Hello all, Due to the (unexpected) popularity of my plugin to color 2 backbones according to their RMSD (color_rmsd.py), I managed to have a working website of my lab from which you can download that plugins and other scripts I have coded. The site is: http://mrcc.ciq.uchile.cl/ and has a "software" link on the left.
*The GUIs of plugins are pretty ugly but I just don't have time to learn tk. *All the plugins (they are not so many) have been tested on my machine. If someone has any problem, just drop me a line and I will try to fix it *I Will upload new plugins soon. *If you modify a plugin, please send me you version. I will add the website and the plugin to the pymol wiki as soon as possible. Hope it helps, Raúl --- El dom 28-sep-08, pymol-users-requ...@lists.sourceforge.net <pymol-users-requ...@lists.sourceforge.net> escribió: > De: pymol-users-requ...@lists.sourceforge.net > <pymol-users-requ...@lists.sourceforge.net> > Asunto: PyMOL-users Digest, Vol 28, Issue 15 > A: pymol-users@lists.sourceforge.net > Fecha: domingo, 28 septiembre, 2008, 1:28 am > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > 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 > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. select ATP hetatm? (Paul Shannon) > 2. Re: select ATP hetatm? (gilleain torrance) > 3. Re: RMSD and color between two very similar > structures (Ra?l Mera) > 4. Electron density map in pymol (Jhon Thomas) > 5. Re: Electron density map in pymol (Folmer Fredslund) > 6. apbs plugin for MacPyMOL? (Paul Shannon) > 7. Re: about unassigned atoms (Haiming Cao) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 23 Sep 2008 11:18:49 -0700 > From: Paul Shannon <pshan...@systemsbiology.org> > Subject: [PyMOL] select ATP hetatm? > To: pymol-users@lists.sourceforge.net > Cc: Paul Shannon <pshan...@systemsbiology.org> > Message-ID: > <2b4c8d85-daa8-4594-bb18-1d090e64e...@systemsbiology.org> > Content-Type: text/plain; charset=US-ASCII; format=flowed; > delsp=yes > > What command will select a HETATM of ATP? I am looking at > 1ATP.pdb, > in which the ATP molecule appears > as shown below. > > I found 'select hetatm' but found no way to be more > specific, in the > spirit of > > 'select hetatm and name=ATP' > > Thanks! > > - Paul > > > HETATM 2937 O2 PO3 E 338 18.820 34.274 -7.166 > 1.00 > 45.64 O > HETATM 2938 O3 PO3 E 338 17.963 34.737 -4.940 > 1.00100.00 O > HETATM 2939 PG ATP 1 16.223 8.151 -1.015 > 1.00 > 18.11 P > HETATM 2940 O1G ATP 1 17.550 8.536 -0.515 > 1.00 > 17.95 O > HETATM 2941 O2G ATP 1 15.748 6.835 -0.427 > 1.00 > 15.57 O > HETATM 2942 O3G ATP 1 16.255 8.014 -2.438 > 1.00 > 6.59 O > HETATM 2943 PB ATP 1 14.471 10.520 -1.490 > 1.00 > 22.96 P > HETATM 2944 O1B ATP 1 13.929 9.920 -2.700 > 1.00 > 13.08 O > HETATM 2945 O2B ATP 1 15.318 11.737 -1.637 > 1.00 > 19.59 O > HETATM 2946 O3B ATP 1 15.196 9.363 -0.681 > 1.00 > 13.80 O > HETATM 2947 PA ATP 1 11.968 9.868 -0.260 > 1.00 > 19.49 P > HETATM 2948 O1A ATP 1 11.100 9.880 -1.430 > 1.00 > 13.47 O > HETATM 2949 O2A ATP 1 12.426 8.514 0.144 > 1.00 > 25.00 O > HETATM 2950 O3A ATP 1 13.242 10.795 -0.567 > 1.00 > 21.72 O > HETATM 2951 O5' ATP 1 11.333 10.591 1.011 > 1.00 > 14.92 O > HETATM 2952 C5' ATP 1 12.092 10.373 2.227 > 1.00 > 58.54 C > HETATM 2953 C4' ATP 1 11.238 9.922 3.406 > 1.00 > 15.72 C > HETATM 2954 O4' ATP 1 10.003 10.681 3.386 > 1.00 > 30.04 O > HETATM 2955 C3' ATP 1 10.722 8.498 3.395 > 1.00 > 9.26 C > HETATM 2956 O3' ATP 1 11.705 7.533 3.717 > 1.00 > 33.78 O > HETATM 2957 C2' ATP 1 9.560 8.606 4.401 > 1.00 > 1.00 C > HETATM 2958 O2' ATP 1 9.942 8.562 5.764 > 1.00 > 48.53 O > HETATM 2959 C1' ATP 1 8.988 9.957 4.085 > 1.00 > 12.71 C > HETATM 2960 N9 ATP 1 7.778 