Re: [PyMOL] Automatic mutation introduction
Thanks! I'll try all pf this possibilities- especially I'm interesting in Modeller because its 1) python-based and 2) produce suitable input for MD (fixing side-chains or loops missed in the X-ray input data) James 2013/11/11 Ron Jacak > Hi James, > > SCWRL is a good suggestion. You may also want to take a look at Rosetta ( > https://www.rosettacommons.org/). It uses the Dunbrack 2010 rotamer > library but also includes a dozen or so other score terms to aid in > repacking and minimizing mutations. There's also a server ( > http://rosettadesign.med.unc.edu/), since the installation and > compilation can take some time. > > Best, > -Ron > > On Nov 10, 2013, at 2:27 PM, James Starlight wrote: > > > Dear PyMol users! > > > > > > I'm looking for the possible python script which using the pymol source > would introduce selected mutations in the defined PDB file and produce PDB > output containing such protein with the selected substitution residues. It > would be also good if rotamers for mutation residues would be backbone > dependent or taken from the existing rotamer libraries (although its not > essence because I can run minimization on the mutants) > > > > Previously I've done such tasks with selectivity mutations via pymol-GUI > but now I'd like to obtain big series of the mutant of studied protein for > further examinations of such mutants by means of molecular dynamics > simulation. > > Could someone provide me with such script if it could not be very > complicated to make it? > > > > > > Thanks for help, > > > > James > > > -- > > November Webinars for C, C++, Fortran Developers > > Accelerate application performance with scalable programming models. > Explore > > techniques for threading, error checking, porting, and tuning. Get the > most > > from the latest Intel processors and coprocessors. See abstracts and > register > > > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Pymol sas
Hi, I could not find the the algorithm by which pymol calculates the solvent ASA. What I understood is that pymol adds the vdw radii of atom and probe, makes the sphere around the center of selected atoms, puts some dots and according to the density of dots it calculates the SASA. or it simply uses the Richard & Lee algorithm of rolling water. Please clarify my doubts. -- Best regards Neshatul Haque PhD, Dpt of Biotechnology university of hyderabad -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Secondary structure for C-alpha only and coarse-grained models
Thanks a lot Tsjerk,
It iw really going to be helpful. I will update you when I play with it.
best,
Abhi
On Sat, Nov 9, 2013 at 12:46 PM, Tsjerk Wassenaar wrote:
>
> Hey :)
>
> I thought there was a post recently about showing secondary structure in
> C-alpha only models. I can't find it anymore, but in any case it's
> something popping up now and again. For reconstruction of high-resolution
> models out of coarse-grained ones, I came up with a very simple algorithm
> for rebuilding the backbone based on C-alpha atoms only. I realized that
> that could work for determining secondary structure, and made a function
> out of it. It's not perfect, as sometimes a residue gets a flipped
> backbone, but overall it seems to work pretty nicely. The following can be
> put in a script (bbpredict.py):
>
> from pymol import cmd
> import math
>
> def oprod(a,b): return
> a[1]*b[2]-a[2]*b[1],a[2]*b[0]-a[0]*b[2],a[0]*b[1]-a[1]*b[0]
> def vsub(a,b): return [i-j for i,j in zip(a,b)]
> def cest(u,v,w): return [i+0.37*j+0.45*k for i,j,k in zip(u,v,w)]
> def oest(u,v,w): return [i+0.37*j+1.75*k for i,j,k in zip(u,v,w)]
> def hest(u,v,w): return [i-0.37*j-1.45*k for i,j,k in zip(u,v,w)]
> def nest(u,v,w): return [i-0.37*j-0.45*k for i,j,k in zip(u,v,w)]
> def norm(a): return math.sqrt(sum([i**2 for i in a]))
> def vdiv(a,b): return [i/b for i in a]
>
> def bbpredict(selection,name="bbpred"):
> m=cmd.get_model(selection+' and n. ca')
> x=m.get_coord_list()
