From conrad at cgl.ucsf.edu  Wed Nov  1 11:14:51 2006
From: conrad at cgl.ucsf.edu (Conrad Huang)
Date: Wed, 01 Nov 2006 11:14:51 -0800
Subject: [Chimera-users] Chimera under FreeBSD
In-Reply-To: <1161112863.45352d1fa09e8@lehrer.ucsf.edu>
References: <1161112863.45352d1fa09e8@lehrer.ucsf.edu>
Message-ID: <4548F22B.7070005@cgl.ucsf.edu>

Devon Ryan wrote:
> Has anyone had success getting chimera to run under FreeBSD? I can get the linux
> version to start (under the linuxulator), but it crashes after ~20 seconds when
> the bundled version of python core dumps. I'm running FreeBSD 6.1 on an intel
> architecture. Thanks
> 

Thanks to Devon's offer to use his machine, we now have a FreeBSD 
snapshot of Chimera available on the download page.  The build is not 
thoroughly tested but will at least start up and display a molecule.  If 
there is enough interest, we will consider adding FreeBSD as a supported 
platform.

Conrad


From goddard at cgl.ucsf.edu  Thu Nov  2 12:07:45 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 2 Nov 2006 12:07:45 -0800 (PST)
Subject: [Chimera-users] Per-model clipping plane command
In-Reply-To: <20061102185431.355641DB02@handler12.mail.rice.edu>
	(triffo@rice.edu)
References: <20061102185431.355641DB02@handler12.mail.rice.edu>
Message-ID: <200611022007.kA2K7jZT1874318@guanine.cgl.ucsf.edu>

Hi Jeff,

  There isn't yet a Chimera command for per-model clipping.
Below is some Python code that can do it.  Open a density map
and then open this Python code in Chimera to clip it.  Some
more code can make it loop through different depths.  There is
some trickiness to making it update the graphics window in such
a loop.  Ask for details if you want that.

	Tom

> From: Jeff
> To: <goddard at cgl.ucsf.edu>
> Subject: per-model clipping plane question (or similar)
> Date: Thu, 2 Nov 2006 10:54:26 -0800
> 
> hi Tom,
> 
> was wondering if I can control the per-model clipping plane
> orientation/parameters/etc via command line or shortcuts -
> 
> would like to be able to methodically push a clipping plane in 'slab mode'
> through my model to compare it w/ other 2D/projection tools I use - I know I
> can click 'orient' on the model and it will orient to a default
> position/rotation (and I can click orient on the per-model clipping plane
> and therefore register them both), but is there then a way that I can
> specify (say, along one axis, like z) where the slab/clipping plane is
> positioned, like in pixels? 
> 
> can I control the angular position of the clipping plane via command line,
> too?
> 
> thanks,
> 
> Jeff

-----
Python code clip.py.

# -----------------------------------------------------------------------------
# Python function to control per-model clipping (like menu entry
# Tools / Depiction / Per-Model Clipping).  The clip plane rotates with
# the model (PDB structure, density map, ...).
#
# Parameters:
#   model is a Chimera Model
#   origin is (x,y,z) of point on clip plane.
#   normal is (nx,ny,nz) pointing towards clipped (invisible) half of plane.
#   slab_thickness is in data length units (usually Angstroms).
#
# Origin and normal are relative to the data coordinate system, for example,
# the x,y,z coordinates of a PDB atoms or axes of a density map.  The clip
#
def set_clipping(model, origin, normal, slab_thickness = None):

  p = model.clipPlane
  from chimera import Point, Vector
  p.origin = Point(*origin)
  p.normal = Vector(*normal)
  model.clipPlane = p
  model.useClipPlane = True
  if slab_thickness == None:
    model.useClipThickness = False
  else:
    model.clipThickness = slab_thickness
    model.useClipThickness = True

