pymol-users Mailing List for PyMOL Molecular Graphics System

Dear all,
when I open my pdb file in Pymol one residue in each subunit of my
protein dimer is not visible.  I know it's there as I can select it and
it is visible as sticks or lines with all bons present.  I have tried
using a pdb of just the 2 helices in my dimer but the residue still
isn't visible.  I have also checked the pdb and everything seems fine
(the residue can be seen in 'O' and is joined to its neighboring
residues).  I am using version 0.90 in Windows and have used version
0.68 in Unix.
Does anyone have any ideas how I can overcome this?
Thanks,
Claire

Hi,

When attempting to import pymol 0.90 using "import
pymol", I get the following error:

Traceback (most recent call last):
  File "<pyshell#0>", line 1, in ?
    import pymol
  File
"C:\Python22\Lib\site-packages\pymol\__init__.py",
line 300, in ?
    import _cmd
ImportError: No module named _cmd

Can somebody point me to a solution?

Much thanks!



__________________________________
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Hello PyMOL users,

There are some recent improvements and bugfixes to the rTools suite 
available. The package rTools 0.6.0 can be regarded as beta, it is 
available from:

http://www.rubor.de/bioinf

New features include:
- more detailed instructions for Win and MacOSX users.
- states can be freely assigned to movie frames.
- separate mvTurn and (as suggested by Richard Ball)
- color fading in movies. (written by Tserk Wassenaar)

rTools for PyMOL is a collection of useful stuff not yet contained in 
PyMOL itself. It includes.

- some dialog boxes for rapidly running scripts etc.
- access to the PDB from PyMOL.
- integration of external applications (DSSP, PASS, HBExplore, calc-surface)
- commands for easier creation of animations


As rTools is not really mature, i still like to hear of bugs in it 
(kri...@ch...).

Yours,

Kristian Rother

Protein Structure Theory Group
Institute of Biochemistry
Humboldt University Berlin

Richard,

	"layer0/MemoryCache.c", needs to be added to the source list in
setup.py.  Sorry for the inconvenience...

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of rb...@uc...
> Sent: Sunday, July 27, 2003 5:01 PM
> To: pym...@li...
> Subject: [PyMOL] installing 0.90 from scratch
> 
> Dear All,
> 
> I tried installing 0.90 from source, using "option 1", i.e.
> 
> python setup1.py install
> python setup2.py
> 
> But when I try to run the executable pymol.com, I get the error:
> 
> Traceback (most recent call last):
>   File "/usr/lib/python2.2/site-packages/pymol/__init__.py", line 92,
in ?
>     import pymol
>   File "/usr/lib/python2.2/site-packages/pymol/__init__.py", line 300,
in
> ?
>     import _cmd
> ImportError: /usr/lib/python2.2/site-packages/pymol/_cmd.so: undefined
> symbol:
> MemoryCacheDone
> 
> Any advice appreciated,
> 
> Richard Baxter
> 
> 
> -------------------------------------------------------
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Milton,

	To get a complete list of commands, hit TAB on a blank command
line.

	My apologies that PyMOL isn't more obvious, but thanks for the
reminder -- I'm working on making life easier!

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Milton H. Werner, Ph.D.
> Sent: Sunday, July 27, 2003 3:28 AM
> To: pym...@li...
> Subject: [PyMOL] command list in Mac OSX
> 
> After struggling for an extend time and viewing the command list in
> 'help command', I finally found that the 'align' command exists in v.
> 0.9x and can nicely fit dissimilar molecules.
> 
> Is there an additional way to get a complete command list?
> 
> Milton H. Werner, Ph.D.
> --
> Associate Professor and Head, Laboratory of Molecular Biophysics
> The Rockefeller University
> 1230 York Avenue, Box 42
> New York, NY  10021
> 
> 212/327-7221
> 212/327-7222 FAX
> mw...@po...
> http://www.rockefeller.edu/labheads/werner/werner-lab.html
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> Data Reports, E-commerce, Portals, and Forums are available now.
> Download today and enter to win an XBOX or Visual Studio .NET.
> http://aspnet.click-
> url.com/go/psa00100003ave/direct;at.aspnet_072303_01/01
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Dear All,

I tried installing 0.90 from source, using "option 1", i.e.

python setup1.py install
python setup2.py

But when I try to run the executable pymol.com, I get the error:

Traceback (most recent call last):
  File "/usr/lib/python2.2/site-packages/pymol/__init__.py", line 92, in ?
    import pymol
  File "/usr/lib/python2.2/site-packages/pymol/__init__.py", line 300, in ?
    import _cmd
ImportError: /usr/lib/python2.2/site-packages/pymol/_cmd.so: undefined symbol:
MemoryCacheDone

Any advice appreciated,

Richard Baxter

After struggling for an extend time and viewing the command list in 
'help command', I finally found that the 'align' command exists in v. 
0.9x and can nicely fit dissimilar molecules.

Is there an additional way to get a complete command list?

Milton H. Werner, Ph.D.
-- 
Associate Professor and Head, Laboratory of Molecular Biophysics
The Rockefeller University
1230 York Avenue, Box 42
New York, NY  10021

212/327-7221
212/327-7222 FAX
mw...@po...
http://www.rockefeller.edu/labheads/werner/werner-lab.html

Hello to all,
Can anybody tell why the labels disappear after the rendering and if
there is a way to include labels in the ray-traced images.
Alex 

=20

No, actually I didn't, I thought is was enabled by default, so I must =
admit
I overlooked it in the driver instructions. I have to add the line

Option "Stereo" "1"

to the XF86Config file. That's a pity - the FX1000 is probably faster =
than
the 750XGL :-)  Well - the supplier accidentially swapped my and=20
another costumer's orders - so I was honest and sent it back :-)

Also, even with the cheap GeForce 4MX card currently in the machine, =
the
(mono) graphic performance is incredible - I guess it's an order of
magnitude faster than the VPro6 graphics on our SGIs :-)
=20
Cheers,

Esben

-----Original Message-----
From: Warren L. DeLano
To: EPF (Esben Peter Friis)
Sent: 21-07-03 18:19
Subject: RE: [PyMOL] Nuvision stereo glasses?=20

Esben,

	Are you sure you correctly configured the nVidia driver
(XF86Config) for Stereo?  It's not automatic, but as AFAIK, all the =
FX's
are QBS capable.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of EPF (Esben Peter Friis)
> Sent: Sunday, July 20, 2003 11:39 PM
> To: pym...@li...
> Subject: RE: [PyMOL] Nuvision stereo glasses?
>=20
>=20
>=20
> Hi all!
>=20
> > My personal bias is that the added cost to obtain real QBS hardware
with
> built-in stereo support
> > is well worth the money in terms of time saved on bugs and hassles
such
> as
> this.
>=20
> Yes! Real quad-buffered stereo is IMHO crucial for molecular =
modelling
> work
> ;-)
>=20
> > Under Linux, the nVidia Quadro4 750XGL does a fine job, has a
three-pin
> stereo sync plug,
> > and works with the Nuvision glasses and emitters. While I haven't
tested
> the higher-end FX series,
> > I have every reason to believe that they would also work just fine
given
> nVidia's unified driver
> > architecture.
>=20
> I doesn't work for me :-(   I ordered a Quadro4 750XGL, and the =
vendor
> sent
> me a Quadro FX1000 by mistake. I didn't notice at first, and just
> installed
> the card. Works fine and very fast with the 1.0-4363 version of the
Linux
> driver - but neither PyMOL or VMD detects any hardware stereo.... I
have
> to
> get it replaced by a 750XGL or 900XGL.
>=20
> We have some older stereographics glasses, which I expect will work
with
> the
> Nvidia cards. But we have also bought a set of Eye3D premium glasses.
They
> come with a VGA pass-through cable, which can catch the sync signal
from
> any
> VGA output. They also support different stereo modes, including
> interlacing,
> page-flipping, sync-doubling, and line-blanking. You get two sets of
> glasses
> (one wired, one IR) for =88179 or $199. This works nice with PyMOL =
and
the
> Xig
> X-server on an ATI Radeon 9000 card, and the "Scanline interleave"
> (interlaced) stereo mode in VMD works fine with these glasses and any
> graphics adapter. Maybe "scanline interleave" could be a stereo =
option
in
> PyMOL - it is definitely inferior to quad-buffered stereo, but it
works
> with
> _any_ graphics card and doesn't require a special driver. (I would
still
> go
> for QBS, though :-)
>=20
>=20
> Cheers
>=20
> Esben
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: VM Ware
> With VMware you can run multiple operating systems on a single
machine.
> WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at
the
> same time. Free trial click here: =
http://www.vmware.com/wl/offer/345/0
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

On Fri, Jul 18, 2003 at 11:59:17AM +0300, Dr. Daniel James White PhD wrote:

> ATI radeon 8500 works with the xig.com Summit Xserver, with stereographics
> stereo enabler cable (takes sync from the monitor cable) and infra red
> emitter box E2 with stereographics infra red shutter glasses. i don't know
> if this emitter and enabler cable work with nuvision glasses?

They do in my hands, using the NuVision NSR (for non stereo-ready cards like
the 8500) glasses.

--Joe
_____________________________________
D. Joe Anderson, Asst. Sci.                    
http://www.public.iastate.edu/~deejoe	

Regarding the h-bond code I posted the other day,

(1) The formatting got all screwed up in the e-mail.  (Thanks to Cameron
Mura for pointing this out)

(2) Michael Lerner mailed me an improved version of the code which can
automatically number the h-bond objects hbond01, hbond02 etc, if
explicit names aren't supplied

The new version, with correct indenting, is available for download at 
	
	http://www.ebi.ac.uk/~gareth/work/pymol

Gareth

-- 
Gareth Stockwell <ga...@eb...>
European Bioinformatics Institute

Hi all!

> My personal bias is that the added cost to obtain real QBS hardware =
with
built-in stereo support=20
> is well worth the money in terms of time saved on bugs and hassles =
such as
this.

Yes! Real quad-buffered stereo is IMHO crucial for molecular modelling =
work
;-)

> Under Linux, the nVidia Quadro4 750XGL does a fine job, has a =
three-pin
stereo sync plug,=20
> and works with the Nuvision glasses and emitters. While I haven't =
tested
the higher-end FX series,=20
> I have every reason to believe that they would also work just fine =
given
nVidia's unified driver
> architecture.

I doesn't work for me :-(   I ordered a Quadro4 750XGL, and the vendor =
sent
me a Quadro FX1000 by mistake. I didn't notice at first, and just =
installed
the card. Works fine and very fast with the 1.0-4363 version of the =
Linux
driver - but neither PyMOL or VMD detects any hardware stereo.... I =
have to
get it replaced by a 750XGL or 900XGL.

We have some older stereographics glasses, which I expect will work =
with the
Nvidia cards. But we have also bought a set of Eye3D premium glasses. =
They
come with a VGA pass-through cable, which can catch the sync signal =
from any
VGA output. They also support different stereo modes, including =
interlacing,
page-flipping, sync-doubling, and line-blanking. You get two sets of =
glasses
(one wired, one IR) for =88179 or $199. This works nice with PyMOL and =
the Xig
X-server on an ATI Radeon 9000 card, and the "Scanline interleave"
(interlaced) stereo mode in VMD works fine with these glasses and any
graphics adapter. Maybe "scanline interleave" could be a stereo option =
in
PyMOL - it is definitely inferior to quad-buffered stereo, but it works =
with
_any_ graphics card and doesn't require a special driver. (I would =
still go
for QBS, though :-)


Cheers

Esben

Hi,

On Unix-like systems, stock pymol installs all images/data files/demo
stuff under /usr/lib/python2.x/site-packages/pymol/. I believe this is a
violation of the File Hierachy Standard (FHS) (well, at least its
spirit, I'm not sure about the letter), as only architecture-dependent
files should be under /usr/lib. 

