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From: James S. <jms...@gm...> - 2011-11-26 06:39:05
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Dear PyMol users! As I've understood there are no posible ways to represent H-bonds in proteins in explicit manner. So I'm looking for possible way to do it via some plugin or another way. In particular I need 1) to visualize H-bonds in some structural motifs like coiled coil wich are dimers of alpha helices ( so I'd like to see H-bonds beetwen separate alpha helices ) 2) to visualize H-bonds in spicified SS structure ( e.g during formation of the alpha helices)- so I'd like to see H-bonds beetwen amide and Carboxy groups in specified amino acid sequence. 3) Finally I'd like to check H-bond in protein-ligand complex ( beetwenn specified ligand groups as well as some amino acid residues of the ligand binding pocket) Thanks, James |
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From: Thomas H. <sp...@us...> - 2011-11-26 08:21:00
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Hi James, > As I've understood there are no posible ways to represent H-bonds in > proteins in explicit manner. So I'm looking for possible way to do it > via some plugin or another way. PyMOL can find polar contacts and represent them as dashed lines. You don't need any extra plugin. http://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts It's the "distance" command with mode=2 that does the job. http://pymolwiki.org/index.php/Distance There are various dash_* settings that control the appearance of the dashed lines: http://pymolwiki.org/index.php/Dash_Length http://pymolwiki.org/index.php/Dash_color (and many others...) > In particular I need > 1) to visualize H-bonds in some structural motifs like coiled coil wich > are dimers of alpha helices ( so I'd like to see H-bonds beetwen > separate alpha helices ) Try this (lets say helix 1 is resi 1-100 and helix 2 is resi 101-200): # add hydrogens (if not already present) h_add donors # detect polar contacts distance hb_coiled_coil, resi 1-100, resi 101-200, mode=2 > 2) to visualize H-bonds in spicified SS structure ( e.g during formation > of the alpha helices)- so I'd like to see H-bonds beetwen amide and > Carboxy groups in specified amino acid sequence. just like example 1, but with other selections: distance hb_backbone, name O, name N, mode=2 > 3) Finally I'd like to check H-bond in protein-ligand complex ( beetwenn > specified ligand groups as well as some amino acid residues of the > ligand binding pocket) just like before, but with ligand as selection 1 and receptor as selection 2. Hope that helps. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
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From: James S. <jms...@gm...> - 2011-11-26 12:02:33
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Thomas, thank you for so detailed explanation. This way works good but I'd like to ask you about possibe Hbonds in the protein chain. As I remember for protein physics courses the H atom is always donor for only ONE H-bond ( and O or N atoms could be akceptors for 1 or 2 Hbonds) But In my case there are some cases where H atom ( white ) is donor for the 2 Hbonds. By the way I found the same on the picture in WIKI too. How it could be explaned ? James |
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From: Edward A. B. <Be...@up...> - 2011-11-26 18:55:19
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While the single acceptor H-bond is most common, bifurcated (or three-centred) H-bods are not uncommon in crystal structures, as described starting page 22 of GA Jeffrey's book: http://www.amazon.com/Introduction-Hydrogen-Bonding-Physical-Chemistry/dp/0195095499/ref=sr_1_2?ie=UTF8&qid=1322331503&sr=8-2 James Starlight wrote: > Thomas, thank you for so detailed explanation. > > This way works good but I'd like to ask you about possibe Hbonds in the protein chain. > > As I remember for protein physics courses the H atom is always donor for only ONE H-bond ( > and O or N atoms could be akceptors for 1 or 2 Hbonds) > > But In my case there are some cases where H atom ( white ) is donor for the 2 Hbonds. By > the way I found the same on the picture in WIKI too. > > How it could be explaned ? > > 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... |
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From: James S. <jms...@gm...> - 2011-11-28 13:58:24