# -----------------------------------------------------------------------------
# Cap holes left when clipping a surface.  Controls graphical interface
# shown by menu entry Tools / Depiction / Surface Capping.
#
# Parameters:
#   cap_color is (r,g,b) or (r,g,b,a) where values in range 0-1
#   cap_mesh is True or False for mesh or solid cap appearance
#   cap_subdivision of 2 makes cap mesh twice as fine for detailed coloring.
#   cap_offset in data length units (usually Angstroms) for large models
#     sometimes needs to be larger to avoid cap itself being clipped due to
#     finite floating point precision in OpenGL.
#
def show_surface_caps(show, cap_color = None, cap_mesh = False,
                      cap_subdivision = 1, cap_offset = 0.001):

  from SurfaceCap.gui import capper_dialog
  d = capper_dialog(create = True)
  d.Close()
  use_color = (cap_color != None)
  if use_color:
    d.use_cap_color.set(use_color)
    d.cap_color.showColor(cap_color)
  if cap_mesh:
    d.cap_style.set('mesh')
  else:
    d.cap_style.set('solid')
  d.subdivision_factor.set(cap_subdivision)
  d.cap_offset.set(cap_offset)
  d.show_caps.set(show)

# -----------------------------------------------------------------------------
# Example using set_clipping().
#
from chimera import openModels
mlist = openModels.list()
m = mlist[0]
set_clipping(m, (.5,0,1), (0,1,1), 8)
show_surface_caps(True, (1,0,0), True)        # Red mesh caps


From goddard at cgl.ucsf.edu  Thu Nov  2 13:46:21 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 2 Nov 2006 13:46:21 -0800 (PST)
Subject: [Chimera-users] Chimera length units
In-Reply-To: <20061102212616.3E1D01DB0D@handler2.mail.rice.edu>
	(triffo@rice.edu)
References: <20061102212616.3E1D01DB0D@handler2.mail.rice.edu>
Message-ID: <200611022146.kA2LkLX91887294@guanine.cgl.ucsf.edu>


Hi Jeff,

  Chimera does not know what units you are using, the data coordinates
are just numbers as far as it is concerned.  If you open a PDB atomic
model the coordinates are always Angstroms.  If you open a density
map, say an MRC file, the header may include the voxel size.  That
value could be in Angstroms or nanometers.  Often maps don't have the
true voxel size in the header, often they say it is 1.  In such cases
you can use the Chimera volume dialog menu entry "Features / Origin and
Scale" to set the voxel size in Angstroms or nanometers so that the map
can be aligned with other models or maps.  If you open a PDB model in
Angstroms and a map with the scale set in nanometers then the map will
look 10 times smaller than it should be relative to the model.

	Tom


> From: Jeff
> To: "'Thomas Goddard'" <goddard at cgl.ucsf.edu>
> Date: Thu, 2 Nov 2006 13:26:11 -0800
> 
> thanks Tom,
> 
> sorry for a goofy question, but how do I know what units chimera is using
> (for measuring distances, having the output is nice in Angstroms, but
> sometimes (like with orienting a clipping plane) using unitless/pixels is
> more handy for displacements/etc)
> 
> thanks,
> 
> -jeff


From hsosa at aecom.yu.edu  Thu Nov  2 14:53:49 2006
From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu)
Date: Thu, 02 Nov 2006 17:53:49 -0500
Subject: [Chimera-users] stereo
Message-ID: <454A76FD.4090001@aecom.yu.edu>



How can I use stereo (sequential mode)  ?. If  I click the stereo button 
in the camera dialog or start chimera using the command chimera 
--stereo. I get the error message:


Unable to turn on stereo viewing
Unable to find hardware stereo support
(coulddm't choose stereo pixel format
Couldn't figure togl widget)


My graphic cards is a NVIDIA Quadro4 900  XGL.
The Nvdia Stereo driver (v: 91.31) is installed and enabled.
Chimera version is: 1 build 2255 2006/06/23

Monitors: Two (dual) digital DELL 1900 FP
Computer: Dual Xeon 1.4 Ghz, 1GB of RAM. Running Windows XP

Thanks

Hernando


--




From gregc at cgl.ucsf.edu  Thu Nov  2 15:14:23 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 2 Nov 2006 15:14:23 -0800 (PST)
Subject: [Chimera-users] stereo
In-Reply-To: <454A76FD.4090001@aecom.yu.edu>
References: <454A76FD.4090001@aecom.yu.edu>
Message-ID: <Pine.OSF.4.63.0611021506510.1901476@guanine.cgl.ucsf.edu>

On Thu, 2 Nov 2006, hsosa at aecom.yu.edu wrote:

