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 <pymol-users-requ...@lists.sourceforge.net>:
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> 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 <jmsstarli...@gmail.com>
> Subject: [PyMOL] Analysis of docking poses from 2 nmr-ensembles
> To: pymol-users <pymol-users@lists.sourceforge.net>
> Message-ID:
> <
> caalqopzzjtykby+j_evphgvpp2_k_mhmv2holhjgf2d5pnr...@mail.gmail.com>
> 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." <jms2...@cumc.columbia.edu>
> Subject: Re: [PyMOL] Analysis of docking poses from 2 nmr-ensembles
> To: James Starlight <jmsstarli...@gmail.com>
> Cc: pymol-users <pymol-users@lists.sourceforge.net>
> Message-ID: <fdab34d6-3ff3-4737-b61a-a80343979...@columbia.edu>
> 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 <jmsstarli...@gmail.com
> <mailto:jmsstarli...@gmail.com>> 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
>
>
> ------------------------------------------------------------------------------
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> ------------------------------
>
> Message: 3
> Date: Mon, 13 Jun 2016 09:56:36 +0000
> From: "McIntyre, Patrick" <pm...@leicester.ac.uk>
> Subject: [PyMOL] Selective valency on bond
> To: "pymol-users@lists.sourceforge.net"
> <pymol-users@lists.sourceforge.net>
> Message-ID: <a67054c6-d4f4-4237-bfa0-8fef10783...@leicester.ac.uk>
> 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 <4ndreas.warne...@gmail.com>
> Subject: Re: [PyMOL] Selective valency on bond
> To: "McIntyre, Patrick" <pm...@leicester.ac.uk>
> Cc: "pymol-users@lists.sourceforge.net"
> <pymol-users@lists.sourceforge.net>
> Message-ID:
> <
> caeyfqbufiodrvnoydhtegst5hmkq_ji5bqwnglko9tvibtt...@mail.gmail.com>
> 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...@leicester.ac.uk
> >
> 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 (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
> -------------- 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
>
> ------------------------------
>
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>
> End of PyMOL-users Digest, Vol 121, Issue 3
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