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Another question also linked with the non-covalent interaction. In particular I wounder to know how i Could represent all hydrophobic ( Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd like to represent the hydrophobic core of the proteins made from those residues. Thanks, James 2011/11/27 Edward A. Berry <Be...@up...> > Yes i think the strongest H-bonds are single acceptor and straight > (angle at H = 180*). but these other bonds have significant > strength also. > Sorry, I'm a complete beginner at pymol. I have no idea how to > do these things. > > ed > > > James Starlight wrote: > >> Thanks Edward >> >> but recently I've studied generation of the Hbond in the water crystalls >> ( ice ) where H >> could be as the donor of only one H-bond. It seems that I need to refresh >> my protein >> physics course again :) >> >> By the way as I understtod the mode=2 way shows not only H-bonds but also >> others >> electrostatic bonds ( e.g as the salt bridges) >> 1- Is there any way to make clear difference betwen two distinguished >> electostatic contacts? >> >> 2- Also I'm looking for the most trivial way to show S-S bonds ( between >> 2 Cys resiudes) >> in the specified chain as well as between differen chains ( as in the >> inslulin for instance ). >> >> >> Thanks again, >> >> James >> >> 2011/11/26 Edward A. Berry <Be...@up... <mailto:Be...@up... >> >> >> >> >> While the single acceptor H-bond is most common, bifurcated (or >> three-centred) H-bods >> are not uncommon in crystal structures, as described starting page 22 >> of GA Jeffrey's >> book: >> http://www.amazon.com/__**Introduction-Hydrogen-Bonding-** >> __Physical-Chemistry/dp/__**0195095499/ref=sr_1_2?ie=UTF8&** >> __qid=1322331503&sr=8-2<http://www.amazon.com/__Introduction-Hydrogen-Bonding-__Physical-Chemistry/dp/__0195095499/ref=sr_1_2?ie=UTF8&__qid=1322331503&sr=8-2> >> >> <http://www.amazon.com/**Introduction-Hydrogen-Bonding-** >> Physical-Chemistry/dp/**0195095499/ref=sr_1_2?ie=UTF8&** >> qid=1322331503&sr=8-2<http://www.amazon.com/Introduction-Hydrogen-Bonding-Physical-Chemistry/dp/0195095499/ref=sr_1_2?ie=UTF8&qid=1322331503&sr=8-2> >> > >> >> James Starlight wrote: >> >> Thomas, thank you for so detailed explanation. >> >> This way works good but I'd like to ask you about possibe Hbonds >> in the protein chain. >> >> As I remember for protein physics courses the H atom is always >> donor for only ONE >> H-bond ( >> and O or N atoms could be akceptors for 1 or 2 Hbonds) >> >> But In my case there are some cases where H atom ( white ) is >> donor for the 2 >> Hbonds. By >> the way I found the same on the picture in WIKI too. >> >> How it could be explaned ? >> >> 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<http://p.sf.net/sfu/splunk-__novd2d>< >> http://p.sf.net/sfu/splunk-**novd2d <http://p.sf.net/sfu/splunk-novd2d>> >> >> >> >> ______________________________**___________________ >> PyMOL-users mailing list (PyMOL-users@lists.__sourcefor**ge.net<http://sourceforge.net> >> <mailto:PyMOL-users@lists.**sourceforge.net<PyM...@li...> >> >) >> Info Page: https://lists.sourceforge.net/** >> __lists/listinfo/pymol-users<https://lists.sourceforge.net/__lists/listinfo/pymol-users> >> <https://lists.sourceforge.**net/lists/listinfo/pymol-users<https://lists.sourceforge.net/lists/listinfo/pymol-users> >> **> >> Archives: http://www.mail-archive.com/__** >> pym...@li....**__net<http://www.mail-archive.com/__p...@li....__net> >> <http://www.mail-archive.com/**pym...@li....**net<http://www.mail-archive.com/pym...@li...> >> > >> >> >> >> > |
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From: Thomas H. <sp...@us...> - 2011-11-28 14:35:14
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Hi James, most trivial manner: as cartoon show sticks, resn LEU+ILE+VAL set cartoon_side_chain_helper and eventually something like this: show spheres, resn LEU+ILE+VAL and not name N+O+C set sphere_transparency, 0.5 Cheers, Thomas On 11/28/2011 02:58 PM, James Starlight wrote: > Another question also linked with the non-covalent interaction. > > In particular I wounder to know how i Could represent all hydrophobic ( > Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd > like to represent the hydrophobic core of the proteins made from those > residues. > > Thanks, > > James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
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From: James S. <jms...@gm...> - 2011-11-29 14:44:37