> d=[(vsub(j,i),vsub(k,i)) for i,j,k in zip(x,x[1:],x[2:])]
> o=[oprod(*i) for i in d]
> no=[vdiv(i,norm(i)) for i in o]
>
> CA = [("ATOM %5d CA %3s %1s%4d"+("%8.3f%8.3f%8.3f"%tuple(i)))
> for i in x]
> N = [("ATOM %5d N %3s %1s%4d
> "+("%8.3f%8.3f%8.3f"%tuple(nest(i,j[0],k for i,j,k in zip(x[1:],d,no)]
> H = [("ATOM %5d H %3s %1s%4d
> "+("%8.3f%8.3f%8.3f"%tuple(hest(i,j[0],k for i,j,k in zip(x[1:],d,no)]
> C = [("ATOM %5d C %3s %1s%4d
> "+("%8.3f%8.3f%8.3f"%tuple(cest(i,j[0],k for i,j,k in zip(x,d,no)]
> O = [("ATOM %5d O %3s %1s%4d
> "+("%8.3f%8.3f%8.3f"%tuple(oest(i,j[0],k for i,j,k in zip(x,d,no)]
>
> j = m.atom[0]
> bb= [CA[0]%(3,j.resn,j.chain,int(j.resi))]
> bb.append(C[0]%(4,j.resn,j.chain,int(j.resi)))
> bb.append(O[0]%(5,j.resn,j.chain,int(j.resi)))
> stuff = zip(m.atom[1:],zip(N,H,CA[1:],C[1:],O[1:]))
> bb.extend([ i%(num,j.resn,j.chain,int(j.resi)) for j,k in stuff for
> i,num in zip(k,range(5)) ])
>
> cmd.read_pdbstr("\n".join(bb),name)
>
> END
>
> Then it can be used e.g. as follows (yes, a full atomistic structure for
> demonstration):
>
> run bbpredict.py
> fetch 6lzm
> bbpredict('6lzm','pred')
> dss pred
>
>
> I'll see if I can get the flips out and tidy the code up a bit. Then I'll
> add this to the wiki. I hope it'll be of some use to anyone. The routine is
> explained in a manuscript we just submitted.
>
> Cheers,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
>
> --
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models.
> Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and
> register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
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Re: [PyMOL] rotate cell
Thanks Folmer for the response. The move command doesnot help. But I could see a command "turn" will does what I want. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Nov 12, 2013 at 1:25 PM, Folmer Fredslund wrote: > Dear Chandan, > > I think you want to use the "move" command ( > http://pymolwiki.org/index.php/Move) which moves the camera around the > molecule, instead of the "rotate" command ( > http://pymolwiki.org/index.php/Rotate) which alters the coordinates of > the object you are looking at. > > Hope this helps > Folmer > > > > 2013/11/12 Chandan Choudhury > >> Dear PyMOL users, >> >> I want to rotate/revolve the loaded structure. The cell parameter should >> also rotate. >> I am aware of rotate command. >> eg. rotate X, 90. >> >> But when I view the cell. The rotation does not happen here. >> >> My purpose is to generated a snapshot showing the boundaries. >> How can this be acheived? >> >> Chandan >> >> -- >> Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> >> -- >> November Webinars for C, C++, Fortran Developers >> Accelerate application performance with scalable programming models. >> Explore >> techniques for threading, error checking, porting, and tuning. Get the >> most >> from the latest Intel processors and coprocessors. See abstracts and >> register >> >> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > > -- > Folmer Fredslund > -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] apply spectrum per MODEL in PyMOL script
Hello Jason, thanks for your hint. Unfortunately, I can not produce what I want: Let assume that I read a local PDB file with different MODELS and I would like to colour the first model in red, the senond in blue: what would be the MPL script coaamnd ? Thanks in advance, Jerome On 11/11/13 19:17, Jason Vertrees wrote: > Hi Jerome, > > fetch 1nmr, discrete=1, async=0 > as ribbon > set all_states > for x in range(cmd.count_states()): cmd.color(str(x), "state %s" % x) > > You can substitute the spectrum command for the color command. > > Cheers, > > --- Jason > > On Sat, Nov 9, 2013 at 8:54 PM, Jerome BENOIT wrote: >> Hello List, >> >> is there a way in PML script to apply a specific spectrum to each MODEL (as >> define in PDB data file) ? >> >> Thanks in advance, >> Jerome >> >> -- >> November Webinars for C, C++, Fortran Developers >> Accelerate application performance with scalable programming models. Explore >> techniques for threading, error checking, porting, and tuning. Get the most >> from the latest Intel processors and coprocessors. See abstracts and register >> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > -- DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] apply spectrum per MODEL in PyMOL script