> How can I use stereo (sequential mode)  ?. If  I click the stereo button
> in the camera dialog or start chimera using the command chimera
> --stereo. I get the error message:
>
>
> Unable to turn on stereo viewing
> Unable to find hardware stereo support
> (coulddm't choose stereo pixel format
> Couldn't figure togl widget)
>
>
> My graphic cards is a NVIDIA Quadro4 900  XGL.
> The Nvdia Stereo driver (v: 91.31) is installed and enabled.
> Chimera version is: 1 build 2255 2006/06/23
>
> Monitors: Two (dual) digital DELL 1900 FP
> Computer: Dual Xeon 1.4 Ghz, 1GB of RAM. Running Windows XP

I've made your mistake, you need to remove the NVidia Consumer Stereo 
driver -- the Quadro driver supports stereo natively.  The Consumer Stereo 
driver is for GeForce graphics cards (ie., consumer graphics cards, not 
workstation graphics cards).

The lastest Quadro driver is version 91.36.

You still need to configure the Quadro graphics driver for stereo after 
you install it.

 	Greg Couch
 	UCSF Computer Graphics Lab


From goddard at cgl.ucsf.edu  Thu Nov  2 16:05:50 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 2 Nov 2006 16:05:50 -0800 (PST)
Subject: [Chimera-users] Chimera length units
In-Reply-To: <20061102223035.36DB81DB01@handler11.mail.rice.edu>
	(triffo@rice.edu)
References: <20061102223035.36DB81DB01@handler11.mail.rice.edu>
Message-ID: <200611030005.kA305ofJ1941817@guanine.cgl.ucsf.edu>

Hi Jeff,

  Chimera clipping and other tools use xyz coordinates and do not use
voxel or pixel measures.  The volume dialog region bounds panel and
the volume dialog step size are exceptions where voxel index positions
are used.

  The notion of a voxel is only relevant to density maps, not atomic
models and clippping applies to all kinds of data, not just maps.

  Screen pixels are a 2 dimensional concept so it is an awkward
measure to use especially with perspective 3-d viewing for measuring
lengths.

	Tom


> From: Jeff
> To: "'Thomas Goddard'" <goddard at cgl.ucsf.edu>
> Subject: RE: Chimera length units
> Date: Thu, 2 Nov 2006 14:30:30 -0800
> 
> does this mean that I can't refer to a given coordinate by pixel/voxel
> location without resetting the voxel size to '1 1 1' (which I might not want
> to do - does chimera not keep the mrc file (or other voxel data) inside of a
> similar kind of array) 
> 
> > -----Original Message-----
> > From: Thomas Goddard [mailto:goddard at cgl.ucsf.edu] 
> > Sent: Thursday, November 02, 2006 1:46 PM
> > Cc: chimera-users at cgl.ucsf.edu
> > Subject: Chimera length units
> > 
> > 
> > Hi Jeff,
> > 
> >   Chimera does not know what units you are using, the data 
> > coordinates are just numbers as far as it is concerned.  If 
> > you open a PDB atomic model the coordinates are always 
> > Angstroms.  If you open a density map, say an MRC file, the 
> > header may include the voxel size.  That value could be in 
> > Angstroms or nanometers.  Often maps don't have the true 
> > voxel size in the header, often they say it is 1.  In such 
> > cases you can use the Chimera volume dialog menu entry 
> > "Features / Origin and Scale" to set the voxel size in 
> > Angstroms or nanometers so that the map can be aligned with 
> > other models or maps.  If you open a PDB model in Angstroms 
> > and a map with the scale set in nanometers then the map will 
> > look 10 times smaller than it should be relative to the model.
> > 
> > 	Tom


From David_Belnap at byu.edu  Thu Nov  2 16:54:51 2006
From: David_Belnap at byu.edu (David Belnap)
Date: Thu, 2 Nov 2006 17:54:51 -0700
Subject: [Chimera-users] X11 updated for Mac OS X, stereo now?
Message-ID: <451248E3-B863-4EF8-84AC-1A0213C3B20C@byu.edu>

Apple has released an update for X11 with the following comment:

This update addresses several issues in the X11 for Mac OS X package,  
enabling it to better handle:

- GLX stereo visuals
- offscreen rendering to GLX Pbuffers and Pixmaps

I downloaded it and tried to run Chimera (beta version 1 build 2199  
2006/01/24) in stereo.  It didn't work.  Does the X11 update have the  
stereo-in-a-window capability now that Chimera needs?  Is there a  
newer version of Chimera that will run in stereo on the Mac?