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Thanks, Thomas, Jason both of the methods are useable :) By the way I've forced with the problem of the representation of the active sites of different enzymes. I need to view all my protein as the cartoons and the ligand as the shpere in the ligand binding pocket. Besides I need to mark residues wich are contact with the ligand ( E.g I want to mark it as the lines and with the individual colour ). Finally I want to represent Hbonds between active site residues and the ligand. I've done this manually but its very long if I want to study 20-30 different enzymes during evening :) Also I've found such sollution wich could do all that i want http://www.pymolwiki.org/index.php/PLoS#Case_2:_Ligand-binding_sites_.28.E2.89.A5_novice.2Fintermediate.29 but this way also I need to rewrite script for specified enzyme ( e.g mark the active site residues and the distances for Hbonds etc ) Is there any semi-avtomated way to find ligand binding pocket and do all such things ? James 2011/11/28 Thomas Holder <sp...@us...> > Hi James, > > most trivial manner: > > as cartoon > show sticks, resn LEU+ILE+VAL > set cartoon_side_chain_helper > > and eventually something like this: > > show spheres, resn LEU+ILE+VAL and not name N+O+C > set sphere_transparency, 0.5 > > > Cheers, > Thomas > > > On 11/28/2011 02:58 PM, James Starlight wrote: > >> Another question also linked with the non-covalent interaction. >> >> In particular I wounder to know how i Could represent all hydrophobic ( >> Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd >> like to represent the hydrophobic core of the proteins made from those >> residues. >> >> Thanks, >> >> James >> > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |
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From: Jason V. <jas...@sc...> - 2011-11-29 14:49:54
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James, > Is there any semi-avtomated way to find ligand binding pocket and do all > such things ? For your given object, click A > preset > ligands sites > cartoon. Try other options under that menu. Cheers, -- Jason > 2011/11/28 Thomas Holder <sp...@us...> >> >> Hi James, >> >> most trivial manner: >> >> as cartoon >> show sticks, resn LEU+ILE+VAL >> set cartoon_side_chain_helper >> >> and eventually something like this: >> >> show spheres, resn LEU+ILE+VAL and not name N+O+C >> set sphere_transparency, 0.5 >> >> >> Cheers, >> Thomas >> >> On 11/28/2011 02:58 PM, James Starlight wrote: >>> >>> Another question also linked with the non-covalent interaction. >>> >>> In particular I wounder to know how i Could represent all hydrophobic ( >>> Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd >>> like to represent the hydrophobic core of the proteins made from those >>> residues. >>> >>> Thanks, >>> >>> James >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen > > > ------------------------------------------------------------------------------ > 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 |
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From: James S. <jms...@gm...> - 2011-11-30 06:33:51
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Thanks Jason. It works quite well in case of not very compliated ligands ( e.g bonds beetween aa-tRNA and the aa-tRNA syntase were correct ) but in the sugar-bound enzyme there were some mistakes in representation of the H-bonds netween water/ligand/active center ( some water also partisipate in the ligand binding but in case where water and some residues of the active sites were positioned iclosely the bonds were incorect ). So a I understood I can fix this mistakes only manually ? By the way, on what assumptions helix elements of my proteins were colored after representation of the ligand binding with the cartoons ? Finally how I could represent ionic contacts in the ion-binding proteins ? E.g now I'm studing calmodulin wich has Ef-hand Ca-binding motifs. I've tried to represent bonds beetwen some polar residues of the active site with the ligand but failed :( Thanks again, James 2011/11/29 Jason Vertrees <jas...@sc...> > James, > > > Is there any semi-avtomated way to find ligand binding pocket and do all > > such things ? > > For your given object, click A > preset > ligands sites > cartoon. Try > other options under that menu. > > Cheers, > > -- Jason > > > > 2011/11/28 Thomas Holder <sp...@us...> > >> > >> Hi James, > >> > >> most trivial manner: > >> > >> as cartoon > >> show sticks, resn LEU+ILE+VAL > >> set cartoon_side_chain_helper > >> > >> and eventually something like this: > >> > >> show spheres, resn LEU+ILE+VAL and not name N+O+C > >> set sphere_transparency, 0.5 > >> > >> > >> Cheers, > >> Thomas > >> > >> On 11/28/2011 02:58 PM, James Starlight wrote: > >>> > >>> Another question also linked with the non-covalent interaction. > >>> > >>> In particular I wounder to know how i Could represent all hydrophobic ( > >>> Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd > >>> like to represent the hydrophobic core of the proteins made from those > >>> residues. > >>> > >>> Thanks, > >>> > >>> James > >> > >> -- > >> Thomas Holder > >> MPI for Developmental Biology > >> Spemannstr. 35 > >> D-72076 Tübingen > > > > > > > ------------------------------------------------------------------------------ > > 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 > |
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From: James S. <jms...@gm...> - 2011-12-06 16:31:17
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Dear all :) I want to find Hbonds beetween different helices in the membrane receptor ( H bonds beetween sidechains only) I know possible way to do it wihin selection if I defined different helixes but is there any way to find almost all Hbonds between polar sidecains groups ? Could I use find-> polar contact-> sidechain only for this purpose ? James 2011/11/30 Jason Vertrees <jas...@sc...> > James, > > > It works quite well in case of not very compliated ligands ( e.g bonds > > beetween aa-tRNA and the aa-tRNA syntase were correct ) but in the > > sugar-bound enzyme there were some mistakes in representation of the > H-bonds > > netween water/ligand/active center ( some water also partisipate in the > > ligand binding but in case where water and some residues of the active > sites > > were positioned iclosely the bonds were incorect ). So a I understood I > can > > fix this mistakes only manually ? > > Please ask the pymol-users about this. > > > > By the way, on what assumptions helix elements of my proteins were > colored > > after representation of the ligand binding with the cartoons ? > > It's colored rainbow from start to end. > > > > Finally how I could represent ionic contacts in the ion-binding proteins > ? > > E.g now I'm studing calmodulin wich has Ef-hand Ca-binding motifs. I've > > tried to represent bonds beetwen some polar residues of the active site > with > > the ligand but failed :( > > Please ask the pymol-users about this. > > I'm gearing up for the PyMOL v1.5.0 release, so I won't have time > right now to personally answer your questions. Please keep relying on > the pymol-users list--they're very knowledgeable about PyMOL. > > Cheers, > > -- Jason > > > > > > 2011/11/29 Jason Vertrees <jas...@sc...> > >> > >> James, > >> > >> > Is there any semi-avtomated way to find ligand binding pocket and do > all > >> > such things ? > >> > >> For your given object, click A > preset > ligands sites > cartoon. Try > >> other options under that menu. > >> > >> Cheers, > >> > >> -- Jason > >> > >> > >> > 2011/11/28 Thomas Holder <sp...@us...> > >> >> > >> >> Hi James, > >> >> > >> >> most trivial manner: > >> >> > >> >> as cartoon > >> >> show sticks, resn LEU+ILE+VAL > >> >> set cartoon_side_chain_helper > >> >> > >> >> and eventually something like this: > >> >> > >> >> show spheres, resn LEU+ILE+VAL and not name N+O+C > >> >> set sphere_transparency, 0.5 > >> >> > >> >> > >> >> Cheers, > >> >> Thomas > >> >> > >> >> On 11/28/2011 02:58 PM, James Starlight wrote: > >> >>> > >> >>> Another question also linked with the non-covalent interaction. > >> >>> > >> >>> In particular I wounder to know how i Could represent all > hydrophobic > >> >>> ( > >> >>> Ley Ile Val etc) sidechains in my proteins in most trivial manner? > I'd > >> >>> like to represent the hydrophobic core of the proteins made from > those > >> >>> residues. > >> >>> > >> >>> Thanks, > >> >>> > >> >>> James > >> >> > >> >> -- > >> >> Thomas Holder > >> >> MPI for Developmental Biology > >> >> Spemannstr. 35 > >> >> D-72076 Tübingen > >> > > >> > > >> > > >> > > ------------------------------------------------------------------------------ > >> > 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 > > > > > > > > > ------------------------------------------------------------------------------ > > 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 > |
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