Deal all!
I'm intresting about representation of the polarr contacts between ligand
and protein
1) Usually I'm ussing Present-> Ligand sites option for that purposes but
in my current case I'm working with GFP where tree residues form chromofore
group of that protein.
So I want to assign that three residues as the ligand and finally find
polar contacts between that chromophore and surrounding polar residues. How
I could do this assignment?
2) Also I'm looking in possible way to represent Names of residues wich
forrm my ligand binding pocket. Always I represent names of residues via
Label option. But if I choose Label -> res.names all names will be
represented but i want to represent only the names of residues wich form
polar contact with ligand.
James
2012/1/10 Jason Vertrees <jason.vertr...@schrodinger.com>
> James,
>
> Please take these questions to the pymol-users list. I'm getting ready
> for the PyMOL v1.5 release, so you'll get faster answers there.
>
> Cheers,
>
> -- Jason
>
> On Tue, Jan 10, 2012 at 6:22 AM, James Starlight <jmsstarli...@gmail.com>
> wrote:
> > Hi Jason
> >
> > Thank you for help again.
> >
> > I've also question about representation of the polarr contacts between
> > ligand and protein
> >
> > Usually I'm ussing Present-> Ligand sites option for that purposes but
> in my
> > current case I'm working with GFP where tree residues form chromofore
> group
> > of that protein.
> >
> > So I want to assign that three residues as the ligand and finally find
> polar
> > contacts between that chromophore and surrounding polar residues. How I
> > could do this assignment?
> >
> > Thanks again
> >
> > James
> >
> >
> > 2012/1/9 Jason Vertrees <jason.vertr...@schrodinger.com>
> >>
> >> Hi James,
> >>
> >> I see you want chains A and B in one object to become just chain AA,
> >> for example, in another object? If so,
> >>
> >> create newObj, (oldObj1 and chain A) or (oldObj2 and chain B)
> >>
> >> alter newObj, chain=AA
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >> On Mon, Jan 9, 2012 at 2:26 AM, James Starlight <jmsstarli...@gmail.com
> >
> >> wrote:
> >> > Jason hello!
> >> >
> >> > I've tried exactly that command with OR operator
> >> >
> >> > but new object consitsted of 2 different chains like initial
> structure (
> >> > this was equal to the simple coppy of the 2g16 to the 2g16new object
> >> > without
> >> > deleation of initial one). But I want that 2g16new will consist of
> only
> >> > 1
> >> > chain wich would contait residues from both A and B of initial object.
> >> >
> >> > James
> >> >
> >> >>
> >> >> Cheers,
> >> >>
> >> >> -- JAson
> >> >>
> >> >> On Sun, Jan 8, 2012 at 1:35 AM, James Starlight
> >> >> <jmsstarli...@gmail.com>
> >> >> wrote:
> >> >> > Jason hello!
> >> >> >
> >> >> > I've tried use Create command to merge 2 chains from one object
> into
> >> >> > the united chain in new object but failed.
> >> >> >
> >> >> > create 2g16new, 2g16 and chain A 2g16 and chain B
> >> >> >
> >> >> > It's because of my new object also consist of 2 chains ( like
> >> >> > initial
> >> >> > one) but I want to obtain new object only with one chain wich would
> >> >> > consist of atoms from both chains of initial object. ( A+B)
> >> >> >
> >> >> > How I could solve that problem?
> >> >> >
> >> >> > James
> >> >> >
> >> >> > 2011/11/27, Jason Vertrees <jason.vertr...@schrodinger.com>:
> >> >> >> James,
> >> >> >>
> >> >> >> Please look up the 'create'
> >> >> >> (http://www.pymolwiki.org/index.php/Create)
> >> >> >> comand.