David

============================================
   David M. Belnap
   Department of Chemistry and Biochemistry
   Brigham Young University
   Provo, Utah 84602  USA

   Phone:  801-422-9163
   FAX:      801-422-0153
   David_Belnap at byu.edu
============================================




From gregc at cgl.ucsf.edu  Thu Nov  2 17:17:08 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 2 Nov 2006 17:17:08 -0800 (PST)
Subject: [Chimera-users] X11 updated for Mac OS X, stereo now?
In-Reply-To: <451248E3-B863-4EF8-84AC-1A0213C3B20C@byu.edu>
References: <451248E3-B863-4EF8-84AC-1A0213C3B20C@byu.edu>
Message-ID: <Pine.OSF.4.63.0611021700300.1901476@guanine.cgl.ucsf.edu>

On Thu, 2 Nov 2006, David Belnap wrote:

> Apple has released an update for X11 with the following comment:
>
> This update addresses several issues in the X11 for Mac OS X package,
> enabling it to better handle:
>
> - GLX stereo visuals
> - offscreen rendering to GLX Pbuffers and Pixmaps

This is good news.  Still no multisampling though.

> I downloaded it and tried to run Chimera (beta version 1 build 2199
> 2006/01/24) in stereo.  It didn't work.  Does the X11 update have the
> stereo-in-a-window capability now that Chimera needs?  Is there a
> newer version of Chimera that will run in stereo on the Mac?

To see if your graphics card supports stereo, run the 
/usr/X11R6/bin/glxinfo program inside of xterm and there should be an 
occasional y in the st/ro column.  That will only be true for Macs with 
the NVidia Quadro graphics cards.  So if you didn't buy a PowerMac or Mac 
Pro with the high-end NVidia graphics card, you're out of luck.

FYI, the latest version of chimera can switch into stereo on the fly by 
changing the camera mode in the Camera tool.

 	Greg Couch
 	UCSF Computer Graphics Lab



From goddard at cgl.ucsf.edu  Thu Nov  2 19:30:00 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 2 Nov 2006 19:30:00 -0800 (PST)
Subject: [Chimera-users] Showing data set axes
In-Reply-To: <20061103013035.8B5B61DB02@handler4.mail.rice.edu>
	(triffo@rice.edu)
References: <20061103013035.8B5B61DB02@handler4.mail.rice.edu>
Message-ID: <200611030330.kA33U0le1892604@guanine.cgl.ucsf.edu>

Hi Jeff,

  Chimera supports a format for making geometric objects called BILD
described in the Chimera manual:

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html

Below is a 6 line BILD file that when opened in Chimera shows cylindrical
arrows for the X (red), (green), and Z (blue) axes in the style of the
program VMD.  I made the axes 20 units long, with radius 1 and cone shaped
tip with a radius of 2.

	Tom

-----
File axes.bld:

.color 1 0 0
.arrow 0 0 0 20 0 0 1 2
.color 0 1 0
.arrow 0 0 0 0 20 0 1 2
.color 0 0 1
.arrow 0 0 0 0 0 20 1 2




> From: Jeff
> To: "'Thomas Goddard'" <goddard at cgl.ucsf.edu>
> Subject: RE: Chimera length units
> Date: Thu, 2 Nov 2006 17:30:29 -0800
> 
> i figured some of that but is good to hear it from the source.
> 
> one last question - if i want to make an origin with axes (like a CAD
> program might have) so i don't get lost after rotating my volumes a jillion
> times and have to click 'orient', is there a way for me to make a
> marker-based model (two markers for each axis) and put it slightly
> off-origin (like in the -,-,- octant) so that i have a visual on my axes as
> i rotate the scene?
> 
> as in, is there a simple way for me to hand-write a marker model that i can
> just load and fix to the scene?
> 
> thanks,
> 
> -jeff


From hsosa at aecom.yu.edu  Fri Nov  3 08:32:15 2006
From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu)
Date: Fri, 03 Nov 2006 11:32:15 -0500
Subject: [Chimera-users] stereo
In-Reply-To: <Pine.OSF.4.63.0611021506510.1901476@guanine.cgl.ucsf.edu>
References: <454A76FD.4090001@aecom.yu.edu>
	<Pine.OSF.4.63.0611021506510.1901476@guanine.cgl.ucsf.edu>
Message-ID: <454B6F0F.6020705@aecom.yu.edu>

I didn't know that nvidia had workstation and consumer version of their 
drivers. In any case the only 91.36 version that I found was at 
http://www.nvidia.com/object/winxp_2k_91.36
If I install this driver I don't see any stereo setting when I get to 
the video driver setting menu. Chimera stereo doesn't work either.

