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[PyMOL] Re: PyMOL-users digest, Vol 1 #1176 - 1 msg
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From: Liu S. <sy...@md...> - 2006-04-04 09:39:16
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http://www.ebi.ac.uk/~gareth/pymol/images/walls.png how to draw this walls.png ? On Mon, 3 Apr 2006 pym...@li... wrote: > Send PyMOL-users mailing list submissions to > pym...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pym...@li... > > You can reach the person managing the list at > pym...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. RE: Angstrom-squared values for solvent/protein contact surface per residue (Seth Harris) > > --__--__-- > > Message: 1 > Date: Mon, 3 Apr 2006 15:56:23 -0700 > From: "Seth Harris" <se...@gm...> > To: pym...@li... > Subject: [PyMOL] RE: Angstrom-squared values for solvent/protein contact surface per residue > > ------=_Part_19793_7876172.1144104983332 > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > Just to throw my 2 cents in following Warren's invitation, I think > Mark Gerstein's programs work well for this (calcsurf.exe or > something...they're on his web site) > ccp4's areaimol does something similar, though I can't recall whether > its output was atom by atom. > In either case, you may have to add up the component atom parts if you > want residue by residue. > > Despite Warren's comment, I think last time I was doing this Pymol's > results compared well with the above methods, but that was for large > areas of a protein interface > and perhaps if you want very fine residue level resolution you'd heed > his caveat. I though, which is reiterated in the notes accompanying a > former post of his... > > -Seth > > if I may quote Warren: > > For a solvent accessible PSA approximation: > > set dot_density, 3 > remove hydro > remove solvent > show dots > set dot_solvent, on > get_area elem N+O > get_area elem C+S > get_area all > > For molecular PSA approximation > > set dot_density, 3 > remove hydro > remove solvent > set dot_solvent, off > get_area elem N+O > get_area elem C+S > get_area all > > Showing dots isn"t mandatory, but it"s a good idea to confirm that you"re > getting the value for the atom dot surface you think you"re using. > > Please realize that the resulting numbers are only approximate, reflecting > the sum of partial surface areas for all the dots you see. To increase > accuracy, set dot_density to 4, but be prepared to wait... > Cheers, > Warren > > > > > > ---------------------------------------------------------------------------= > -------------------- > Melanie, > > At present, PyMOL isn't the right tool for this, but perhaps someone > on the mailing list will know what is... > > Cheers, > Warren > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 USA > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:wa...@de... > > >> -----Original Message----- >> From: pym...@li... >> [mailto:pym...@li...] On Behalf Of >> Melanie Rogers >> Sent: Monday, April 03, 2006 10:36 AM >> To: pym...@li... >> Subject: [PyMOL] Angstrom-squared values for solvent/protein >> contact surface per residue >> >> Dear Pymol Users, >> >> Is it possible to extract numerical values, (i.e. Angstrom-squared per >> residue) >> for the solvent/protein contact surface for individual >> residues in a crystal structure using Pymol? >> >> Thank you, >> >> Melanie Rogers >> University of Leeds >> >> > > ------=_Part_19793_7876172.1144104983332 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > <pre>Just to throw my 2 cents in following Warren's invitation, I think Mar= > k Gerstein's programs work well for this (calcsurf.exe or something...they'= > re on his web site)<br>ccp4's areaimol does something similar, though I can= > 't recall whether its output was atom by atom.=20 > <br>In either case, you may have to add up the component atom parts if you = > want residue by residue. <br><br>Despite Warren's comment, I think last tim= > e I was doing this Pymol's results compared well with the above methods, bu= > t that was for large areas of a protein interface=20 > <br>and perhaps if you want very fine residue level resolution you'd heed h= > is caveat. I though, which is reiterated in the notes accompanying a former= > post of his...<br><br>-Seth<br><br>if I may quote Warren:<br><br>For a sol= > vent accessible PSA approximation: > <br> <br> set dot_density, 3<br> remove hydro<br> remove solvent<br> show d= > ots<br> set dot_solvent, on<br> get_area elem N+O<br> get_area elem C+S<br>= > get_area all<br> <br> For molecular PSA approximation<br> <br> set dot_den= > sity, 3 > <br> remove hydro<br> remove solvent<br> set dot_solvent, off<br> get_area = > elem N+O<br> get_area elem C+S<br> get_area all<br> <br> Showing dots isn&q= > uot;t mandatory, but it"s a good idea to confirm that you"re<br> > getting the value for the atom dot surface you think you"re using. <= > br> <br> Please realize that the resulting numbers are only approximate, re= > flecting<br> the sum of partial surface areas for all the dots you see. To= > increase > <br> accuracy, set dot_density to 4, but be prepared to wait...<br> Cheers= > ,<br> Warren<br><br><br><br><br><br>--------------------------------------= > ---------------------------------------------------------<br>Melanie,<br> > <br>At present, PyMOL isn't the right tool for this, but perhaps someone on= > the mailing list will know what is...<br><br>Cheers,<br>Warren<br><br>--<b= > r>Warren L. DeLano, Ph.D. <br>Principal Scientist<br> > <br>. DeLano Scientific LLC <br>. 400 Oyster Point Blvd., Suite 213 = > <br>. South San Francisco, CA 94080 USA <br>. Biz:(650)-872-0942 Tec= > h:(650)-872-0834 <br>. Fax:(650)-872-0273 Cell:(650)-346-1154<br>. mai= > lto: > <a href=3D"mailto:wa...@de...">wa...@de...</a> <br> <br><b= > r>> -----Original Message-----<br>> From: <a href=3D"mailto:pymol-use= > rs-...@li...">pym...@li...</a> > <br>> [mailto:<a href=3D"mailto:pym...@li...= > ">pym...@li...</a>] On Behalf Of <br>> Melani= > e Rogers <br>> Sent: Monday, April 03, 2006 10:36 AM<br>> To: <a href= > =3D"mailto:pym...@li..."> > pym...@li...</a><br>> Subject: [PyMOL] Angstrom-squ= > ared values for solvent/protein <br>> contact surface per residue<br>>= > ; <br>> Dear Pymol Users, <br>> <br>> Is it possible to extract nu= > merical values, ( > i.e. Angstrom-squared per<br>> residue)<br>> for the solvent/protein = > contact surface for individual <br>> residues in a crystal structure usi= > ng Pymol? <br>> <br>> Thank you,<br>> <br>> Melanie Rogers > <br>> University of Leeds <br>> <br>> </pre> > > ------=_Part_19793_7876172.1144104983332-- > > > > --__--__-- > > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest > |
