From Klaas.Decanniere at pandora.be  Thu Dec  4 11:50:56 2003
From: Klaas.Decanniere at pandora.be (Klaas Decanniere)
Date: Thu, 04 Dec 2003 20:50:56 +0100
Subject: [Chimera-users] delphi potenital map viewing
Message-ID: <3FCF9020.4060302@pandora.be>


Hello,


Thinking that more is better I ended up with Delphi potential maps on a 
rather large grid which I would like to visualize with chimera (gsize=213)
Chimera seems to think the grid is to large.
Is there an easy way to have chimera accept bigger grids (speed is not 
really an issue)?
Alternatively, what is the largest grid that chimera can accept?

Thanks for your help.

Klaas Decanniere


From goddard at cgl.ucsf.edu  Thu Dec  4 15:23:15 2003
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 4 Dec 2003 15:23:15 -0800 (PST)
Subject: [Chimera-users] delphi potenital map viewing
In-Reply-To: <3FCF9020.4060302@pandora.be> (message from Klaas Decanniere on
	Thu, 04 Dec 2003 20:50:56 +0100)
References: <3FCF9020.4060302@pandora.be>
Message-ID: <200312042323.hB4NNFul628895@adenine.cgl.ucsf.edu>

Hi Klaas,

  The size of the Delphi potential map Chimera can display is only
limited by the size of your computer memory.

  If you open a large map it does not get shown immediately if the map
is larger than 1 Mvoxels (~100^3).  This is controlled by an option
under the Volume Viewer options pane "Show data when opened if smaller
than XXX Mvoxels".  If you open a large data set, you need to press
the Show button at the bottom of the Volume Viewer dialog to display
it.  This is intended to allow you to adjust the bounds to show a
subregion and avoid loading the whole map.  This setting can be
changed to specify a larger volume limit, or always show the data
immediately when opened.

  When you press Show to display the large map, it will show a
subsampled version, for example skipping every other plane along
each axis.  This is indicated in the "Step" menu near the top of
the Volume Viewer dialog.  The automatic subsampling happens because
of another Volume Viewer / Options setting "Adjust step to show at
most XXX MVoxels".  The default setting is to subsample for data
sets larger than 2 MVoxels.  You can change the step to not do
subsampling using the Step menu (set it to "1 1 1").  You can turn
off the automatic subsampling option or increase the volume size
limit.

  Delphi grid values are 4 byte floats, so a 213^3 map will take
about 38 Mb (213^3 * 4), plus some additional memory will be used
to make a surface representation.  I've worked with 256^3 maps with
no problem.  Probably the practical limit is around 512^3 for a
machine with a gigabyte of memory.

	Tom


From goddard at cgl.ucsf.edu  Fri Dec  5 13:30:28 2003
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Fri, 5 Dec 2003 13:30:28 -0800 (PST)
Subject: [Chimera-users] delphi potenital map viewing
In-Reply-To: <3FD0E62C.3050906@pandora.be> (message from Klaas Decanniere on
	Fri, 05 Dec 2003 21:10:20 +0100)
References: <3FCF9020.4060302@pandora.be>
	<200312042323.hB4NNFul628895@adenine.cgl.ucsf.edu>
	<3FD0E62C.3050906@pandora.be>
Message-ID: <200312052130.hB5LUSQO837800@adenine.cgl.ucsf.edu>

Hi Klaas,

  The Delphi Viewer is the only tool that can color a molecular surface
according to the potential value.

  Can you email me the Python traceback you get when the "_cubes error: ..."
occurs?  This shows exactly where in the code the error happened.  You find
it by looking at Favorites/Reply Log.

  Having the traceback alone might be enough for me to figure out and
correct the problem.  If you could put the phi file on the web so I could
download it I would almost certainly be able to figure out the problem.

  The Delphi Viewer is supposed to be able handle maps of any size.
It will be much slower than volume viewer, but it should not generate
an error with a large map.

	 Tom


> Date: Fri, 05 Dec 2003 21:10:20 +0100
> From: Klaas Decanniere <Klaas.Decanniere at pandora.be>
> Reply-To: Klaas.Decanniere at pandora.be
> To: Thomas Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] delphi potenital map viewing
> 
> Thomas Goddard wrote:
> 
> >Hi Klaas,
> >
> >  The size of the Delphi potential map Chimera can display is only
> >limited by the size of your computer memory.
> >
> >  If you open a large map it does not get shown immediately if the map
> >is larger than 1 Mvoxels (~100^3). 
> >  
> >
> 
> When I tried using the "delphi viewer" option, I get _cubes error: grid 
> index out of range
> Using the volume viewer I can indeed load everything.
> Is there a way to tie the volume viewer thing to a molecular surface? 
> With a colour gradient showing different levels of potential? (As in the 
> Molecular surface option in the Delphiviewer)
> Or maybe I can save the subsampled map somehow and then read it into the 
> delphiviewer thing?
> 
> Thanks again for your help.
> 
> Klaas
> 
> P.S.: I like the program more each day.
> P.P.S.: If you ever have a day with nothing to do: the automatic 
> fetching of pdb files doesn't work for me as I'm behind a proxy server.