Thus, I've cleaned up my current patch for pymol-0.88, replacing
$PYMOL_PATH with $PYMOL_DATA_PATH and $CHEMPY_DATA_PATH, under the
observation that $PYMOL_PATH is 99% only needed in order for the
examples and other stuff to find data.

Currently, I put everything under data/{pymol,chempy) under
/usr/share/pymol and test/dat/*, data/tut/*, examples/devel/cgo03.py
into /usr/share/pymol/demo. This can of course be tuned at will.

One needs to set $PYMOL_DATA_PATH and $CHEMPY_DATA_PATH of course, I'm
doing this in a small wrapper script:

#!/bin/sh
# debian wrapper script for pymol

export PYMOL_DATA_PATH=/usr/share/pymol
export CHEMPY_DATA_PATH=/usr/share/chempy

python /usr/lib/python2.2/site-packages/pymol/__init__.py


I've attached the patch, do you think that would make sense for pymol
proper as well? If not, I'll have to keep maintaining it in the debian
package.


cheers,

Michael

Warren,

Great - that's what I needed.  For those who are interested, I've
attached code below which draws a dashed line between two atoms, with an
arrow on it.  It's called with pretty much the same syntax as the
'distance' command.

Gareth


#------------------------------------------------------------------------

from pymol.cgo import *
from pymol import cmd
from math import *


#-------------------------------------------------
# Draw a hydrogen bond
#---------------------------------

def hbond(name,s1,s2,r=1.0,g=1.0,b=0.2):

      '''
DESCRIPTION

   "hbond" creates a dashed line between two selections, marked with an
arrow.

USAGE

   distance name, (selection1), (selection1) , [, r, [, g, [, b] ] ]

   name = name of distance object 
   selection1,selection2 = atom selections
   r, g, b = colour

   '''	


	# Convert arguments into floating point values
	rr = float(r)
	gg = float(g)
	bb = float(b)

	# Get dash length, gap length and dash radius from PyMOL
	# settings
	dl = float(cmd.get_setting_tuple("dash_length")[1][0])
	gl = float(cmd.get_setting_tuple("dash_gap")[1][0])
	dr = float(cmd.get_setting_tuple("dash_radius")[1][0])

	# Get tuple containing object and index of atoms in these
	# selections
	x1 = cmd.index(s1,1)	
	x2 = cmd.index(s2,1)

	# Get number of atoms in each selection	
	n1 = len(x1)
	n2 = len(x2)
	if(n1 < 1):
		print "Error: selection " + s1 + " has no atoms"
		return
	if(n2 < 1):
		print "Error: selection " + s2 + " has no atoms"
		return

	# Get objects and atom indices
	o1 = x1[0][0]
	i1 = x1[0][1]
	o2 = x2[0][0]
	i2 = x2[0][1]

	# Get ChemPy models
	m1 = cmd.get_model(o1)
	m2 = cmd.get_model(o2)

	# Get atoms
	a1 = m1.atom[i1-1]
	a2 = m2.atom[i2-1]

	# Get coords
	x1 = a1.coord[0]
	y1 = a1.coord[1]
	z1 = a1.coord[2]
	x2 = a2.coord[0]
	y2 = a2.coord[1]
	z2 = a2.coord[2]

	# Make some nice strings for user feedback
	s1 = o1 + "/" + a1.chain + "/" + a1.resn + "." + a1.resi + "/" 
		+ a1.name
	print s1 + "(" + str(x1) + "," + str(y1) + "," + str(z1) + ")"
	s2 = o2 + "/" + a2.chain + "/" + a2.resn + "." + a2.resi + "/" 
		+ a2.name
	print s2 + "(" + str(x2) + "," + str(y2) + "," + str(z2) + ")"

	# Calculate distances 
	dx = x2 - x1
	dy = y2 - y1
	dz = z2 - z1
	d  = math.sqrt((dx*dx) + (dy*dy) + (dz*dz))
	print "distance = " + str(d) + "A"

	# Work out how many times (dash_len + gap_len) fits into d
	dash_tot = dl + gl
	n_dash = math.floor(d / dash_tot)

	# Work out step lengths
	dx1 = (dl / dash_tot) * (dx / n_dash)
	dy1 = (dl / dash_tot) * (dy / n_dash)
	dz1 = (dl / dash_tot) * (dz / n_dash)
	dx2 = (dx / n_dash)
	dy2 = (dy / n_dash)
	dz2 = (dz / n_dash)


	# Empty CGO object
	obj = []


	# Generate dashes
	x = x1
	y = y1
	z = z1
	for i in range(n_dash):
		
		# Generate a dash cylinder
		obj.extend( [ CYLINDER, x, y, z, x+dx1, y+dy1, z+dz1,
			dr, rr, gg, bb, rr, gg, bb ] )

		# Move to start of next dash
		x = x + dx2
		y = y + dy2
		z = z + dz2


	# Add an arrow half way along
	# Calculate midpoint
	xm = (x1 + x2) / 2	
	ym = (y1 + y2) / 2
	zm = (z1 + z2) / 2

	# Vector pointing along the bond
	xv = (3.5 * dr / d) * dx
	yv = (3.5 * dr / d) * dy
	zv = (3.5 * dr / d) * dz

	# Rotate step vector 90deg around X axis
	xxv = xv
	yyv = -1 * zv
	zzv = yv

	# Add lines
	obj.extend( [ CYLINDER, xm-xv-xxv, ym-yv-yyv, zm-zv-zzv,
		xm+xv, ym+yv, zm+zv, dr, rr, gg, bb, rr, gg, bb ] )
	obj.extend( [ CYLINDER, xm-xv+xxv, ym-yv+yyv, zm-zv+zzv,
		xm+xv, ym+yv, zm+zv, dr, rr, gg, bb, rr, gg, bb ] )