zip it like this colors = [‘red’,’blue’] fetch 1nmr, discrete=1, async=0 as ribbon set all_states for color, model in zip(range(cmd.count_states()),colors): cmd.color(str(color), "state %s" % x) On Nov 12, 2013, at 11:32 PM, Jerome BENOIT wrote: > Hello Jason, > > thanks for your hint. > > Unfortunately, I can not produce what I want: > > Let assume that I read a local PDB file with different MODELS and > I would like to colour the first model in red, the senond in blue: > what would be the MPL script coaamnd ? > > Thanks in advance, > Jerome > > On 11/11/13 19:17, Jason Vertrees wrote: >> Hi Jerome, >> >> fetch 1nmr, discrete=1, async=0 >> as ribbon >> set all_states >> for x in range(cmd.count_states()): cmd.color(str(x), "state %s" % x) >> >> You can substitute the spectrum command for the color command. >> >> Cheers, >> >> --- Jason >> >> On Sat, Nov 9, 2013 at 8:54 PM, Jerome BENOIT wrote: >>> Hello List, >>> >>> is there a way in PML script to apply a specific spectrum to each MODEL (as >>> define in PDB data file) ? >>> >>> Thanks in advance, >>> Jerome >>> >>> -- >>> November Webinars for C, C++, Fortran Developers >>> Accelerate application performance with scalable programming models. Explore >>> techniques for threading, error checking, porting, and tuning. Get the most >>> from the latest Intel processors and coprocessors. See abstracts and >>> register >>> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk >>> ___ >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> >> > > -- > DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps > OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access > Free app hosting. Or install the open source package on any LAMP server. > Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! > http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] apply spectrum per MODEL in PyMOL script
rather :) colors = [‘red’,’blue’] fetch 1nmr, discrete=1, async=0 as ribbon set all_states for model,color in zip(range(cmd.count_states()),colors): cmd.color(str(color), "state %s" % x) On Nov 13, 2013, at 12:23 AM, Jordan Willis wrote: > zip it like this > > colors = [‘red’,’blue’] > fetch 1nmr, discrete=1, async=0 > as ribbon > set all_states > for color, model in zip(range(cmd.count_states()),colors): > cmd.color(str(color), "state %s" % x) > On Nov 12, 2013, at 11:32 PM, Jerome BENOIT wrote: > >> Hello Jason, >> >> thanks for your hint. >> >> Unfortunately, I can not produce what I want: >> >> Let assume that I read a local PDB file with different MODELS and >> I would like to colour the first model in red, the senond in blue: >> what would be the MPL script coaamnd ? >> >> Thanks in advance, >> Jerome >> >> On 11/11/13 19:17, Jason Vertrees wrote: >>> Hi Jerome, >>> >>> fetch 1nmr, discrete=1, async=0 >>> as ribbon >>> set all_states >>> for x in range(cmd.count_states()): cmd.color(str(x), "state %s" % x) >>> >>> You can substitute the spectrum command for the color command. >>> >>> Cheers, >>> >>> --- Jason >>> >>> On Sat, Nov 9, 2013 at 8:54 PM, Jerome BENOIT wrote: Hello List, is there a way in PML script to apply a specific spectrum to each MODEL (as define in PDB data file) ? Thanks in advance, Jerome -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >>> >>> >>> >> >> -- >> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps >> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access >> Free app hosting. Or install the open source package on any LAMP server. >> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! >> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