In the NVIDIA web site there is a consumer stereo driver at:
http://www.nvidia.com/object/3dstereo_91.31
The web site  says that it requires 91.31 ForceWare Graphics drivers to run.

I have tried the following permutations so far and I always get an error 
message when trying to go in stereo mode with chimera.

1 - NVIDIA driver  for Quadro4 downloaded from DELL support web site. 
(driver version?. date 2004)). This one seems to have native stereo 
support (at least it has a menu saying so).
2 - NVIDIA ForceWare driver 91.36 & Consumer stereo driver 91.31.
3 - NVIDIA ForceWare driver 91.31 & Consumer stereo driver 91.31.

With options 2 and 3 there are is a test option in the driver menu. This 
test seem to run OK (i.e. I can see the two stereo images in a scene 
alternating rapidly). Yet chimera gives an error message when I tried 
the stereo mode (or calling the program with chimera --stereo).

Maybe none of the above are the correct drivers ?.  Maybe  I need to 
reinstall chimera after installing the drivers ?.

Thanks

Hernando


Greg Couch wrote:
> On Thu, 2 Nov 2006, hsosa at aecom.yu.edu wrote:
>
>> How can I use stereo (sequential mode)  ?. If  I click the stereo button
>> in the camera dialog or start chimera using the command chimera
>> --stereo. I get the error message:
>>
>>
>> Unable to turn on stereo viewing
>> Unable to find hardware stereo support
>> (coulddm't choose stereo pixel format
>> Couldn't figure togl widget)
>>
>>
>> My graphic cards is a NVIDIA Quadro4 900  XGL.
>> The Nvdia Stereo driver (v: 91.31) is installed and enabled.
>> Chimera version is: 1 build 2255 2006/06/23
>>
>> Monitors: Two (dual) digital DELL 1900 FP
>> Computer: Dual Xeon 1.4 Ghz, 1GB of RAM. Running Windows XP
>
> I've made your mistake, you need to remove the NVidia Consumer Stereo 
> driver -- the Quadro driver supports stereo natively.  The Consumer 
> Stereo driver is for GeForce graphics cards (ie., consumer graphics 
> cards, not workstation graphics cards).
>
> The lastest Quadro driver is version 91.36.
>
> You still need to configure the Quadro graphics driver for stereo 
> after you install it.
>
>     Greg Couch
>     UCSF Computer Graphics Lab
>
>

-- 
-----------------------------------
Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone	(718) 430-3456
FAX	(718) 430-8819
email	hsosa at aecom.yu.edu
-----------------------------------





From gregc at cgl.ucsf.edu  Fri Nov  3 10:23:57 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 3 Nov 2006 10:23:57 -0800 (PST)
Subject: [Chimera-users] stereo
In-Reply-To: <454B6F0F.6020705@aecom.yu.edu>
References: <454A76FD.4090001@aecom.yu.edu>
	<Pine.OSF.4.63.0611021506510.1901476@guanine.cgl.ucsf.edu>
	<454B6F0F.6020705@aecom.yu.edu>
Message-ID: <Pine.OSF.4.63.0611030944330.1677410@guanine.cgl.ucsf.edu>

What you need to do is a variation of option 1.  Here is a rehash of 
everything you have to do.  I don't have access to the a Quadro today, 
so some of the latter details will be from memory.

First, remove the consumer stereo driver.  The Quadro driver has its own 
stereo support.

Next go to www.nvidia.com, select "Download Drivers".  In the three 
columns, pick "Graphics Driver" in column 1, pick "Quadro" in column 2, 
and pick "Windows XP/2000" in column 3. Then press the "Go!" button. 
That takes you to 
<http://www.nvidia.com/page/partner_certified_drivers.html>.

Next, since chimera isn't listed, pick the "Windows XP/2000" link in the 
Quadro FX.  The driver works for the Quadro4 as well.

I believe you have already successfully done all of the above steps.

