Hi Clarisa,
you can save an alignment using the create and save commands, e.g.:
fetch 1oky 1t46, async=0
as ribbon
align 1oky, 1t46
create aligned, all
save aligned.pdb, aligned
You can also save the alignment in clustalw format, see
http://pymolwiki.org/index.php/Align.
I hope this is what you were looking for?
Cheers,
Julian
On Fri, Jun 24, 2016 at 3:10 PM Clarisa Alvarez <clarisae.alva...@gmail.com>
wrote:
> 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
>>
>>
>> ------------------------------------------------------------------------------
>> 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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>> PyMOL-users@lists.sourceforge.net>)
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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
>>
>> ------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> PyMOL-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>> End of PyMOL-users Digest, Vol 121, Issue 3
>> *******************************************
>>
>
>
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