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.vertrees@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 <jmsstarlight@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.vertrees@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 <jmsstarlight@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
>> >> <jmsstarlight@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.vertrees@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
>> >> >> <jmsstarlight@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.tyndall@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:jmsstarlight@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 <jmsstarlight@gmail.com>
>> >> >>>>
>> >> >>>> Thanks Joel, it's clear now :)
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> >> >>>> 2011/11/14 Joel Tyndall <joel.tyndall@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:jmsstarlight@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.tyndall@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:jmsstarlight@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.Vertrees@schrodinger.com
>> >> >> (o) +1 (603) 374-7120
>> >> >>
>> >>
>> >>
>> >>
>> >> --
>> >> Jason Vertrees, PhD
>> >> PyMOL Product Manager
>> >> Schrodinger, LLC
>> >>
>> >> (e) Jason.Vertrees@schrodinger.com
>> >> (o) +1 (603) 374-7120
>> >
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jason.Vertrees@schrodinger.com
>> (o) +1 (603) 374-7120
>
>



--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120