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Re: [PyMOL] loading gro files
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From: Joseph A. <and...@gm...> - 2011-08-18 07:54:13
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Hi Tsjerk,
Thanks for the script. It works great on my protein. However when I try to
load the solvated system > 100.000 atoms I have problems with water
molecules. Is it possible to handle gro files with more than 100.000 atoms
and 9999 residues?
Best
On Thu, Aug 18, 2011 at 9:39 AM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hey :)
>
> Here is an all Python solution to load a .gro file, including the box
> vectors. It simply converts to PDB format and calls cmd.read_pdbstr...
> It supports multimodel files. I'll probably add a mechanism to
> identify chains from breaks, as the .gro format does not use chain
> identifiers, and may add gzip support. Later I'll also add MARTINI
> coarse graining, while I'm at it :)
>
> Hope it helps,
>
> Tsjerk
>
>
> ###
>
> from pymol import cmd
> import math
>
> _pdbline = "ATOM %5i %-3s %3s%2s%4i %8.3f%8.3f%8.3f%6.2f%6.2f
> %1s \n"
> _pdbBoxLine = "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1\n"
>
> d2r = math.pi/180
>
> def cos_angle(a,b):
> p = sum([i*j for i,j in zip(a,b)])
> q = math.sqrt(sum([i*i for i in a])*sum([j*j for j in b]))
> return min(max(-1,p/q),1)
>
> def norm2(a):
> return sum([i*i for i in a])
>
> def norm(a):
> return math.sqrt(norm2(a))
>
> def groBoxRead(a):
> b = [10*float(i) for i in a.split()] + 6*[0] # Padding for rectangular
> boxes
> return b[0],b[3],b[4],b[5],b[1],b[6],b[7],b[8],b[2]
>
> def groAtom(a):
> #012345678901234567890123456789012345678901234567890
> # 1PRN N 1 4.168 11.132 5.291
> ## ===> atom name, res name, res id, chain
> x, y, z
> return (a[10:15].strip(),a[5:10].strip(),int(a[:5]),"
> ",10*float(a[20:28]),10*float(a[28:36]),10*float(a[36:44]))
>
> # Simple GRO iterator
> def groFrameIterator(stream):
> while True:
> title = stream.readline()
> natoms = stream.readline().strip()
> if not natoms:
> break
> natoms = int(natoms)
> atoms = [groAtom(stream.readline()) for i in range(natoms)]
> box = groBoxRead(stream.readline())
> yield title, atoms, box
>
> def pdbOut(atom,i=1):
> return _pdbline%((i,) + (atom[0][:3],) + (atom[1],) + (atom[3],) +
> (atom[2],) + atom[4:] + (1,40) + (atom[0][0],))
>
> def pdbBoxString(box):
> nu = math.sqrt(norm2(box[0:3]))
> nv = math.sqrt(norm2(box[3:6]))
> nw = math.sqrt(norm2(box[6:9]))
>
> alpha = nv*nw == 0 and 90 or math.acos(cos_angle(box[3:6],box[6:9]))/d2r
> beta = nu*nw == 0 and 90 or math.acos(cos_angle(box[0:3],box[6:9]))/d2r
> gamma = nu*nv == 0 and 90 or math.acos(cos_angle(box[0:3],box[6:9]))/d2r
>
> return _pdbBoxLine %
> (norm(box[0:3]),norm(box[3:6]),norm(box[6:9]),alpha,beta,gamma)
>
> def gro(filename):
> objname = filename[1+filename.rfind("/"):filename.rfind(".")]
> pdb = []
> model = 1
> for title, atoms, box in groFrameIterator(open(filename)):
> pdb.append("MODEL %8d"%model)
> pdb.append(pdbBoxString(box))
> pdb.extend([pdbOut(atom,i) for atom, i in
> zip(atoms,range(1,len(atoms)+1))])
> pdb.append("ENDMDL")
> model += 1
> cmd.read_pdbstr("\n".join(pdb),objname)
>
> cmd.extend("gro",gro)
>
> ###
>
> On Wed, Aug 17, 2011 at 5:11 AM, Jason Vertrees
> <jas...@sc...> wrote:
> > Hi Michael,
> >
> > PyMOL knows about gromacs files, but needs to better handle .gro
> > files, specifically. Currently you have to export to a PDB to read the
> > topology.
> >
> > Please file this on the open-source tracker
> > (https://sourceforge.net/tracker/?group_id=4546) and I'll get to it
> > ASAP.
> >
> > Cheers,
> >
> > -- Jason
> >
> > On Mon, Aug 15, 2011 at 8:19 PM, Michael Daily <mda...@gm...>
> wrote:
> >> Hi all,
> >>
> >> Is there a direct way to load a gromacs structure file (.gro) in PyMOL?
> I
> >> know it's simple to convert them to pdb using editconf, but I want to
> load
> >> gro files directly (as you can in vmd) because they permit higher max.
> atom
> >> and residue numbers (100K vs. 10K for pdb) and permit longer residue
> names
> >> (4 chars vs. 3 for vmd).
> >>
> >> Thanks,
> >> Mike
> >>
> >> --
> >> ====================================
> >> Michael D. Daily
> >> Postdoctoral research associate
> >> Pacific Northwest National Lab (PNNL)
> >> 509-375-4581
> >> (formerly Qiang Cui group, University of Wisconsin-Madison)
> >>
> >>
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> >
> >
> >
> > --
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schrodinger, LLC
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
> >
> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
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> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
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--
Joseph ANDRE
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