From lgc4r at virginia.edu  Mon Dec  8 13:17:08 2003
From: lgc4r at virginia.edu (Luis Cuello)
Date: Mon, 8 Dec 2003 16:17:08 -0500
Subject: [Chimera-users] B-Factor
Message-ID: <002901c3bdd0$a3987230$9f118f80@Magneto>

Hello, My name is Luis Cuello and I am a graduate student at the University
of Virginia..I started using chimera recently but I have not been able to
colored my files by B-factors values, Is there any way to do that with
chimera software??? If you could help me in this matter I would
appreciated..Sincerely

 

 

 

 

Luis Cuello

University of Virginia

Molecular Physiology

1(434)9245473

e-mail:lgc4r at virginia.edu

 

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From pett at cgl.ucsf.edu  Mon Dec  8 22:34:29 2003
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 8 Dec 2003 22:34:29 -0800
Subject: [Chimera-users] B-Factor
In-Reply-To: <002901c3bdd0$a3987230$9f118f80@Magneto>
Message-ID: <BDA3C48A-2A11-11D8-AEEF-0003933D1350@cgl.ucsf.edu>


On Monday, December 8, 2003, at 01:17  PM, Luis Cuello wrote:

> Hello, My name is Luis Cuello and I am a graduate student at the  
> University of Virginia?.I started using chimera recently but I have  
> not been able to colored my files by B-factors values, Is there any  
> way to do that with chimera software??? If you could help me in this  
> matter I would appreciated?.

Hi Luis,
	We intend to make a nice interface for coloring structures by  
associated numerical values (such as B factors), but for now a series  
of typed commands will do what you want to do.  To color a structure so  
that B factors less than 10 are shown as green, between 10 and 20 as  
yellow, and over 20 as red, do:

	color green
	color yellow @/bfactor>10
	color red @/bfactor>20

Obviously, use whatever numerical cutoffs and colors you want.  There  
is a discussion of the the atom/residue/model attributes you can use in  
commands at  
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
atom_spec.html#descriptors .

	Eric Pettersen
	UCSF Computer Graphics Lab
	pett at cgl.ucsf.edu


From goddard at cgl.ucsf.edu  Wed Dec 10 23:36:11 2003
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 10 Dec 2003 23:36:11 -0800 (PST)
Subject: [Chimera-users] Re: Gaussians
In-Reply-To: <C718948D-2A9F-11D8-AC6E-000393CD9B40@cgl.ucsf.edu> (message from
	Eric Pettersen on Tue, 9 Dec 2003 15:31:13 -0800)
References: <C718948D-2A9F-11D8-AC6E-000393CD9B40@cgl.ucsf.edu>
Message-ID: <200312110736.hBB7aBxp561273@adenine.cgl.ucsf.edu>

Hi Lars,

  I'm not sure what you mean by visualizing some Gaussians.  If you
mean you want to make a volume which contains some specified Gaussians
then I can give you a separate Python program that will do that.
I already wrote it for another user.  It is included at the end of
this email.  It outputs a netcdf format volume file.

     Tom

% ./spots.py
Make a volume array that is the sum of specified Gaussians.
The first line of the input file has the grid cell size.
Each subsequent line has 5 fields giving x, y, z, width, height.
A volume grid is made that includes each Gaussian out to 3 widths.
The resulting volume is written in netcdf format.
Syntax: spots.py <infile> <outfile>

% cat spotfile
.5
15.49100  7.05000 17.16500   0.38   1.00
14.94600  7.55000 15.88800   0.35   1.00
16.01100  7.60400 14.81400   0.34   1.00
...

% ./spots.py spotfile gspottest.nc

The spots.py code follows.  Note that it contains a path to your
Chimera installation because it needs Chimera modules to write the
netcdf volume.


