Hi Michael,
Proteins are actually very easy, because of the fixed connectivity...
I'll post a few scripts soon to coarse grain a protein in Pymol, and
to fix/show the connectivity. I'll have to combine some things from
scriptlets here and there, though.
Cheers,
Tsjerk
On Thu, Aug 18, 2011 at 9:07 PM, Michael Lerner <mgler...@gmail.com> wrote:
>
>
> On Thu, Aug 18, 2011 at 3:39 AM, Tsjerk Wassenaar <tsje...@gmail.com> 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 :)
>
> Do you have a fairly complete Python library for parsing GROMACS topology
> files? I tend to write ad hoc scripts that add CONECT records to MARTINI
> models. It's easy to do that for lipid bilayers, but I'd love a more general
> solution that makes it easy to load proteins correctly.
> Cheers,
> -Michael
>
>>
>> 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
>> <jason.vertr...@schrodinger.com> 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 <mdaily.w...@gmail.com>
>> > 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) jason.vertr...@schrodinger.com
>> > (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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>
>
>
> --
> Michael Lerner
> Department of Physics and Astronomy
> Earlham College - Drawer 111
> 801 National Road West
> Richmond, IN 47374-4095
>
--
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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