	# Load the object into PyMOL
	cmd.load_cgo(obj, name)


# Add to PyMOL API
cmd.extend("hbond",hbond)

#------------------------------------------------------------------------




On Fri, 2003-07-18 at 18:25, Warren L. DeLano wrote:
> Gareth,
> 
> 	cmd.identify returns the input indexing, which will correspond
> to the PDB file.
> 
> 	cmd.index returns the internal indexing, which will correspond
> to cmd.get_model
> 
> help identify
> help index
> 
> Cheers,
> Warren
> 
> 
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154 
> Fax   (650)-593-4020
> 
> > -----Original Message-----
> > From: Gareth Stockwell [mailto:ga...@eb...]
> > Sent: Friday, July 18, 2003 8:50 AM
> > To: Warren L. DeLano
> > Cc: 'pymol-users'
> > Subject: RE: [PyMOL] H-bond display
> > 
> > Warren,
> > 
> > I started having a look at this, but I am getting stuck with atom 
> > indices.  If I make two selections, (lb) and (rb), by clicking on 
> > atoms in an object called 'x', then I can get the indices and objects 
> > of those atoms by doing
> > 
> > x1 = cmd.identify("lb",1)
> > x2 = cmd.identify("rb",1)
> > 
> > In my example, printing out x1 and x2 gives the following: [('x', 2)]
> > [('x', 16)]
> > 
> > As I clicked on these atoms, the GUI told me that they were,
> > respectively:
> > VAL: /x/1ATP/E/15/CA
> > LYS: /x/1ATP/E/16/NZ
> > 
> > But now, if I dump out the contents of the model.atom array, using 
> > this
> > code:
> > 
> > m = cmd.get_model("x")
> > 	i = 1
> > 	for a in m.atom:
> > 		print str(i) + " -> " + a.chain + "/" + a.resn + "." \
> > 			 + a.resi + "/" + a.name
> > 		i = i+1
> > 
> > Then I see the following
> > 1 -> E/VAL.15/N
> > 2 -> E/VAL.15/CA
> > 3 -> E/VAL.15/CB
> > 4 -> E/VAL.15/CG1
> > 5 -> E/VAL.15/CG2
> > 6 -> E/VAL.15/C
> > 7 -> E/VAL.15/O
> > 8 -> E/LYS.16/N
> > 9 -> E/LYS.16/CA
> > 10 -> E/LYS.16/CB
> > 11 -> E/LYS.16/CG
> > 12 -> E/LYS.16/CD
> > 13 -> E/LYS.16/CE
> > 14 -> E/LYS.16/NZ
> > 15 -> E/LYS.16/C
> > 16 -> E/LYS.16/O
> > 17 -> E/GLU.17/N
> > 18 -> E/GLU.17/CA
> > 19 -> E/GLU.17/C
> > 20 -> E/GLU.17/O
> > 
> > So atom number 2 is correct (VAL.15/CA), but in this array, atom 16 is
> 
> > the O, not NZ in LYS.16.  I presume that ChemPy is re-ordering the 
> > atoms some time during the get_model call - how do I resolve this?
> > 
> > Gareth
> > 
> > 
> > On Fri, 2003-07-18 at 16:36, Warren L. DeLano wrote:
> > > Gareth,
> > >
> > > 	CGO is currently the way to go...
> > >
> > > Cheers,
> > > Warren
> > >
> > >
> > > --
> > > mailto:wa...@de...
> > > Warren L. DeLano, Ph.D.
> > > Principal Scientist
> > > DeLano Scientific LLC
> > > Voice (650)-346-1154
> > > Fax   (650)-593-4020
> > >
> > > > -----Original Message-----
> > > > From: pym...@li... [mailto:pymol-users-
> 
> > > > ad...@li...] On Behalf Of Gareth Stockwell
> > > > Sent: Friday, July 18, 2003 2:46 AM
> > > > To: pymol-users
> > > > Subject: [PyMOL] H-bond display
> > > >
> > > >
> > > > I am using distance objects at the moment, to display h-bonding 
> > > > contacts.  My question is ... is there any easy way to display the
> 
> > > > direction of an h-bond using distances (i.e. putting a little 
> > > > arrow on the dashed line)?
> > > >
> > > > I am prepared to bash out some functions which do this using CGOs,
> 
> > > > but of course I won't if it's already implemented!
> > > >
> > > > Gareth
> > > >
> > > >
> > > > --
> > > > Gareth Stockwell <ga...@eb...>
> > > > European Bioinformatics Institute
> > > >
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > This SF.net email is sponsored by: VM Ware
> > > > With VMware you can run multiple operating systems on a single
> > > machine.
> > > > WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines 
> > > > at
> > > the
> > > > same time. Free trial click here: 
> > > > http://www.vmware.com/wl/offer/345/0
> > > > _______________________________________________
> > > > PyMOL-users mailing list
> > > > PyM...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.net email is sponsored by: VM Ware
> > > With VMware you can run multiple operating systems on a single 
> > > machine. WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual 
> > > machines at the same time. Free trial click here: 
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> > > _______________________________________________
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> > --
> > Gareth Stockwell <ga...@eb...>
> > European Bioinformatics Institute
> 
> 
> 
> -------------------------------------------------------
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> With VMware you can run multiple operating systems on a single machine.
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-- 
Gareth Stockwell <ga...@eb...>
European Bioinformatics Institute

Gareth,

	cmd.identify returns the input indexing, which will correspond
to the PDB file.