#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Make a volume array that is the sum of specified Gaussians.
# The resulting volume is written in netcdf format.
#
# Syntax: spots.py <infile> <outfile>
#
# The input file has a grid cell size on the first line followed by one
# line per gaussian with 5 fields specifying x, y, z, width, height.
#
import os.path
import sys

# Need Chimera path to use VolumeData and Numeric modules
CHIMERA_PATH = '/usr/local/chimera'

sys.path.insert(0, os.path.join(CHIMERA_PATH, 'lib'))
sys.path.insert(0, os.path.join(CHIMERA_PATH, 'share'))

import Numeric

# -----------------------------------------------------------------------------
#
def make_spot_grid(path):

    step_size, spot_parameters = read_spots(path)
    
    range = 3         # in spot widths
    xyz_min, xyz_max = bounding_box(spot_parameters, range)
    xyz_origin = xyz_min
    xyz_step = (step_size, step_size, step_size)
    xyz_size = map(lambda a,b: a - b, xyz_max, xyz_min)
    import math
    grid_size = map(lambda s, step, math=math: 1 + int(math.ceil(s/step)),
                    xyz_size, xyz_step)

    a = spot_array(spot_parameters, range, xyz_origin, step_size, grid_size)
    from VolumeData import Array_Grid_Data
    g = Array_Grid_Data(a, xyz_origin, xyz_step)

    return g

# -----------------------------------------------------------------------------
#
def read_spots(path):

    f = open(path, 'r')
    lines = f.readlines()
    f.close()

    step_size = float(lines[0])

    spot_params = []
    for line in lines[1:]:
        params = map(float, line.split())
        spot_params.append(params)

    return step_size, spot_params

# -----------------------------------------------------------------------------
#
def bounding_box(spot_parameters, range):

    xmin = ymin = zmin = None
    xmax = ymax = zmax = None
    for x, y, z, w, h in spot_parameters:
        pad = range * w
        if xmin == None or x - pad < xmin: xmin = x - pad
        if ymin == None or y - pad < ymin: ymin = y - pad
        if zmin == None or z - pad < zmin: zmin = z - pad
        if xmax == None or x + pad > xmax: xmax = x + pad
        if ymax == None or y + pad > ymax: ymax = y + pad
        if zmax == None or z + pad > zmax: zmax = z + pad

    return (xmin, ymin, zmin), (xmax, ymax, zmax)

# -----------------------------------------------------------------------------
#
def spot_array(spot_parameters, range, xyz_origin, step_size, grid_size):

    shape = list(grid_size)
    shape.reverse()             # array indices are z, y, x.
    array = Numeric.zeros(shape, Numeric.Float)
    for x, y, z, width, height in spot_parameters:
        add_spot((x,y,z), width, height, range, xyz_origin, step_size, array)
    return array

# -----------------------------------------------------------------------------
#
def add_spot(xyz, width, height, srange, xyz_origin, step_size, array):

    ijk = map(lambda a,b,s=step_size: (a - b)/s, xyz, xyz_origin)
    w = width / step_size
    w2 = w * w
    r = srange * width / step_size
    import math
    imin, jmin, kmin = map(lambda l, r=r, math=math: int(math.floor(l-r)), ijk)
    imax, jmax, kmax = map(lambda l, r=r, math=math: int(math.ceil(l+r)), ijk)
    for k in range(kmin, kmax+1):
        for j in range(jmin, jmax+1):
            for i in range(imin, imax+1):
                di, dj, dk = i-ijk[0], j-ijk[1], k-ijk[2]
                s2 = di*di + dj*dj + dk*dk
                e = height * math.exp(-s2/(2*w2))
                array[k,j,i] += e

# -----------------------------------------------------------------------------
#
def bfactor_backbone_spots(path, molecule = None):

    if molecule == None:
        import chimera
        molecule = chimera.openModels.list()[0]
    out = open(path, 'w')
    out.write('.5\n')     # step size
    import math
    for a in molecule.atoms:
        if a.name in ('C', 'N', 'CA') and hasattr(a, 'bfactor'):
            x, y, z = a.coord().xyz.data()
            w = math.sqrt(a.bfactor / (8 * math.pi**2))
            h = 1
            out.write('%8.5f %8.5f %8.5f %6.2f %6.2f\n' % (x,y,z,w,h))
    out.close()

# -----------------------------------------------------------------------------
#
def syntax():
  
  msg = ('Make a volume array that is the sum of specified Gaussians.\n' +
         'The first line of the input file has the grid cell size.\n' +
         'Each subsequent line has 5 fields giving x, y, z, width, height.\n' +
         'A volume grid is made that includes each Gaussian out to 3 widths.\n' +
         'The resulting volume is written in netcdf format.\n' +
         'Syntax: spots.py <infile> <outfile>\n')
  sys.stderr.write(msg)
  sys.exit(1)

