj, sel2), "{} and > {}".format(obj, sel3)) > print "{}: '{}' to '{}' distance = {}".format(obj, sel1, sel2, d12) > print "{}: '{}' to '{}' distance = {}".format(obj, sel2, sel3, d23) > python end > > This is just a very quick example; really there are many different ways to > do this, and you'll have to find what kind of analysis your particular > structure needs. Also, if you want to look at H-bonds, it will be more > complicated, because the angle is important as well. In this case you may > want to look at Thomas' Polarpairs< > http://pymolwiki.org/index.php/Polarpairs> script. > > Hope that helps. > > Cheers, > Jared > > > > On Jun 13, 2016, at 9:41 AM, James Starlight <jms...@gm... > <mailto:jms...@gm...>> wrote: > > Dear Pymol users! > > I am studying protein-protein assosiation using 2 different proteins > as test case by means of variety of computational methods. > For my particular caseI need to compare binding poses emerged as the > result of protein-protein docking (ensemble 1: which consists of 20 > snapshots according to docking ranking) as well as MD simulation > (ensemble 2: which consists of 10 snapshots each of which represents > binding pose which has been established during long MD run). > Loading those two ensembles in pymol as 2 different models (in > NMR-like model format) I need to performs some analysis to find some > shared trends in each of them e.g RMSD of the distances between common > residues-pairs found in contact map analysis > or something else. What are most trivial suggestions might be in that > particular case? > > > Thanks for the suggestions! > > > James > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > _______________________________________________ > PyMOL-users mailing list (PyM...@li...<mailto: > PyM...@li...>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 3 > Date: Mon, 13 Jun 2016 09:56:36 +0000 > From: "McIntyre, Patrick" <pm...@le...> > Subject: [PyMOL] Selective valency on bond > To: "pym...@li..." > <pym...@li...> > Message-ID: <A67...@le...> > Content-Type: text/plain; charset="us-ascii" > > Dear PyMol users, > > I have a crystal structure of my protein with an unnatural amino acid > present. This amino acid has a double bond within it, which I would like to > display as such. However I would like the surrounding protein side chains > to not show double bond character. Is this possible at all? > > So far, I can either keep valence mode set to '0' and see no double bonds > across the whole protein, or set to '1' and see all of the double bonds, > which I don't want. > > My question is, is it possible to selectively 'set valency' onto a single > bond, or is it a global command which is not capable of this fine-tuning? I > am using MacPyMol if this makes a difference at all? > > Thanks for your help, > Patrick > > > ------------------------------ > > Message: 4 > Date: Tue, 14 Jun 2016 16:01:04 +0200 > From: Andreas Warnecke <4nd...@gm...> > Subject: Re: [PyMOL] Selective valency on bond > To: "McIntyre, Patrick" <pm...@le...> > Cc: "pym...@li..." > <pym...@li...> > Message-ID: > < > CAE...@ma...> > Content-Type: text/plain; charset="utf-8" > > The easiest way to deal with this is setting the valence or valence_mode > individually for the object. > > set valence, 0, object1 > set valence, 1, object2 > > Cheers, > > Andreas > > On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick <pm...@le... > > > wrote: > > > Dear PyMol users, > > > > I have a crystal structure of my protein with an unnatural amino acid > > present. This amino acid has a double bond within it, which I would like > to > > display as such. However I would like the surrounding protein side > chains > > to not show double bond character. Is this possible at all? > > > > So far, I can either keep valence mode set to '0' and see no double bonds > > across the whole protein, or set to '1' and see all of the double bonds, > > which I don't want. > > > > My question is, is it possible to selectively 'set valency' onto a single > > bond, or is it a global command which is not capable of this > fine-tuning? I > > am using MacPyMol if this makes a difference at all? > > > > Thanks for your help, > > Patrick > > > > > ------------------------------------------------------------------------------ > > What NetFlow Analyzer can do for you? Monitors network bandwidth and > > traffic > > patterns at an interface-level. Reveals which users, apps, and protocols > > are > > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > > J-Flow, sFlow and other flows. Make informed decisions using capacity > > planning reports. > https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > > ------------------------------ > > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest, Vol 121, Issue 3 > ******************************************* > |