pymol-users

[PyMOL] loading gro files

[Michael D. <mda...@gm...>]

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)

Re: [PyMOL] loading gro files

[Marius R. <mar...@gm...>]

Maybe this can help you

http://sourceforge.net/mailarchive/message.php?msg_id=19472192

Cheers,
Marius

On Tue, Aug 16, 2011 at 2:19 AM, 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)
>
> ------------------------------------------------------------------------------
> uberSVN's rich system and user administration capabilities and model
> configuration take the hassle out of deploying and managing Subversion and
> the tools developers use with it. Learn more about uberSVN and get a free
> download at:  http://p.sf.net/sfu/wandisco-dev2dev
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Re: [PyMOL] loading gro files

[Jason V. <jas...@sc...>]

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)
>
> ------------------------------------------------------------------------------
> uberSVN's rich system and user administration capabilities and model
> configuration take the hassle out of deploying and managing Subversion and
> the tools developers use with it. Learn more about uberSVN and get a free
> download at:  http://p.sf.net/sfu/wandisco-dev2dev
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Re: [PyMOL] loading gro files

[Tsjerk W. <ts...@gm...>]

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)
>>
>> ------------------------------------------------------------------------------
>> uberSVN's rich system and user administration capabilities and model
>> configuration take the hassle out of deploying and managing Subversion and
>> the tools developers use with it. Learn more about uberSVN and get a free
>> download at:  http://p.sf.net/sfu/wandisco-dev2dev
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
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

Re: [PyMOL] loading gro files

[Joseph A. <and...@gm...>]

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)
> >>
> >>
> ------------------------------------------------------------------------------
> >> uberSVN's rich system and user administration capabilities and model
> >> configuration take the hassle out of deploying and managing Subversion
> and
> >> the tools developers use with it. Learn more about uberSVN and get a
> free
> >> download at:  http://p.sf.net/sfu/wandisco-dev2dev
> >>
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >>
> >
> >
> >
> > --
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schrodinger, LLC
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
> >
> >
> ------------------------------------------------------------------------------
> > 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
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
>
> --
> 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
>
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Joseph ANDRE

Re: [PyMOL] loading gro files

[Tsjerk W. <ts...@gm...>]

Hi Joseph,

Sorry about that. A bit naive with the numbering. To fix it, change the function

def pdbOut(atom,i=1):
   return _pdbline%((i,) + (atom[0][:3],) + (atom[1],) + (atom[3],) +
(atom[2],) + atom[4:] + (1,40) + (atom[0][0],))

to

def pdbOut(atom,i=1):
    stuff = [i%1e5,atom[0][:3],atom[1],atom[3],atom[2]%1e4]+list(atom[4:])+[1,40,atom[0][0]]
    return _pdbline % tuple(stuff)

It worked for me on a .gro file with 160k atoms :)

Cheers,

Tsjerk

2011/8/18 Joseph André <and...@gm...>:
> 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)
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >> uberSVN's rich system and user administration capabilities and model
>> >> configuration take the hassle out of deploying and managing Subversion
>> >> and
>> >> the tools developers use with it. Learn more about uberSVN and get a
>> >> free
>> >> download at:  http://p.sf.net/sfu/wandisco-dev2dev
>> >>
>> >> _______________________________________________
>> >> PyMOL-users mailing list (PyM...@li...)
>> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >> Archives: http://www.mail-archive.com/pym...@li...
>> >>
>> >
>> >
>> >
>> > --
>> > Jason Vertrees, PhD
>> > PyMOL Product Manager
>> > Schrodinger, LLC
>> >
>> > (e) Jas...@sc...
>> > (o) +1 (603) 374-7120
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > 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
>> > _______________________________________________
>> > PyMOL-users mailing list (PyM...@li...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pym...@li...
>> >
>>
>>
>>
>> --
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> --
> Joseph ANDRE
>
>
>



-- 
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

Re: [PyMOL] loading gro files

[Thomas H. <sp...@us...>]

To keep the original residue numbers from the gro file, you could also 
temporarily store additional numbering in the segment identifier, and 
after loading get it back from there:

_pdbline    = "ATOM  %5i  %-3s %3s%2s%4i" +\
     "    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s  \n"

def pdbOut(atom,i=1):
     segi = '%02d%02d' % (i/100000,atom[2]/10000)
     stuff = [i%1e5,atom[0][:3],atom[1],atom[3],atom[2]%1e4] +\
             list(atom[4:])+[1,40,segi,atom[0][0]]
     return _pdbline % tuple(stuff)

And after cmd.read_pdbstr:

     cmd.alter(objname, '(ID,resi,segi)=' +\
         '(ID+100000*int(segi[:2]), resv+10000*int(segi[2:]), "")')

Cheers,
   Thomas

On 08/18/2011 10:40 AM, Tsjerk Wassenaar wrote:
> Hi Joseph,
>
> Sorry about that. A bit naive with the numbering. To fix it, change the function
>
> def pdbOut(atom,i=1):
>     return _pdbline%((i,) + (atom[0][:3],) + (atom[1],) + (atom[3],) +
> (atom[2],) + atom[4:] + (1,40) + (atom[0][0],))
>
> to
>
> def pdbOut(atom,i=1):
>      stuff = [i%1e5,atom[0][:3],atom[1],atom[3],atom[2]%1e4]+list(atom[4:])+[1,40,atom[0][0]]
>      return _pdbline % tuple(stuff)
>
> It worked for me on a .gro file with 160k atoms :)
>
> Cheers,
>
> Tsjerk
>
> 2011/8/18 Joseph André<and...@gm...>:
>> 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

-- 
Thomas Holder
MPI for Developmental Biology

Re: [PyMOL] loading gro files

[Michael L. <mgl...@gm...>]

On Thu, Aug 18, 2011 at 3:39 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 :)
>

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
> <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)
> >>
> >>
> ------------------------------------------------------------------------------
> >> uberSVN's rich system and user administration capabilities and model
> >> configuration take the hassle out of deploying and managing Subversion
> and
> >> the tools developers use with it. Learn more about uberSVN and get a
> free
> >> download at:  http://p.sf.net/sfu/wandisco-dev2dev
> >>
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >>
> >
> >
> >
> > --
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schrodinger, LLC
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
> >
> >
> ------------------------------------------------------------------------------
> > 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
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
>
> --
> 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
>
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner
Department of Physics and Astronomy
Earlham College - Drawer 111
801 National Road West
Richmond, IN   47374-4095

Re: [PyMOL] loading gro files

[Tsjerk W. <ts...@gm...>]

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 <mgl...@gm...> wrote:
>
>
> On Thu, Aug 18, 2011 at 3:39 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 :)
>
> 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
>> <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)
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >> uberSVN's rich system and user administration capabilities and model
>> >> configuration take the hassle out of deploying and managing Subversion
>> >> and
>> >> the tools developers use with it. Learn more about uberSVN and get a
>> >> free
>> >> download at:  http://p.sf.net/sfu/wandisco-dev2dev
>> >>
>> >> _______________________________________________
>> >> PyMOL-users mailing list (PyM...@li...)
>> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >> Archives: http://www.mail-archive.com/pym...@li...
>> >>
>> >
>> >
>> >
>> > --
>> > Jason Vertrees, PhD
>> > PyMOL Product Manager
>> > Schrodinger, LLC
>> >
>> > (e) Jas...@sc...
>> > (o) +1 (603) 374-7120
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > 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
>> > _______________________________________________
>> > PyMOL-users mailing list (PyM...@li...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pym...@li...
>> >
>>
>>
>>
>> --
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> --
> 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