# -----------------------------------------------------------------------------
#
def run_command():

    if len(sys.argv) != 3:
        syntax()

    inpath = sys.argv[1]
    outpath = sys.argv[2]

    grid = make_spot_grid(inpath)

    from VolumeData.netcdf.netcdf_grid import write_grid_as_netcdf
    write_grid_as_netcdf(grid, outpath)

# -----------------------------------------------------------------------------
#
if __name__ == '__main__':
    run_command()
    

From mryan1 at nc.rr.com  Fri Dec 12 15:34:42 2003
From: mryan1 at nc.rr.com (Morgan Ryan)
Date: Fri, 12 Dec 2003 18:34:42 -0500
Subject: [Chimera-users] Chimera export to VRML?
Message-ID: <C299F048-2CFB-11D8-A469-000393923A52@nc.rr.com>

VRML seems to be a native internal format for (the magnificent) 
Chimera. Is it possible to export VRML models from Chimera? Or do you 
worldly folks know of a mechanism for converting msms output into vrml 
files?
	Thanks! Morgan Ryan, enthusiastic amateur

____________________
Morgan Ryan
Development editor
W H Freeman
209 Adams Way
Chapel Hill NC 27516
phone: 919 942 4890
fax: 651 846 5265
mryan at whfreeman.com 
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From amutha_ramu at yahoo.com  Mon Dec 15 08:57:23 2003
From: amutha_ramu at yahoo.com (amutha ramaswamy)
Date: Mon, 15 Dec 2003 08:57:23 -0800 (PST)
Subject: [Chimera-users] help
Message-ID: <20031215165723.28854.qmail@web21110.mail.yahoo.com>

Dear sir
 
I am using the Chimera molecular visualising software. I am not able to color the PDB structure according to the B-factors. could you plase let me know how do i color accroding to the bfactor. 
 
i would greatly apprecuate your help in this regard
 
sincerely
amutha



Dr Amutha Ramaswamy
Postdoctoral Fellow, Department of Biomedical Informatics
3184 Graves Hall, 333 West 10th Avenue
The Ohio state University, Columbus, OHIO 43210
Phone: 614-688-3236 (Office); 614-291-0071(Residence)
Fax:    614-292-7659 (Office)
 
 








---------------------------------
Do you Yahoo!?
New Yahoo! Photos - easier uploading and sharing
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From pett at cgl.ucsf.edu  Mon Dec 15 13:59:30 2003
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 15 Dec 2003 13:59:30 -0800
Subject: [Chimera-users] help
In-Reply-To: <20031215165723.28854.qmail@web21110.mail.yahoo.com>
Message-ID: <F5369B08-2F49-11D8-8582-000393CD9B40@cgl.ucsf.edu>


On Monday, December 15, 2003, at 08:57 AM, amutha ramaswamy wrote:

> Dear sir
> ?
> I am using the Chimera molecular visualising software. I am not able  
> to color the PDB structure according to the B-factors. could you plase  
> let me know how do i color accroding to the bfactor.
> ?
> i would greatly apprecuate your help in this regard

Dear Amutha,
	We just got a question very similar to yours on the list a few days  
ago.  I should say that we are working on an interface to allow  
coloring of ribbons/atoms/surfaces by any attribute, using any number  
colors in either a continuous spectrum, or as discrete "color bars".   
The interface isn't ready yet and will not be ready for the snapshot  
release that will be out in a few days.  We hope it will be ready for  
the release after that.  Until then, you can use typed-in commands to  
color by B-factor in discrete ranges, as described in the part of the  
previous mail that I've quoted below.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu

> To color a structure so that B factors less than 10 are shown as  
> green, between 10 and 20 as   yellow, and over 20 as red, do:
>
>         color green
>         color yellow @/bfactor>10
>         color red @/bfactor>20
>
> Obviously, use whatever numerical cutoffs and colors you want. There  
> is a discussion of the the atom/residue/model attributes you can use  
> in commands at  
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
> atom_spec.html#descriptors .
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From pett at cgl.ucsf.edu  Mon Dec 15 14:24:00 2003
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 15 Dec 2003 14:24:00 -0800
Subject: [Chimera-users] Chimera export to VRML?
In-Reply-To: <C299F048-2CFB-11D8-A469-000393923A52@nc.rr.com>
Message-ID: <615FA04C-2F4D-11D8-8582-000393CD9B40@cgl.ucsf.edu>