Next bring up the Display dialog (start / Control Panel / Display), switch 
to the Settings tab and press the Advanced button.  The resulting dialog 
should have many tabs (General, Adapter, Monitor, etc.) and one of the 
tabs will be the name of your graphics card, in this case Quadro4 900 XGL.
Pick the graphics card tab and you'll see the NVidia control panel.

Here come the crucial step.  NVidia has moved the stereo settings around 
in the control panel from one driver release to another.  Sometimes you 
will see various Stereo items listed in the associated popup menu to the 
left of the dialog, like what you see when the consumer stereo driver is 
loaded.  But if that is not there, you will need to go to the "Performance 
& Quality Setting" subpanel, and change the View from "Basic settings" to 
"Advanced settings", then in the scrolled table just below it, you will 
see the stereo options.  And after you set the right stereo options, you 
will get stereo.

If the above doesn't work, on Monday I can sit down in front of a Windows 
XP machine with a Quadro4 900 XGL and find out exactly what needs to be 
done.

 	- Greg

On Fri, 3 Nov 2006, hsosa at aecom.yu.edu wrote:

> Date: Fri, 03 Nov 2006 11:32:15 -0500
> From: hsosa at aecom.yu.edu
> To: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] stereo
> 
> I didn't know that nvidia had workstation and consumer version of their
> drivers. In any case the only 91.36 version that I found was at
> http://www.nvidia.com/object/winxp_2k_91.36
> If I install this driver I don't see any stereo setting when I get to
> the video driver setting menu. Chimera stereo doesn't work either.
>
> In the NVIDIA web site there is a consumer stereo driver at:
> http://www.nvidia.com/object/3dstereo_91.31
> The web site  says that it requires 91.31 ForceWare Graphics drivers to run.
>
> I have tried the following permutations so far and I always get an error
> message when trying to go in stereo mode with chimera.
>
> 1 - NVIDIA driver  for Quadro4 downloaded from DELL support web site.
> (driver version?. date 2004)). This one seems to have native stereo
> support (at least it has a menu saying so).
> 2 - NVIDIA ForceWare driver 91.36 & Consumer stereo driver 91.31.
> 3 - NVIDIA ForceWare driver 91.31 & Consumer stereo driver 91.31.
>
> With options 2 and 3 there are is a test option in the driver menu. This
> test seem to run OK (i.e. I can see the two stereo images in a scene
> alternating rapidly). Yet chimera gives an error message when I tried
> the stereo mode (or calling the program with chimera --stereo).
>
> Maybe none of the above are the correct drivers ?.  Maybe  I need to
> reinstall chimera after installing the drivers ?.
>
> Thanks
>
> Hernando
>
>
> Greg Couch wrote:
>> On Thu, 2 Nov 2006, hsosa at aecom.yu.edu wrote:
>>
>>> How can I use stereo (sequential mode)  ?. If  I click the stereo button
>>> in the camera dialog or start chimera using the command chimera
>>> --stereo. I get the error message:
>>>
>>>
>>> Unable to turn on stereo viewing
>>> Unable to find hardware stereo support
>>> (coulddm't choose stereo pixel format
>>> Couldn't figure togl widget)
>>>
>>>
>>> My graphic cards is a NVIDIA Quadro4 900  XGL.
>>> The Nvdia Stereo driver (v: 91.31) is installed and enabled.
>>> Chimera version is: 1 build 2255 2006/06/23
>>>
>>> Monitors: Two (dual) digital DELL 1900 FP
>>> Computer: Dual Xeon 1.4 Ghz, 1GB of RAM. Running Windows XP
>>
>> I've made your mistake, you need to remove the NVidia Consumer Stereo
>> driver -- the Quadro driver supports stereo natively.  The Consumer
>> Stereo driver is for GeForce graphics cards (ie., consumer graphics
>> cards, not workstation graphics cards).
>>
>> The lastest Quadro driver is version 91.36.
>>
>> You still need to configure the Quadro graphics driver for stereo
>> after you install it.
>>
>>     Greg Couch
>>     UCSF Computer Graphics Lab
>>
>>
>
> -- 
> -----------------------------------
> Hernando Sosa
> Dept. of Physiology and Biophysics
> Albert Einstein College of Medicine
> 1300 Morris Park Av.
> Bronx NY 10461
> phone	(718) 430-3456
> FAX	(718) 430-8819
> email	hsosa at aecom.yu.edu
> -----------------------------------
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>


From hsosa at aecom.yu.edu  Fri Nov  3 11:38:51 2006
From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu)
Date: Fri, 03 Nov 2006 14:38:51 -0500
Subject: [Chimera-users] stereo
In-Reply-To: <Pine.OSF.4.63.0611030944330.1677410@guanine.cgl.ucsf.edu>
References: <454A76FD.4090001@aecom.yu.edu>
	<Pine.OSF.4.63.0611021506510.1901476@guanine.cgl.ucsf.edu>
	<454B6F0F.6020705@aecom.yu.edu>
	<Pine.OSF.4.63.0611030944330.1677410@guanine.cgl.ucsf.edu>
Message-ID: <454B9ACB.7020200@aecom.yu.edu>

Thanks, now it seems to work. The original problem was that I did not 
find to find the stereo settings in the Nvdia 91.36 driver menu. After 
finding/setting them the  stereo option now  is working in Chimera.
Now another question: is there any particular 3D glasses recommended ?

Thanks

Hernando



Greg Couch wrote:
> What you need to do is a variation of option 1.  Here is a rehash of 
> everything you have to do.  I don't have access to the a Quadro today, 
> so some of the latter details will be from memory.
>
> First, remove the consumer stereo driver.  The Quadro driver has its 
> own stereo support.
>
> Next go to www.nvidia.com, select "Download Drivers".  In the three 
> columns, pick "Graphics Driver" in column 1, pick "Quadro" in column 
> 2, and pick "Windows XP/2000" in column 3. Then press the "Go!" 
> button. That takes you to 
> <http://www.nvidia.com/page/partner_certified_drivers.html>.
>
> Next, since chimera isn't listed, pick the "Windows XP/2000" link in 
> the Quadro FX.  The driver works for the Quadro4 as well.
>
> I believe you have already successfully done all of the above steps.
>
> Next bring up the Display dialog (start / Control Panel / Display), 
> switch to the Settings tab and press the Advanced button.  The 
> resulting dialog should have many tabs (General, Adapter, Monitor, 
> etc.) and one of the tabs will be the name of your graphics card, in 
> this case Quadro4 900 XGL.
> Pick the graphics card tab and you'll see the NVidia control panel.
>
> Here come the crucial step.  NVidia has moved the stereo settings 
> around in the control panel from one driver release to another.  
> Sometimes you will see various Stereo items listed in the associated 
> popup menu to the left of the dialog, like what you see when the 
> consumer stereo driver is loaded.  But if that is not there, you will 
> need to go to the "Performance & Quality Setting" subpanel, and change 
> the View from "Basic settings" to "Advanced settings", then in the 
> scrolled table just below it, you will see the stereo options.  And 
> after you set the right stereo options, you will get stereo.
>
> If the above doesn't work, on Monday I can sit down in front of a 
> Windows XP machine with a Quadro4 900 XGL and find out exactly what 
> needs to be done.
>
>     - Greg
>
> On Fri, 3 Nov 2006, hsosa at aecom.yu.edu wrote:
>
>> Date: Fri, 03 Nov 2006 11:32:15 -0500
>> From: hsosa at aecom.yu.edu
>> To: chimera-users at cgl.ucsf.edu
>> Subject: Re: [Chimera-users] stereo
>>
>> I didn't know that nvidia had workstation and consumer version of their
>> drivers. In any case the only 91.36 version that I found was at
>> http://www.nvidia.com/object/winxp_2k_91.36
>> If I install this driver I don't see any stereo setting when I get to
>> the video driver setting menu. Chimera stereo doesn't work either.
>>
>> In the NVIDIA web site there is a consumer stereo driver at:
>> http://www.nvidia.com/object/3dstereo_91.31
>> The web site  says that it requires 91.31 ForceWare Graphics drivers 
>> to run.
>>
>> I have tried the following permutations so far and I always get an error
>> message when trying to go in stereo mode with chimera.
>>
>> 1 - NVIDIA driver  for Quadro4 downloaded from DELL support web site.
>> (driver version?. date 2004)). This one seems to have native stereo
>> support (at least it has a menu saying so).
>> 2 - NVIDIA ForceWare driver 91.36 & Consumer stereo driver 91.31.
>> 3 - NVIDIA ForceWare driver 91.31 & Consumer stereo driver 91.31.
>>
>> With options 2 and 3 there are is a test option in the driver menu. This
>> test seem to run OK (i.e. I can see the two stereo images in a scene
>> alternating rapidly). Yet chimera gives an error message when I tried
>> the stereo mode (or calling the program with chimera --stereo).
>>
>> Maybe none of the above are the correct drivers ?.  Maybe  I need to
>> reinstall chimera after installing the drivers ?.
>>
>> Thanks
>>
>> Hernando
>>
>>
>> Greg Couch wrote:
>>> On Thu, 2 Nov 2006, hsosa at aecom.yu.edu wrote:
>>>
>>>> How can I use stereo (sequential mode)  ?. If  I click the stereo 
>>>> button
>>>> in the camera dialog or start chimera using the command chimera
>>>> --stereo. I get the error message:
>>>>
>>>>
>>>> Unable to turn on stereo viewing
>>>> Unable to find hardware stereo support
>>>> (coulddm't choose stereo pixel format
>>>> Couldn't figure togl widget)
>>>>
>>>>
>>>> My graphic cards is a NVIDIA Quadro4 900  XGL.
>>>> The Nvdia Stereo driver (v: 91.31) is installed and enabled.
>>>> Chimera version is: 1 build 2255 2006/06/23
>>>>
>>>> Monitors: Two (dual) digital DELL 1900 FP
>>>> Computer: Dual Xeon 1.4 Ghz, 1GB of RAM. Running Windows XP
>>>
>>> I've made your mistake, you need to remove the NVidia Consumer Stereo
>>> driver -- the Quadro driver supports stereo natively.  The Consumer
>>> Stereo driver is for GeForce graphics cards (ie., consumer graphics
>>> cards, not workstation graphics cards).
>>>
>>> The lastest Quadro driver is version 91.36.
>>>
>>> You still need to configure the Quadro graphics driver for stereo
>>> after you install it.
>>>
>>>     Greg Couch
>>>     UCSF Computer Graphics Lab
>>>
>>>
>>
>> -- 
>> -----------------------------------
>> Hernando Sosa
>> Dept. of Physiology and Biophysics
>> Albert Einstein College of Medicine
>> 1300 Morris Park Av.
>> Bronx NY 10461
>> phone    (718) 430-3456
>> FAX    (718) 430-8819
>> email    hsosa at aecom.yu.edu
>> -----------------------------------
>>
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
>