9.924 3.236 > 1.00 > 19.15 N > HETATM 2961 C8 ATP 1 7.884 9.906 1.879 > 1.00 > 45.84 C > HETATM 2962 N7 ATP 1 6.731 9.904 1.248 > 1.00 > 35.77 N > HETATM 2963 C5 ATP 1 5.796 9.977 2.253 > 1.00 > 24.00 C > HETATM 2964 C6 ATP 1 4.373 10.039 2.244 > 1.00 > 26.67 C > HETATM 2965 N6 ATP 1 3.616 10.001 1.128 > 1.00 > 31.35 N > HETATM 2966 N1 ATP 1 3.756 10.034 3.445 > 1.00 > 19.73 N > HETATM 2967 C2 ATP 1 4.499 10.076 4.582 > 1.00 > 28.79 C > HETATM 2968 N3 ATP 1 5.825 10.053 4.705 > 1.00 > 18.18 N > HETATM 2969 C4 ATP 1 6.425 9.873 3.496 > 1.00 > 37.89 C > HETATM 2970 O HOH 400 8.234 9.392 -4.975 > 1.00 > 37.01 O > HETATM 2971 O HOH 402 -1.957 4.450 -6.367 > 1.00 > 18.24 O > HETATM 2972 O HOH 403 12.337 4.400 -6.581 > 1.00 > 18.55 O > > > > ------------------------------ > > Message: 2 > Date: Tue, 23 Sep 2008 19:46:44 +0100 > From: "gilleain torrance" > <gilleain.torra...@gmail.com> > Subject: Re: [PyMOL] select ATP hetatm? > To: pymol-users <pymol-users@lists.sourceforge.net> > Message-ID: > <d0d153660809231146j264a1dc5j4612365aab732...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > "select hetatm and resname atp" or "select > hetatm and r. atp" > > see also: "help selections" > > gilleain > > On Tue, Sep 23, 2008 at 7:18 PM, Paul Shannon > <pshan...@systemsbiology.org> wrote: > > What command will select a HETATM of ATP? I am > looking at 1ATP.pdb, > > in which the ATP molecule appears > > as shown below. > > > > I found 'select hetatm' but found no way to be > more specific, in the > > spirit of > > > > 'select hetatm and name=ATP' > > > > Thanks! > > > > - Paul > > > > > > HETATM 2937 O2 PO3 E 338 18.820 34.274 -7.166 > 1.00 > > 45.64 O > > HETATM 2938 O3 PO3 E 338 17.963 34.737 -4.940 > > 1.00100.00 O > > HETATM 2939 PG ATP 1 16.223 8.151 -1.015 > 1.00 > > 18.11 P > > HETATM 2940 O1G ATP 1 17.550 8.536 -0.515 > 1.00 > > 17.95 O > > HETATM 2941 O2G ATP 1 15.748 6.835 -0.427 > 1.00 > > 15.57 O > > HETATM 2942 O3G ATP 1 16.255 8.014 -2.438 > 1.00 > > 6.59 O > > HETATM 2943 PB ATP 1 14.471 10.520 -1.490 > 1.00 > > 22.96 P > > HETATM 2944 O1B ATP 1 13.929 9.920 -2.700 > 1.00 > > 13.08 O > > HETATM 2945 O2B ATP 1 15.318 11.737 -1.637 > 1.00 > > 19.59 O > > HETATM 2946 O3B ATP 1 15.196 9.363 -0.681 > 1.00 > > 13.80 O > > HETATM 2947 PA ATP 1 11.968 9.868 -0.260 > 1.00 > > 19.49 P > > HETATM 2948 O1A ATP 1 11.100 9.880 -1.430 > 1.00 > > 13.47 O > > HETATM 2949 O2A ATP 1 12.426 8.514 0.144 > 1.00 > > 25.00 O > > HETATM 2950 O3A ATP 1 13.242 10.795 -0.567 > 1.00 > > 21.72 O > > HETATM 2951 O5' ATP 1 11.333 10.591 > 1.011 1.00 > > 14.92 O > > HETATM 2952 C5' ATP 1 12.092 10.373 > 2.227 1.00 > > 58.54 C > > HETATM 2953 C4' ATP 1 11.238 9.922 > 3.406 1.00 > > 15.72 C > > HETATM 2954 O4' ATP 1 10.003 10.681 > 3.386 1.00 > > 30.04 O > > HETATM 2955 C3' ATP 1 10.722 8.498 > 3.395 1.00 > > 9.26 C > > HETATM 2956 O3' ATP 1 11.705 7.533 > 3.717 1.00 > > 33.78 O > > HETATM 2957 C2' ATP 1 9.560 8.606 > 4.401 1.00 > > 1.00 C > > HETATM 2958 O2' ATP 1 9.942 8.562 > 5.764 1.00 > > 48.53 O > > HETATM 2959 C1' ATP 1 8.988 9.957 > 4.085 1.00 > > 12.71 C > > HETATM 2960 N9 ATP 1 7.778 9.924 3.236 > 1.00 > > 19.15 N > > HETATM 2961 C8 ATP 1 7.884 9.906 1.879 > 1.00 > > 45.84 C > > HETATM 2962 N7 ATP 1 6.731 9.904 1.248 > 1.00 > > 35.77 N > > HETATM 2963 C5 ATP 1 5.796 9.977 2.253 > 1.00 > > 24.00 C > > HETATM 2964 C6 ATP 1 4.373 10.039 2.244 > 1.00 > > 26.67 C > > HETATM 2965 N6 ATP 1 3.616 10.001 1.128 > 1.00 > > 31.35 N > > HETATM 2966 N1 ATP 1 3.756 10.034 3.445 > 1.00 > > 19.73 N > > HETATM 2967 C2 ATP 1 4.499 10.076 4.582 > 1.00 > > 28.79 C > > HETATM 2968 N3 ATP 1 5.825 10.053 4.705 > 1.00 > > 18.18 N > > HETATM 2969 C4 ATP 1 6.425 9.873 3.496 > 1.00 > > 37.89 C > > HETATM 2970 O HOH 400 8.234 9.392 -4.975 > 1.00 > > 37.01 O > > HETATM 2971 O HOH 402 -1.957 4.450 -6.367 > 1.00 > > 18.24 O > > HETATM 2972 O HOH 403 12.337 4.400 -6.581 > 1.00 > > 18.55 O > > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move > Developer's challenge > > Build the coolest Linux based applications with Moblin > SDK & win great prizes > > Grand prize is a trip for two to an Open Source event > anywhere in the world > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > ------------------------------ > > Message: 3 > Date: Thu, 25 Sep 2008 10:36:32 -0700 (PDT) > From: Ra?l Mera <butil_li...@yahoo.com> > Subject: Re: [PyMOL] RMSD and color between two very > similar > structures > To: pymol-users@lists.sourceforge.net > Message-ID: > <778380.67459...@web53005.mail.re2.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > Hi all, > > I coded a little plugin that performs what Horacio asked > for: > It takes 2 selections with the same number of residues > calculates RMSD for the backbone atoms and assigns each > backbone atom's b-factor the corresponding RMSD. > (assigns 0.0 to non-backbone atoms) > (It only work for aminoacidic sequences) > At this time I don't have any website to upload it, but > I'll email it to whoever drops me a line asking for it > > Cheers, > > Raul > > > Hi, > > > > Given two very similar pdb structures, do you know if > it is > > possible to > > colour them in relationship with the RMSD between the > 2 > > structures ? I > > mean that for instance the backbone is practically the > same > > in both > > proteines, so it gets some same color in both, but for > some > > chains which > > are different, the colors start to diferentiate in > relation > > to the RMSD. > > > > Thanks in advance > > > > Horacio > > > > > -- > > > > > > ____________________________________________________________________________________ > Yahoo! MTV Blog & Rock >?Cu?ntanos tu historia, > inspira una canci?n y g?nate un viaje a los Premios MTV! > Participa aqu? http://mtvla.yahoo.com/ > > > > ------------------------------ > > Message: 4 > Date: Fri, 26 Sep 2008 16:44:58 +0530 > From: "Jhon Thomas" > <jhon1.tho...@gmail.com> > Subject: [PyMOL] Electron density map in pymol > To: pymol-users@lists.sourceforge.net > Message-ID: > <78c9aa6f0809260414v13b7a11ch58e322b7d5a8a...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello all pymol users > > I am new to pymol and trying to open a .xplor map file in > pymol to get the > electron density map of publication grade. > The command i write for pymol to open the file and show > electron density > map is - > > 1) I convert ccp4 .map file into the .xplor file through > mapman. > > # mymap.xplor loaded as " mymap" loaded as state > 0. > 2) Then i load the .xplor map file into pymol and write the > following > commands- > > *isomesh map, mymap.xplor, 2.0, site, carve=1.6 > > * > > isomesh: map or brick object "*mymap.xplor*" not > found. > > > What could be the problem? can any one give suggestion to > solve it? > > Thanks in advance > > Jhon > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 5 > Date: Fri, 26 Sep 2008 14:12:53 +0200 > From: "Folmer Fredslund" > <folm...@gmail.com> > Subject: Re: [PyMOL] Electron density map in pymol > To: "Jhon Thomas" <jhon1.tho...@gmail.com> > Cc: pymol-users@lists.sourceforge.net > Message-ID: > <991070400809260512s69e23a23pd83d9f6a0f9b1...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 2008/9/26 Jhon Thomas <jhon1.tho...