On Friday, December 12, 2003, at 03:34 PM, Morgan Ryan wrote:

> VRML seems to be a native internal format for (the magnificent) 
> Chimera. Is it possible to export VRML models from Chimera? Or do you 
> worldly folks know of a mechanism for converting msms output into vrml 
> files?
> 	Thanks! Morgan Ryan, enthusiastic amateur

Hi Morgan,
	Although VRML is one of the model types that Chimera supports, we 
don't convert MSMS output into VRML.  It is instead made into its own 
model type (MSMSModel) so that we can preserve information about the 
correspondence between surface points and atoms, which would be lost if 
we had used a VRML model.
	A Python routine _could_ be written that would convert the MSMSModel 
information into its VRML equivalent, but before "going there" perhaps 
you could describe why you want MSMS info in VRML format?  There could 
be a better alternative available than writing the conversion routine.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu


From mryan1 at nc.rr.com  Mon Dec 15 17:49:11 2003
From: mryan1 at nc.rr.com (Morgan Ryan)
Date: Mon, 15 Dec 2003 20:49:11 -0500
Subject: [Chimera-users] Chimera export to VRML?
In-Reply-To: <615FA04C-2F4D-11D8-8582-000393CD9B40@cgl.ucsf.edu>
References: <615FA04C-2F4D-11D8-8582-000393CD9B40@cgl.ucsf.edu>
Message-ID: <0B919669-2F6A-11D8-A469-000393923A52@nc.rr.com>

Thanks for your answer, Eric:

> perhaps you could describe why you want MSMS info in VRML format?  
> There could be a better alternative available than writing the 
> conversion routine.

I develop educational stuff--you might know one of my recent outings, 
"Lehninger Principles of Biochemistry 3e" (4e to appear in a couple 
months). I'm the development editor of that book for Freeman, and I'm 
branching out on my own into motion graphics to animate the things we 
talk about in the book. For molecular animations I convert pdb files 
into formats that professional 3D graphics programs can read. I can 
output b&s and vdW models into usable formats in a variety of ways, but 
right now the only route I know of for porting molecular surfaces into 
a 3D app is WebLab->VRML->3D app--imperfect for a variety of reasons 
(expensive, PC only, minimal access to surface parameters, etc).  VMD 
exports VRML, but the output files are _gigantic_ and can't be read 
anyway by any 3D app I've tried. What I crave is a route that would let 
me tune a macromolecular surface with MSMS in a nimble app like 
Chimera, export it into VRML, and open it in any 3D app that reads VRML 
files (most of them). Possible?
	I'm afraid my programing skills are far too primitive to do this 
myself. So how can one get surfaces for enzymes--for the 
ribosome!--into a format that 3D apps can read? Your counsel will be 
greatly appreciated! Morgan


On Dec 15, 2003, at 5:24 PM, Eric Pettersen wrote:

> On Friday, December 12, 2003, at 03:34 PM, Morgan Ryan wrote:
>
>> VRML seems to be a native internal format for (the magnificent) 
>> Chimera. Is it possible to export VRML models from Chimera? Or do you 
>> worldly folks know of a mechanism for converting msms output into 
>> vrml files?
>> 	Thanks! Morgan Ryan, enthusiastic amateur
>
> Hi Morgan,
> 	Although VRML is one of the model types that Chimera supports, we 
> don't convert MSMS output into VRML.  It is instead made into its own 
> model type (MSMSModel) so that we can preserve information about the 
> correspondence between surface points and atoms, which would be lost 
> if we had used a VRML model.
> 	A Python routine _could_ be written that would convert the MSMSModel 
> information into its VRML equivalent, but before "going there" perhaps 
> you could describe why you want MSMS info in VRML format?  There could 
> be a better alternative available than writing the conversion routine.
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         pett at cgl.ucsf.edu
>                         http://www.cgl.ucsf.edu
>
>

____________________
Morgan Ryan
Development editor
W H Freeman
209 Adams Way
Chapel Hill NC 27516
phone: 919 942 4890
fax: 651 846 5265
mryan at whfreeman.com
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From amutha_ramu at yahoo.com  Tue Dec 16 08:32:51 2003
From: amutha_ramu at yahoo.com (amutha ramaswamy)
Date: Tue, 16 Dec 2003 08:32:51 -0800 (PST)
Subject: [Chimera-users] help
In-Reply-To: <F5369B08-2F49-11D8-8582-000393CD9B40@cgl.ucsf.edu>
Message-ID: <20031216163251.41897.qmail@web21105.mail.yahoo.com>

Dear Sir
 
Thank you so much for your kind reply. Yes definitely, the chimera users would grately benifit from the option of coloring the ribbon diagram accoridng to any required parameter..
 
thank you so much
 
regards
amutha

Eric Pettersen <pett at cgl.ucsf.edu> wrote:

On Monday, December 15, 2003, at 08:57 AM, amutha ramaswamy wrote:

> Dear sir
>  
> I am using the Chimera molecular visualising software. I am not able 
> to color the PDB structure according to the B-factors. could you plase 
> let me know how do i color accroding to the bfactor.
>  
> i would greatly apprecuate your help in this regard

Dear Amutha,
We just got a question very similar to yours on the list a few days 
ago. I should say that we are working on an interface to allow 
coloring of ribbons/atoms/surfaces by any attribute, using any number 
colors in either a continuous spectrum, or as discrete "color bars". 
The interface isn't ready yet and will not be ready for the snapshot 
release that will be out in a few days. We hope it will be ready for 
the release after that. Until then, you can use typed-in commands to 
color by B-factor in discrete ranges, as described in the part of the 
previous mail that I've quoted below.

Eric Pettersen
UCSF Computer Graphics Lab
pett at cgl.ucsf.edu
http://www.cgl.ucsf.edu

> To color a structure so that B factors less than 10 are shown as 
> green, between 10 and 20 as yellow, and over 20 as red, do:
>
> color green
> color yellow @/bfactor>10
> color red @/bfactor>20
>
> Obviously, use whatever numerical cutoffs and colors you want. There 
> is a discussion of the the atom/residue/model attributes you can use 
> in commands at 
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
> atom_spec.html#descriptors .

Dr Amutha Ramaswamy
Postdoctoral Fellow, Department of Biomedical Informatics
3184 Graves Hall, 333 West 10th Avenue
The Ohio state University, Columbus, OHIO 43210
Phone: 614-688-3236 (Office); 614-291-0071(Residence)
Fax:    614-292-7659 (Office)
 
 








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From goddard at cgl.ucsf.edu  Tue Dec 16 10:05:26 2003
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 16 Dec 2003 10:05:26 -0800 (PST)
Subject: [Chimera-users] Chimera export to VRML?
In-Reply-To: <0B919669-2F6A-11D8-A469-000393923A52@nc.rr.com> (message from
	Morgan Ryan on Mon, 15 Dec 2003 20:49:11 -0500)
References: <615FA04C-2F4D-11D8-8582-000393CD9B40@cgl.ucsf.edu>
	<0B919669-2F6A-11D8-A469-000393923A52@nc.rr.com>
Message-ID: <200312161805.hBGI5QvL847007@adenine.cgl.ucsf.edu>

Hi Morgan,

  Molecular surfaces produced by the Chimera Actions/Surface/Show menu
entry provide atomic resolution detail.  For a large structure like a
ribosome the VRML file for such a high resolution surface will be
large.  The surface might have a million triangles, and the file will
at least be 30 megabytes.  (In fact the molecular surface calculation
we use, called MSMS, crashes on some ribosome structures like 1jj2.)
Chimera provides lower resolution surfaces with the multi-scale
extension (Tools/Multiscale menu).  Examples showing some viruses and
GroEL are shown on the Chimera image gallery:

	http://www.cgl.ucsf.edu/chimera/ImageGallery/

You can choose the resolution of the multi-scale surfaces.  We don't
currently have VRML output for the multi-scale surfaces but that
could be added fairly easily.  I could look into that.  The Chimera
volume viewer (Tools/Volumes menu) also uses this same type of surface
model.  So a VRML export tool could also export electron and light
microscope 3D data or crystallographic density maps displayed as
isosurfaces.

   Tom

From goddard at cgl.ucsf.edu  Tue Dec 16 11:43:33 2003
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 16 Dec 2003 11:43:33 -0800 (PST)
Subject: [Chimera-users] Chimera export to VRML?
In-Reply-To: <00081A90-2FFF-11D8-A469-000393923A52@nc.rr.com> (message from
	Morgan Ryan on Tue, 16 Dec 2003 14:35:27 -0500)
References: <615FA04C-2F4D-11D8-8582-000393CD9B40@cgl.ucsf.edu>
	<0B919669-2F6A-11D8-A469-000393923A52@nc.rr.com>
	<200312161805.hBGI5QvL847007@adenine.cgl.ucsf.edu>
	<00081A90-2FFF-11D8-A469-000393923A52@nc.rr.com>
Message-ID: <200312161943.hBGJhX1c853596@adenine.cgl.ucsf.edu>

Hi Morgan,

  We hope to have a snapshot Chimera release later this week.  I'll try
to get VRML output of multi-scale and msms surfaces in that release.
Snapshot releases aren't as well tested as production releases, but are
intended for trying out new features like this.

	 Tom

PS: Your email does not go to chimera-users unless you explicitly CC it
to that list.  We like to post to that list so others can benefit from it.
I've included your email below and CC'ed this to chimera-users.  Let me
know if you want to keep your email private.


> From: Morgan Ryan <mryan1 at nc.rr.com>
> Subject: Re: [Chimera-users] Chimera export to VRML?
> Date: Tue, 16 Dec 2003 14:35:27 -0500
> 
> Thanks, Thomas. (Am I broadcasting to the list? I'm not sure if I'm 
> talking to a list or just you and Eric Petterson...)
> 
> >  For a large structure like a
> > ribosome the VRML file ...might have a million triangles, and the file 
> > will
> > at least be 30 megabytes.
> 
> The 3D programs I use have fairly refined mesh management tools for 
> reducing complexity selectively, although being able to choose the mesh 
> density directly through MSMS would be pleasing.
> 
> > You can choose the resolution of the multi-scale surfaces.  We don't
> > currently have VRML output for the multi-scale surfaces but that
> > could be added fairly easily.  I could look into that.
> 
> The advantage of VRML output (or 3dmf, or dxf, or some other 
> interchange format) is that you could open the model in Maya, Studio 
> Max, Strata, Cinema 4D, any of the 3D animation programs, and make 
> startling movies wiith Hollywood special effects--light sabers! 
> Atomic-resolution recreations of enzyme reaction mechanisms! (The 
> latter is what I'm working on...)
> 
> It would be a wonderful extension of Chimera if VRML output were added. 
> Morgan

From goddard at cgl.ucsf.edu  Tue Dec 16 17:04:33 2003
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 16 Dec 2003 17:04:33 -0800 (PST)
Subject: [Chimera-users] Chimera export to VRML?
In-Reply-To: <F83A5E61-3002-11D8-A469-000393923A52@nc.rr.com> (message from
	Morgan Ryan on Tue, 16 Dec 2003 15:03:52 -0500)
References: <615FA04C-2F4D-11D8-8582-000393CD9B40@cgl.ucsf.edu>
	<0B919669-2F6A-11D8-A469-000393923A52@nc.rr.com>
	<200312161805.hBGI5QvL847007@adenine.cgl.ucsf.edu>
	<00081A90-2FFF-11D8-A469-000393923A52@nc.rr.com>
	<200312161943.hBGJhX1c853596@adenine.cgl.ucsf.edu>
	<F83A5E61-3002-11D8-A469-000393923A52@nc.rr.com>
Message-ID: <200312170104.hBH14XFs870336@adenine.cgl.ucsf.edu>

Hi Morgan,

  I've written an extension to export Chimera multi-scale and volume surfaces
as VRML.  I wasn't able to export the molecular (MSMS) surfaces because the
code does not provide access to the surface coloring.  I've submitted a
request to enhance the molecular surface code to make surface colors readable.

  I'm not sure if the VRML surface exporting will make it into the
coming snapshot release.  If it doesn't I will provide it to you by
email.  I'll let you know when we have the snapshot ready, probably later
this week.

	  Tom

From juha.huiskonen at helsinki.fi  Wed Dec 17 03:13:35 2003
From: juha.huiskonen at helsinki.fi (Juha Huiskonen)
Date: 17 Dec 2003 13:13:35 +0200
Subject: [Chimera-users] interactive volume segmentation
Message-ID: <1071659614.340.4031.camel@cryo.pc.helsinki.fi>

Hello,

currently it is possible to select only box-shaped subregions in Volume
Viewer. I would be especially interested in segmenting electron density
maps or their isosurfaces to different subregions with any shape
interactively. Is anyone planning to add a feature like this?

Regards,

Juha Huiskonen



From goddard at cgl.ucsf.edu  Wed Dec 17 10:27:31 2003
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 17 Dec 2003 10:27:31 -0800 (PST)
Subject: [Chimera-users] interactive volume segmentation
In-Reply-To: <1071659614.340.4031.camel@cryo.pc.helsinki.fi> (message from
	Juha Huiskonen on 17 Dec 2003 13:13:35 +0200)
References: <1071659614.340.4031.camel@cryo.pc.helsinki.fi>
Message-ID: <200312171827.hBHIRVnf946217@adenine.cgl.ucsf.edu>

Hi Juha,

  We don't currently have a plan to add volume data segmentation tools
to Chimera.  Some electron microscopy people have expressed interest
in segmentation tools in Chimera.  But this is a big complex problem.
A first step would be to make Chimera volume display able to use mask
files that are produced by segmentation done with programs.