	cmd.index returns the internal indexing, which will correspond
to cmd.get_model

help identify
help index

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: Gareth Stockwell [mailto:ga...@eb...]
> Sent: Friday, July 18, 2003 8:50 AM
> To: Warren L. DeLano
> Cc: 'pymol-users'
> Subject: RE: [PyMOL] H-bond display
> 
> Warren,
> 
> I started having a look at this, but I am getting stuck with atom 
> indices.  If I make two selections, (lb) and (rb), by clicking on 
> atoms in an object called 'x', then I can get the indices and objects 
> of those atoms by doing
> 
> x1 = cmd.identify("lb",1)
> x2 = cmd.identify("rb",1)
> 
> In my example, printing out x1 and x2 gives the following: [('x', 2)]
> [('x', 16)]
> 
> As I clicked on these atoms, the GUI told me that they were,
> respectively:
> VAL: /x/1ATP/E/15/CA
> LYS: /x/1ATP/E/16/NZ
> 
> But now, if I dump out the contents of the model.atom array, using 
> this
> code:
> 
> m = cmd.get_model("x")
> 	i = 1
> 	for a in m.atom:
> 		print str(i) + " -> " + a.chain + "/" + a.resn + "." \
> 			 + a.resi + "/" + a.name
> 		i = i+1
> 
> Then I see the following
> 1 -> E/VAL.15/N
> 2 -> E/VAL.15/CA
> 3 -> E/VAL.15/CB
> 4 -> E/VAL.15/CG1
> 5 -> E/VAL.15/CG2
> 6 -> E/VAL.15/C
> 7 -> E/VAL.15/O
> 8 -> E/LYS.16/N
> 9 -> E/LYS.16/CA
> 10 -> E/LYS.16/CB
> 11 -> E/LYS.16/CG
> 12 -> E/LYS.16/CD
> 13 -> E/LYS.16/CE
> 14 -> E/LYS.16/NZ
> 15 -> E/LYS.16/C
> 16 -> E/LYS.16/O
> 17 -> E/GLU.17/N
> 18 -> E/GLU.17/CA
> 19 -> E/GLU.17/C
> 20 -> E/GLU.17/O
> 
> So atom number 2 is correct (VAL.15/CA), but in this array, atom 16 is

> the O, not NZ in LYS.16.  I presume that ChemPy is re-ordering the 
> atoms some time during the get_model call - how do I resolve this?
> 
> Gareth
> 
> 
> On Fri, 2003-07-18 at 16:36, Warren L. DeLano wrote:
> > Gareth,
> >
> > 	CGO is currently the way to go...
> >
> > Cheers,
> > Warren
> >
> >
> > --
> > mailto:wa...@de...
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154
> > Fax   (650)-593-4020
> >
> > > -----Original Message-----
> > > From: pym...@li... [mailto:pymol-users-

> > > ad...@li...] On Behalf Of Gareth Stockwell
> > > Sent: Friday, July 18, 2003 2:46 AM
> > > To: pymol-users
> > > Subject: [PyMOL] H-bond display
> > >
> > >
> > > I am using distance objects at the moment, to display h-bonding 
> > > contacts.  My question is ... is there any easy way to display the

> > > direction of an h-bond using distances (i.e. putting a little 
> > > arrow on the dashed line)?
> > >
> > > I am prepared to bash out some functions which do this using CGOs,

> > > but of course I won't if it's already implemented!
> > >
> > > Gareth
> > >
> > >
> > > --
> > > Gareth Stockwell <ga...@eb...>
> > > European Bioinformatics Institute
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.net email is sponsored by: VM Ware
> > > With VMware you can run multiple operating systems on a single
> > machine.
> > > WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines 
> > > at
> > the
> > > same time. Free trial click here: 
> > > http://www.vmware.com/wl/offer/345/0
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: VM Ware
> > With VMware you can run multiple operating systems on a single 
> > machine. WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual 
> > machines at the same time. Free trial click here: 
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> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> --
> Gareth Stockwell <ga...@eb...>
> European Bioinformatics Institute

Warren,

I started having a look at this, but I am getting stuck with atom
indices.  If I make two selections, (lb) and (rb), by clicking on atoms
in an object called 'x', then I can get the indices and objects of those
atoms by doing

x1 = cmd.identify("lb",1)
x2 = cmd.identify("rb",1)

In my example, printing out x1 and x2 gives the following:
[('x', 2)]
[('x', 16)]

As I clicked on these atoms, the GUI told me that they were,
respectively:
VAL: /x/1ATP/E/15/CA
LYS: /x/1ATP/E/16/NZ

But now, if I dump out the contents of the model.atom array, using this
code:

m = cmd.get_model("x")
	i = 1
	for a in m.atom:
		print str(i) + " -> " + a.chain + "/" + a.resn + "." \
			 + a.resi + "/" + a.name
		i = i+1

Then I see the following
1 -> E/VAL.15/N
2 -> E/VAL.15/CA
3 -> E/VAL.15/CB
4 -> E/VAL.15/CG1
5 -> E/VAL.15/CG2
6 -> E/VAL.15/C
7 -> E/VAL.15/O
8 -> E/LYS.16/N
9 -> E/LYS.16/CA
10 -> E/LYS.16/CB
11 -> E/LYS.16/CG
12 -> E/LYS.16/CD
13 -> E/LYS.16/CE
14 -> E/LYS.16/NZ
15 -> E/LYS.16/C
16 -> E/LYS.16/O
17 -> E/GLU.17/N
18 -> E/GLU.17/CA
19 -> E/GLU.17/C
20 -> E/GLU.17/O

So atom number 2 is correct (VAL.15/CA), but in this array, atom 16 is
the O, not NZ in LYS.16.  I presume that ChemPy is re-ordering the atoms
some time during the get_model call - how do I resolve this?