@gmail.com>: > > Hello all pymol users > > > > I am new to pymol and trying to open a .xplor map file > in pymol to get the > > electron density map of publication grade. > > The command i write for pymol to open the file and > show electron density > > map is - > > > > 1) I convert ccp4 .map file into the .xplor file > through mapman. > > > > # mymap.xplor loaded as " mymap" loaded as > state 0. > > 2) Then i load the .xplor map file into pymol and > write the following > > commands- > > > > isomesh map, mymap.xplor, 2.0, site, carve=1.6 > > > > isomesh: map or brick object "mymap.xplor" > not found. > > > > I have to "load" the map first! > > Example: > > load mymap.xplor, themap > isomesh themapobject, themap, 2.0, site, carve=1.6 > > > > > > > > > > What could be the problem? can any one give suggestion > to solve it? > > > > Thanks in advance > > > > Jhon > > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move > Developer's challenge > > Build the coolest Linux based applications with Moblin > SDK & win great > > prizes > > Grand prize is a trip for two to an Open Source event > anywhere in the world > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > -- > Folmer Fredslund > Kantatgatan 84 > 21570 Malm? > Sverige > Tlf.: (+46) 40 66 72 194 > Mobil: (+45) 61 468 009 > Mail: folm...@gmail.com > MSN: folm...@gmail.com > Skype: folmerfredslund > -----BEGIN GEEK CODE BLOCK----- > Version: 3.1 > GS/MU$ d>++$ s:>+++:+++ a->? C>++++ UL P+ L++ > E++@ W+ N? o? > K?(+) w-- O- M-->+++$ V? PS+ PE-- Y? PGP- t+++>--- 5 > X+ R*>++++$ > tv++>! b+(+++) DI++(-) !D? G e+++(++++)>* > h---(----)>* r+++ y+++@>$ > ------END GEEK CODE BLOCK------ > > > > ------------------------------ > > Message: 6 > Date: Fri, 26 Sep 2008 17:06:50 -0700 > From: Paul Shannon <pshan...@systemsbiology.org> > Subject: [PyMOL] apbs plugin for MacPyMOL? > To: pymol-users@lists.sourceforge.net > Cc: Paul Shannon <pshan...@systemsbiology.org> > Message-ID: > <7dae82a7-bfc1-475d-b70d-6bb6c163e...@systemsbiology.org> > Content-Type: text/plain; charset=US-ASCII; format=flowed; > delsp=yes > > I've installed apbs and used it from the command line. > Now I'd like > to run it (more conveniently) > as a MacPyMOL plugin. > > Anybody know how I can set this up? > > Thanks! > > - Paul > > > > ------------------------------ > > Message: 7 > Date: Sun, 28 Sep 2008 00:08:57 -0400 > From: "Haiming Cao" <h...@hsph.harvard.edu> > Subject: Re: [PyMOL] about unassigned atoms > To: "Haiming Cao" <h...@hsph.harvard.edu> > Cc: pymol-users@lists.sourceforge.net, > apbs-us...@lists.sourceforge.net > Message-ID: > <48decb1a0200000a0005f...@hsph.harvard.edu> > Content-Type: text/plain; charset=UTF-8 > > I am new to Pymol and have been trying to show > electrostatic potential of a protein. I always got an error > like ?Unable to assign parameters for the x atoms in > selection ?unassigned?. Please either remove these > unassigned atoms and re-start the calculation or fix their > parameters in the generated PQR file and run the calculation > using the modified PQR file?. Any advice to resolve this? > A bit more details, I worked on a Windows XP and the default > folder for pqr file is My Documents. > > Thank you in advance. > > Haiming > > > > > > > ------------------------------ > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move > Developer's challenge > Build the coolest Linux based applications with Moblin SDK > & win great prizes > Grand prize is a trip for two to an Open Source event > anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > ------------------------------ > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest, Vol 28, Issue 15 > ******************************************* ____________________________________________________________________________________ ¡Todo sobre Amor y Sexo! 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