> >> >> >>
> >> >> >> Cheers,
> >> >> >>
> >> >> >> -- Jason
> >> >> >>
> >> >> >> On Sat, Nov 26, 2011 at 6:17 AM, James Starlight
> >> >> >> <jmsstarli...@gmail.com>
> >> >> >> wrote:
> >> >> >>> Dear all! :)
> >> >> >>>
> >> >> >>> I need to merge two chains in one pdb ( object) into one united
> >> >> >>> chain.
> >> >> >>> How
> >> >> >>> I
> >> >> >>> could do it?
> >> >> >>>
> >> >> >>> Thanks
> >> >> >>>
> >> >> >>> James
> >> >> >>>
> >> >> >>> 2011/11/18 Joel Tyndall <joel.tynd...@otago.ac.nz>
> >> >> >>>>
> >> >> >>>> James,
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Please post this to the bulletin board. You can try to click on
> >> >> >>>> the
> >> >> >>>> word
> >> >> >>>> (residues usually default) at the bottom right of the viewer.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Joel
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> From: James Starlight [mailto:jmsstarli...@gmail.com]
> >> >> >>>> Sent: Thursday, 17 November 2011 7:52 a.m.
> >> >> >>>>
> >> >> >>>> To: Joel Tyndall
> >> >> >>>> Subject: Re: [PyMOL] Editing of the pdb structure
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Another question about working with the structure.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> I have structure of the fulerene molecule wich consist of 60
> >> >> >>>> carbon
> >> >> >>>> atoms
> >> >> >>>>
> >> >> >>>> I switch to the Sequence mode-> Atoms and try to select
> individual
> >> >> >>>> carbon
> >> >> >>>> atoms ( e.g I want to find where this atom situated in my
> >> >> >>>> molecule).
> >> >> >>>> But
> >> >> >>>> instead of selection of the individual carbons the whole
> molecule
> >> >> >>>> was
> >> >> >>>> selected. How I can work with individual atoms of my structure ?
> >> >> >>>>
> >> >> >>>> James
> >> >> >>>>
> >> >> >>>> 2011/11/15 James Starlight <jmsstarli...@gmail.com>
> >> >> >>>>
> >> >> >>>> Thanks Joel, it's clear now :)
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> 2011/11/14 Joel Tyndall <joel.tynd...@otago.ac.nz>
> >> >> >>>>
> >> >> >>>> See attached.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> To switch to editing mode click on 3 button viewing or use the
> >> >> >>>> menu
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Mouse > 3 button editing
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> From: James Starlight [mailto:jmsstarli...@gmail.com]
> >> >> >>>> Sent: Monday, 14 November 2011 8:44 p.m.
> >> >> >>>> To: Joel Tyndall
> >> >> >>>> Subject: Re: [PyMOL] Editing of the pdb structure
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Dear all, thank you for the advises :)
> >> >> >>>>
> >> >> >>>> Thomas,
> >> >> >>>>
> >> >> >>>> when I've tried to add ACE cap to the N-tem of the first residue
> >> >> >>>> of
> >> >> >>>> my
> >> >> >>>> peptide I've obtain
> >> >> >>>>
> >> >> >>>> Error: unable to load fragment ''.
> >> >> >>>>
> >> >> >>>> So how I should define dirr from wich those caps groups will be
> >> >> >>>> loaded?
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Joel,
> >> >> >>>>
> >> >> >>>> I could not find such buiilder button :o
> >> >> >>>>
> >> >> >>>> when I've tried to select individual atoms from my FOR residue (
> >> >> >>>> from
> >> >> >>>> sequence panell), the overal residue with all atoms was selected
> >> >> >>>> instead
> >> >> >>>> :o
> >> >> >>>>
> >> >> >>>> James
> >> >> >>>>
> >> >> >>>> 2011/11/11 Joel Tyndall <joel.tynd...@otago.ac.nz>
> >> >> >>>>
> >> >> >>>> Hi James,
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> If I am correct in reading what you want you wish to change the
> >> >> >>>> FOR
> >> >> >>>> group
> >> >> >>>> to an ACE.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> I am using a PC version 1.3. Click on the builder button (right
> >> >> >>>> hand
> >> >> >>>> side
> >> >> >>>> of grey GUI)
> >> >> >>>>
> >> >> >>>> Make sure you are in Mouse mode: 3 button editing.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Click on the carbon of the FOR group and also the oxygen ( a
> white
> >> >> >>>> ball
> >> >> >>>> will appear on each atom)
> >> >> >>>>
> >> >> >>>> Then in the GUI click on the || icon adjacent to “bonds create”.
> >> >> >>>> This
> >> >> >>>> will
> >> >> >>>> give you the carbonyl.
> >> >> >>>>
> >> >> >>>> Now click on the hydrogen attached to the carbonyl carbon and
> then
> >> >> >>>> click
> >> >> >>>> in the GUI, the carbon atom C.
> >> >> >>>>
> >> >> >>>> This has now created your Acetylated nitrogen.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Then save molecule as: and you can edit the text file to change
> >> >> >>>> For
> >> >> >>>> to
> >> >> >>>> ACE.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Given this is some sort of dimer, I have just noticed that the
> >> >> >>>> second
> >> >> >>>> chain will overlap with the first.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Hope this helps
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Joel
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> From: James Starlight [mailto:jmsstarli...@gmail.com]
> >> >> >>>> Sent: Friday, 11 November 2011 1:44 a.m.
> >> >> >>>> To: pymol-users@lists.sourceforge.net
> >> >> >>>> Subject: [PyMOL] Editing of the pdb structure
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Dear PyMol Users!
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Recently I've opened such topic but I didnt obtain answer on
> this
> >> >> >>>> question
> >> >> >>>> so I try to paraphrase my task. Also I want to specify this
> topic
> >> >> >>>> on
> >> >> >>>> questions lincked with the processing of pdbs.
> >> >> >>>>
> >> >> >>>> 1) I need to remove some elements fron my structure described as
> >> >> >>>> the
> >> >> >>>> individual residue and place another element of the same size on
> >> >> >>>> the
> >> >> >>>> place
> >> >> >>>> of the first element.
> >> >> >>>>
> >> >> >>>> In particular I have two different peptides both of wich have
> >> >> >>>> small
> >> >> >>>> cap
> >> >> >>>> groups on C and N termi. ( attached)
> >> >> >>>>
> >> >> >>>> I need to remove all caps ( two caps FOR and ETA because there
> are
> >> >> >>>> two
> >> >> >>>> identical chains in that structure) from the 1MAG structure and
> >> >> >>>> build
> >> >> >>>> exactly on this place another cap groups wich I'd like to copy
> >> >> >>>> from
> >> >> >>>> the
> >> >> >>>> second peptide ( KALP). So I'd like to change FOR- > ACE and
> ETA->
> >> >> >>>> NH2
> >> >> >>>> twisely for the 1MAG dtructure
> >> >> >>>>
> >> >> >>>> How I can perform such task in PyMol?
> >> >> >>>>
> >> >> >>>> James
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >>>
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> >> >> >>> _______________________________________________
> >> >> >>> 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
> >> >> >>>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Jason Vertrees, PhD
> >> >> >> PyMOL Product Manager
> >> >> >> Schrodinger, LLC
> >> >> >>
> >> >> >> (e) jason.vertr...@schrodinger.com
> >> >> >> (o) +1 (603) 374-7120
> >> >> >>
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Jason Vertrees, PhD
> >> >> PyMOL Product Manager
> >> >> Schrodinger, LLC
> >> >>
> >> >> (e) jason.vertr...@schrodinger.com
> >> >> (o) +1 (603) 374-7120
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Jason Vertrees, PhD
> >> PyMOL Product Manager
> >> Schrodinger, LLC
> >>
> >> (e) jason.vertr...@schrodinger.com
> >> (o) +1 (603) 374-7120
> >
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
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