  I'd be the programmer to work on this.  It would help me to have
precise descriptions of exactly how segmentation tools would work.
Then I could better judge how big a programming task it is.

     Tom



From juha.huiskonen at helsinki.fi  Thu Dec 18 00:33:38 2003
From: juha.huiskonen at helsinki.fi (Juha Huiskonen)
Date: 18 Dec 2003 10:33:38 +0200
Subject: [Chimera-users] interactive volume segmentation
In-Reply-To: <200312171827.hBHIRVnf946217@adenine.cgl.ucsf.edu>
References: <1071659614.340.4031.camel@cryo.pc.helsinki.fi>
	 <200312171827.hBHIRVnf946217@adenine.cgl.ucsf.edu>
Message-ID: <1071736418.2782.19.camel@cryo.pc.helsinki.fi>

Hi Tom,

> A first step would be to make Chimera volume display able to use mask
> files that are produced by segmentation done with programs.

A segment file would be another grid with integer values specifying the
segment of the particular voxel. Density would be then divided into
subsets that could be treated as separate grids. Of course, one can also
do this outside chimera, and just read in multiple grids.

More generally, a nice concept would be the possibility of mapping
values from one grid to an isosurface calculated from another grid. The
isosurface would be then colored based on the mapped values. The mapped
value could represent a voxel belonging to some segment, or distance to
some other voxel (e.g. center of the model) etc.

Cheers,

Juha


From goddard at cgl.ucsf.edu  Thu Dec 18 11:38:53 2003
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 18 Dec 2003 11:38:53 -0800 (PST)
Subject: [Chimera-users] interactive volume segmentation
In-Reply-To: <1071736418.2782.19.camel@cryo.pc.helsinki.fi> (message from Juha
	Huiskonen on 18 Dec 2003 10:33:38 +0200)
References: <1071659614.340.4031.camel@cryo.pc.helsinki.fi>
	<1071736418.2782.19.camel@cryo.pc.helsinki.fi>
Message-ID: <200312181938.hBIJcr45773921@adenine.cgl.ucsf.edu>

Hi Juha,

  There is a Chimera tool for coloring a volume isosurface using the
values of another volume data set that was written by Steve Ludke at
the National Center for Macromolecular Imaging.  It is available as
part of the EMAN (single particle EM reconstruction package) source
code.

	http://ncmi.bcm.tmc.edu/~stevel/EMAN/doc/

The code is in eman/chimeraext/FilterKit/Colorizer.py and also requires
a modified version of chimera/share/VolumeViewer/surface.py which is
available for Chimera 1872 in eman/chimeraext/surface.py.  Steve recently
wrote this extension and there is no documentation that I am aware of.
We will have better support for this capability in the coming year.

   Tom

From pett at cgl.ucsf.edu  Mon Dec 22 20:48:24 2003
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 22 Dec 2003 20:48:24 -0800
Subject: [Chimera-users] ribbon+atoms
Message-ID: <3DA9CC20-3503-11D8-ABBF-0003933D1350@cgl.ucsf.edu>

Hi, the 1892 snapshot release we just put out allows control over 
whether backbone atoms can be displayed with ribbons (on a per-model 
basis).  There is a "ribbackbone" command, an entry in the New 
Molecules preference category, and a control in the attributes panel 
(reached via the "attributes..." button in the model panel).

	Eric Pettersen
	UCSF Computer Graphics Lab
	pett at cgl.ucsf.edu


From terry at francisco.compbio.ucsf.edu  Tue Dec 23 13:12:27 2003
From: terry at francisco.compbio.ucsf.edu (Terry Downing)
Date: Tue, 23 Dec 2003 13:12:27 -0800
Subject: [Chimera-users] vdw viewer
Message-ID: <3FE8AFBA.502D187E@francisco.compbio.ucsf.edu>

Hey CGL,

  I would like to be able to visualize several different vdw parameter
sets on the same molecule.  Is there a way to visualize just the vdw
surface?  Can I change the parameter files easily?   As always, thanks
in advance for your help.

Sincerely,
Terry Downing

--
P. Therese Downing
Chemistry and Chemical Biology Graduate Program
Kuntz and James Labs, UCSF
Voice:  (415)476-3986
Fax:    (415)502-1411


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