Gareth


On Fri, 2003-07-18 at 16:36, Warren L. DeLano wrote:
> Gareth,
> 
> 	CGO is currently the way to go...
> 
> Cheers,
> Warren
> 
> 
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154 
> Fax   (650)-593-4020
> 
> > -----Original Message-----
> > From: pym...@li... [mailto:pymol-users-
> > ad...@li...] On Behalf Of Gareth Stockwell
> > Sent: Friday, July 18, 2003 2:46 AM
> > To: pymol-users
> > Subject: [PyMOL] H-bond display
> > 
> > 
> > I am using distance objects at the moment, to display h-bonding
> > contacts.  My question is ... is there any easy way to display the
> > direction of an h-bond using distances (i.e. putting a little arrow on
> > the dashed line)?
> > 
> > I am prepared to bash out some functions which do this using CGOs, but
> > of course I won't if it's already implemented!
> > 
> > Gareth
> > 
> > 
> > --
> > Gareth Stockwell <ga...@eb...>
> > European Bioinformatics Institute
> > 
> > 
> > 
> > -------------------------------------------------------
> > This SF.net email is sponsored by: VM Ware
> > With VMware you can run multiple operating systems on a single
> machine.
> > WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at
> the
> > same time. Free trial click here: http://www.vmware.com/wl/offer/345/0
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: VM Ware
> With VMware you can run multiple operating systems on a single machine.
> WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the
> same time. Free trial click here: http://www.vmware.com/wl/offer/345/0
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
-- 
Gareth Stockwell <ga...@eb...>
European Bioinformatics Institute

Gareth,

	CGO is currently the way to go...

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Gareth Stockwell
> Sent: Friday, July 18, 2003 2:46 AM
> To: pymol-users
> Subject: [PyMOL] H-bond display
> 
> 
> I am using distance objects at the moment, to display h-bonding
> contacts.  My question is ... is there any easy way to display the
> direction of an h-bond using distances (i.e. putting a little arrow on
> the dashed line)?
> 
> I am prepared to bash out some functions which do this using CGOs, but
> of course I won't if it's already implemented!
> 
> Gareth
> 
> 
> --
> Gareth Stockwell <ga...@eb...>
> European Bioinformatics Institute
> 
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: VM Ware
> With VMware you can run multiple operating systems on a single
machine.
> WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at
the
> same time. Free trial click here: http://www.vmware.com/wl/offer/345/0
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Stephen,

	Sorry, the mesh representation right now is limited to rendering
a Cartesian box.  The selection controls the size of the box, but all
atoms within the box are currently always shown.  I will look into
changing this so that the mesh performs more like the other
representations.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users- 
> ad...@li...] On Behalf Of Soisson, Stephen Michael
> Sent: Friday, July 18, 2003 3:27 AM
> To: 'pym...@li...'
> Subject: [PyMOL] mesh question
> 
> Hi everyone-
> 
> I have two interacting monomers, and have selected the contacting 
> resides between them and drawn a solid surface around these selected 
> residues on one monomer.  This worked fine and I had no problem.
> 
> I would now like to draw a mesh surface around the remaining residues 
> in the monomer, that is, everything but the contacting residues.  No 
> matter what selection scheme I try to use, the mesh is always drawn 
> around the entire molecule.
> 
> For instance:
> 
> select contacts=(byres monA and (monB around 4))
> show surface, contacts
> 
> show mesh, (monA and (!contacts)) ****mesh is still drawn around whole

> molecule
> 
> However, the following command does work to color just the mesh 
> surface that is not in contact with the other monomer:
> 
> color grey70, (monA and (!contacts))
> 
> which leads me to believe that my syntax is correct for the selection.
> 
> What am I missing?  Is there a way to just show the mesh over a 
> certain portion of a molecule?
> 
> Many thanks in advance-
> 
> Steve
> 
> ----------------------------------------------------------------------
> ----
> --
> --
> Stephen M. Soisson, Ph.D.
> Senior Research Biochemist
> X-ray Crystallography / Dept. of Medicinal Chemistry
> Merck Research Laboratories
> P.O. Box 2000, RY50-105
> Rahway, NJ  07065
> Phone: 	(732) 594-4349
> Fax:	(732) 594-5042
> ste...@me...
> 
> ----------------------------------------------------------------------
> ----
> ----
> Notice: This e-mail message, together with any attachments, contains
> information of Merck & Co., Inc. (Whitehouse Station, New Jersey,
> USA) that may be confidential, proprietary copyrighted and/or legally
> privileged, and is intended solely for the use of the individual or
entity
> named on this message. If you are not the intended recipient, and
> have received this message in error, please immediately return this by
> e-mail and then delete it.
>
------------------------------------------------------------------------
--
> ----
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: VM Ware
> With VMware you can run multiple operating systems on a single 
> machine. WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual 
> machines at the same time. Free trial click here: 
> http://www.vmware.com/wl/offer/345/0
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

My personal bias is that the added cost to obtain real QBS hardware with
built-in stereo support is well worth the money in terms of time saved
on bugs and hassles such as this.=20

Under Linux, the nVidia Quadro4 750XGL does a fine job, has a three-pin
stereo sync plug, and works with the Nuvision glasses and emitters.
While I haven't tested the higher-end FX series, I have every reason to
believe that they would also work just fine given nVidia's unified
driver architecture.

Quadro4 750XGL ($369)

http://www.cdw.com/shop/products/default.asp?edc=3D389877

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Dr. Daniel James White PhD
> Sent: Friday, July 18, 2003 12:59 AM
> To: pym...@li...
> Subject: Re: [PyMOL] Nuvision stereo glasses?
>=20
> Hi David,
>=20
> ATI radeon 8500 works with the xig.com Summit Xserver,
> with stereographics stereo enabler cable (takes sync from the monitor
> cable)
> and infra red emitter box E2 with stereographics infra red shutter
> glasses.
> i don't know if this emitter and enabler cable work with nuvision
> glasses?
>=20
> (this commercial X server seems to break my sound though.....confirmed
> to me  by xig as a bug)
>=20
> cheers
>=20
> Dan
>=20
>=20
>=20
> On Friday, July 18, 2003, at 06:28 AM,
> pym...@li... wrote:
>=20
> >
> >
> >
> > --__--__--
> >
> > Message: 4
> > Date: Thu, 17 Jul 2003 17:51:27 -0400
> > From: "David A.  Horita" <dh...@wf...>
> > To: <pym...@li...>
> > Subject: [PyMOL] Nuvision stereo glasses?
> >
> > This is a multi-part message in MIME format.
> >
> > ------_=3D_NextPart_001_01C34CAD.92AD614C
> > Content-Type: text/plain;
> > 	charset=3D"iso-8859-1"
> > Content-Transfer-Encoding: quoted-printable
> >
> > Hi,
> > Is anyone using the Nuvision 60GX stereo glasses with FireGL Z1 or =
=3D
> > QuadroFX 500 cards under linux?  Or any other non-nVidia card which
=3D
> > supports quad-buffered stereo but doesn't have a mini-din connector
=3D
> > on-board (i.e., not the 256 Mb FireGL X1).  It would be nice to
avoid =3D
> > the problems with the nVidia stereo drivers, but I'd rather not buy
> > the =3D
> > FX1000+/FireGL X1 level card, and FireGL2/4 are getting old (and
hard
> > to =3D
> > find).  The Nuvision guys told me that their VGA passthrough (the
-100
> > =3D
> > model, not the -NSR model), picks up the stereo sync from nVidia
cards
> > =3D
> > coming through the 15-pin VGA connector.  Is this signal present on
> > ATI =3D
> > cards (or even on dual-DVI-I output cards)?
> > =3D20
> > Thanks,
> > Dave Horita
> > =3D20
> > -----------------------------=3D20
> > David A. Horita, Ph.D.
> > Department of Biochemistry
> > Wake Forest University School of Medicine
> > Winston-Salem, NC 27157-1016=3D20
> > Tel: 336 713-4194
> > Fax: 336 716-7671=3D20
> > email:  dh...@wf...
> > web:  http://www.wfubmc.edu/biochem/faculty/Horita/
> > =3D20
> >
> Dr. Daniel James White BSc. (Hons.) PhD
> Cell Biology
> Department of biological and environmental science
> PO Box  35
> University of Jyv=E4skyl=E4
> Jyv=E4skyl=E4 FIN 40014
> Finland
> +358 (0)14 260 4183 (work)
> +358 (0)414740463 (mob)
>=20
> http://www.chalkie.org.uk
> da...@ch...
> wh...@cc...
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: VM Ware
> With VMware you can run multiple operating systems on a single
machine.
> WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at
the
> same time. Free trial click here: http://www.vmware.com/wl/offer/345/0
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi everyone-

I have two interacting monomers, and have selected the contacting resides
between them and drawn a solid surface around these selected residues on one
monomer.  This worked fine and I had no problem.

I would now like to draw a mesh surface around the remaining residues in the
monomer, that is, everything but the contacting residues.  No matter what
selection scheme I try to use, the mesh is always drawn around the entire
molecule.  

For instance:

select contacts=(byres monA and (monB around 4))
show surface, contacts

show mesh, (monA and (!contacts)) ****mesh is still drawn around whole
molecule

However, the following command does work to color just the mesh surface that
is not in contact with the other monomer:

color grey70, (monA and (!contacts))

which leads me to believe that my syntax is correct for the selection.

What am I missing?  Is there a way to just show the mesh over a certain
portion of a molecule?

Many thanks in advance-

Steve

----------------------------------------------------------------------------
--
Stephen M. Soisson, Ph.D.
Senior Research Biochemist
X-ray Crystallography / Dept. of Medicinal Chemistry
Merck Research Laboratories
P.O. Box 2000, RY50-105
Rahway, NJ  07065
Phone: 	(732) 594-4349
Fax:	(732) 594-5042
ste...@me...

------------------------------------------------------------------------------
Notice: This e-mail message, together with any attachments, contains 
information of Merck & Co., Inc. (Whitehouse Station, New Jersey, 
USA) that may be confidential, proprietary copyrighted and/or legally 
privileged, and is intended solely for the use of the individual or entity
named on this message. If you are not the intended recipient, and
have received this message in error, please immediately return this by 
e-mail and then delete it.
------------------------------------------------------------------------------

I am using distance objects at the moment, to display h-bonding
contacts.  My question is ... is there any easy way to display the
direction of an h-bond using distances (i.e. putting a little arrow on
the dashed line)?

I am prepared to bash out some functions which do this using CGOs, but
of course I won't if it's already implemented!

Gareth


-- 
Gareth Stockwell <ga...@eb...>
European Bioinformatics Institute

Dear PyMOL-ers,

I have just started dabbling in the chempy module, and I have a couple
of questions:


1. If I load in a molecule using the following code...



from chempy import io
from chempy import protein

m = io.pdb.fromFile("/tmp/x.pdb")

# Use the load_object call, specifying the type of object as a chempy
# model (index 8)
cmd.load_object(8,m,"protein")



...there are no bonds displayed.  Is there a chempy call I can make on
the model object (m) to calculate covalent bonds?



2. I can happily iterate over, or select by index, atoms in a chempy
model, using either of the following


# Iterate over all atoms
for a in m.atom:
	# do something

# Random access
a = m.atom[10]



Are there corresponding residue and atom arrays, or does chempy
represent these aggregates simply by the fields of the Atom object
(resn, resi, chain etc)?  As far as I can see, the latter is true, but
like I said, so far I am only a dabbler.




I should mention why I'm doing this, in case anyone has a more elegant
solution.  Basically I have a C++ library which handles molecules,
making selections, identifying h-bonds etc.  I wanted a way to dump out
a molecule object from my library, and display it in PyMOL with all of
its associated selections and bonds.  So basically what I do is:

  1. Write out a PDB file for my molecule
  2. Write out a short Python program which creates PyMOL selections
corresponding to my selections, by way of atom indices.  Basically this
works by grabbing the 'nth' atom from the chempy model, then composing a
selection string which is passed to the cmd.select function.  Missing
out some detail, here is the bare bones:



# Function 1: get a PyMOL selection string from a ChemPy atom
def atom_sel(a,obj_name):

    return "/" + obj_name + "//" + a.chain + "/" + a.resi + "/" + a.name

# Function 2: create a PyMOL selection from an array of atom indices
def make_atom_sel(sel_name,array,model,obj_name):

    sel_str = ""
    for i in range(len(array)):

        sel = atom_sel(model.atom[array[i]],obj_name)
        sel_str += sel 
        if(i < len(array)-1):
            sel_str += " or "

    cmd.select(sel_name, sel_str)

# Similar functions exist for creating an h-bond between ith and jth
# atoms


So to put it all together, given these two functions, the program I
execute in order to reconstitute my molecule in PyMOL looks like


m = io.pdb.fromFile("/tmp/x.pdb")
cmd.load_object(8,m,"protein")
make_atom_sel("my_sel", [0,2,5,8,18,22], m, "protein")


Gareth





-- 
Gareth Stockwell <ga...@eb...>
European Bioinformatics Institute

Hi David,

ATI radeon 8500 works with the xig.com Summit Xserver,
with stereographics stereo enabler cable (takes sync from the monitor=20
cable)
and infra red emitter box E2 with stereographics infra red shutter=20
glasses.
i don't know if this emitter and enabler cable work with nuvision=20
glasses?

(this commercial X server seems to break my sound though.....confirmed=20=

to me  by xig as a bug)

cheers

Dan



On Friday, July 18, 2003, at 06:28 AM,=20
pym...@li... wrote:

>
>
>
> --__--__--
>
> Message: 4
> Date: Thu, 17 Jul 2003 17:51:27 -0400
> From: "David A.  Horita" <dh...@wf...>
> To: <pym...@li...>
> Subject: [PyMOL] Nuvision stereo glasses?
>
> This is a multi-part message in MIME format.
>
> ------_=3D_NextPart_001_01C34CAD.92AD614C
> Content-Type: text/plain;
> 	charset=3D"iso-8859-1"
> Content-Transfer-Encoding: quoted-printable
>
> Hi,
> Is anyone using the Nuvision 60GX stereo glasses with FireGL Z1 or =3D
> QuadroFX 500 cards under linux?  Or any other non-nVidia card which =3D
> supports quad-buffered stereo but doesn't have a mini-din connector =3D
> on-board (i.e., not the 256 Mb FireGL X1).  It would be nice to avoid =
=3D
> the problems with the nVidia stereo drivers, but I'd rather not buy=20
> the =3D
> FX1000+/FireGL X1 level card, and FireGL2/4 are getting old (and hard=20=

> to =3D
> find).  The Nuvision guys told me that their VGA passthrough (the -100=20=

> =3D
> model, not the -NSR model), picks up the stereo sync from nVidia cards=20=

> =3D
> coming through the 15-pin VGA connector.  Is this signal present on=20
> ATI =3D
> cards (or even on dual-DVI-I output cards)?
> =3D20
> Thanks,
> Dave Horita
> =3D20
> -----------------------------=3D20
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine
> Winston-Salem, NC 27157-1016=3D20
> Tel: 336 713-4194
> Fax: 336 716-7671=3D20
> email:  dh...@wf...
> web:  http://www.wfubmc.edu/biochem/faculty/Horita/
> =3D20
>
Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology
Department of biological and environmental science
PO Box  35
University of Jyv=E4skyl=E4
Jyv=E4skyl=E4 FIN 40014
Finland
+358 (0)14 260 4183 (work)
+358 (0)414740463 (mob)

http://www.chalkie.org.uk
da...@ch...
wh...@cc...

Am Donnerstag, 17. Juli 2003 23:05 schrieb Vajdos, Felix:
> Is there a way to append states to objects within pymol?
>
> Here's the scenario:
> Now, each animation is 50 frames (states) long, and runs fine.  What I
> would like to do is at the end of each animation sequence to simply hav=
e
> the final state rock back and forth, as in with the "rock" button on th=
e
> Tcl window. However, I do not want to have the whole thing rocking duri=
ng
> the animation.

Dear Felix,

Though it may sound a little like advertisement, i recommend the rTools=20
package for PyMOL. (http://www.rubor.de/bioinf). =20
Here, you can issue some commands assigning states to frames, like

mvRot 1-500:1-50,z,90
mvRot 501-1000:50-1,z,-90
Which will let states 1 to 50 be shown across the first 500 frames (howev=
er,=20
state 50 is shown only in the last frame). In the second 500 frames, the=20
order is reversed, i.e. the sequence plays backwards.

You can also simply assign commands to frames, leaving the state untouche=
d:
mvSinmove 1001-1100,x,10
mvSinset 1001,1100,transparency,0.0,1.0

To play the animation, just type:
movie

And yes, you can get the structure rocking with these commands.
I apologize it does not run perfectly yet, as a bugfix release of rTools =
is=20
about to appear within a week.

I hope that was not too confusing,

Kristian

Hi,
Is anyone using the Nuvision 60GX stereo glasses with FireGL Z1 or =
QuadroFX 500 cards under linux?  Or any other non-nVidia card which =
supports quad-buffered stereo but doesn't have a mini-din connector =
on-board (i.e., not the 256 Mb FireGL X1).  It would be nice to avoid =
the problems with the nVidia stereo drivers, but I'd rather not buy the =
FX1000+/FireGL X1 level card, and FireGL2/4 are getting old (and hard to =
find).  The Nuvision guys told me that their VGA passthrough (the -100 =
model, not the -NSR model), picks up the stereo sync from nVidia cards =
coming through the 15-pin VGA connector.  Is this signal present on ATI =
cards (or even on dual-DVI-I output cards)?
=20
Thanks,
Dave Horita
=20
-----------------------------=20
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016=20
Tel: 336 713-4194
Fax: 336 716-7671=20
email:  dh...@wf...
web:  http://www.wfubmc.edu/biochem/faculty/Horita/
=20