From: James S. <jms...@gm...> - 2012-01-10 13:43:56
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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 <jas...@sc...> > 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 <jms...@gm...> > 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 <jas...@sc...> > >> > >> 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 <jms...@gm... > > > >> 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 > >> >> <jms...@gm...> > >> >> 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 <jas...@sc...>: > >> >> >> 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 > >> >> >> <jms...@gm...> > >> >> >> 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 <joe...@ot...> > >> >> >>>> > >> >> >>>> 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:jms...@gm...] > >> >> >>>> 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 <jms...@gm...> > >> >> >>>> > >> >> >>>> Thanks Joel, it's clear now :) > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> 2011/11/14 Joel Tyndall <joe...@ot...> > >> >> >>>> > >> >> >>>> See attached. > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> To switch to editing mode click on 3 button viewing or use the > >> >> >>>> menu > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> Mouse > 3 button editing > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> From: James Starlight [mailto:jms...@gm...] > >> >> >>>> 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 <joe...@ot...> > >> >> >>>> > >> >> >>>> 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:jms...@gm...] > >> >> >>>> Sent: Friday, 11 November 2011 1:44 a.m. > >> >> >>>> To: pym...@li... > >> >> >>>> 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 > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>>> > >> >> >>> > >> >> >>> > >> >> >>> > >> >> >>> > ------------------------------------------------------------------------------ > >> >> >>> All the data continuously generated in your IT infrastructure > >> >> >>> contains a definitive record of customers, application > performance, > >> >> >>> security threats, fraudulent activity, and more. Splunk takes > this > >> >> >>> data and makes sense of it. IT sense. And common sense. > >> >> >>> http://p.sf.net/sfu/splunk-novd2d > >> >> >>> _______________________________________________ > >> >> >>> PyMOL-users mailing list (PyM...@li...) > >> >> >>> Info Page: > https://lists.sourceforge.net/lists/listinfo/pymol-users > >> >> >>> Archives: > >> >> >>> http://www.mail-archive.com/pym...@li... > >> >> >>> > >> >> >> > >> >> >> > >> >> >> > >> >> >> -- > >> >> >> Jason Vertrees, PhD > >> >> >> PyMOL Product Manager > >> >> >> Schrodinger, LLC > >> >> >> > >> >> >> (e) Jas...@sc... > >> >> >> (o) +1 (603) 374-7120 > >> >> >> > >> >> > >> >> > >> >> > >> >> -- > >> >> Jason Vertrees, PhD > >> >> PyMOL Product Manager > >> >> Schrodinger, LLC > >> >> > >> >> (e) Jas...@sc... > >> >> (o) +1 (603) 374-7120 > >> > > >> > > >> > >> > >> > >> -- > >> Jason Vertrees, PhD > >> PyMOL Product Manager > >> Schrodinger, LLC > >> > >> (e) Jas...@sc... > >> (o) +1 (603) 374-7120 > > > > > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > |