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Re: [PyMOL] H-bonds representation
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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<" rel="nofollow">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<" rel="nofollow">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. >> <" rel="nofollow">http://p.sf.net/sfu/splunk-__**novd2d<http://p.sf.net/sfu/splunk-__novd2d>< >> http://p.sf.net/sfu/splunk-**novd2d <>" rel="nofollow">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<" rel="nofollow">https://lists.sourceforge.net/__lists/listinfo/pymol-users> >> <https://lists.sourceforge.**net/lists/listinfo/pymol-users<" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users> >> **> >> Archives: http://www.mail-archive.com/__** >> pym...@li....**__net<" rel="nofollow">http://www.mail-archive.com/__p...@li....__net> >> <" rel="nofollow">http://www.mail-archive.com/**pym...@li....**net<http://www.mail-archive.com/pym...@li...> >> > >> >> >> >> > |