-- 
-----------------------------------
Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone	(718) 430-3456
FAX	(718) 430-8819
email	hsosa at aecom.yu.edu
-----------------------------------





From sabuj.pattanayek at vanderbilt.edu  Fri Nov  3 16:00:17 2006
From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek)
Date: Fri, 03 Nov 2006 18:00:17 -0600
Subject: [Chimera-users] font change in v1.2303+
Message-ID: <454BD811.3010905@vanderbilt.edu>

Hi,

The gui font seems to have changed in v1.2303+ . Is there some way to 
change it back to the old font?

Thanks,
Sabuj


From gregc at cgl.ucsf.edu  Fri Nov  3 22:26:41 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Fri, 3 Nov 2006 22:26:41 -0800 (PST)
Subject: [Chimera-users] font change in v1.2303+
In-Reply-To: <454BD811.3010905@vanderbilt.edu>
References: <454BD811.3010905@vanderbilt.edu>
Message-ID: <Pine.OSF.4.63.0611032213210.1881375@guanine.cgl.ucsf.edu>

On Fri, 3 Nov 2006, Sabuj Pattanayek wrote:

> The gui font seems to have changed in v1.2303+ . Is there some way to
> change it back to the old font?

It's actually the same font but drawn with a different technique.  The new 
technique is much faster, so you can have many more labels interactively 
displayed, and works on more graphics cards.  With the new technique, 
labels are roughly the same size as before in the middle of the scene, 
smaller in the back and larger in the front.  In some cases of extreme 
depth, you can see pixelation in the labels in the front.  You can change 
the size and type of font in the Background preferences.

The short answer is no.  But it would be possible to add the old technique 
back if really needed.  The way labels are positioned is very different 
between the two techniques, so an abstraction layer would be needed, but 
it is not hard to do, just questionable if it is worth it or not.

Please email why you want the old technique back and maybe I can fix the 
new technique to address your concerns.

 	Greg Couch
 	UCSF Computer Graphics Lab


From sabuj.pattanayek at vanderbilt.edu  Sat Nov  4 07:44:33 2006
From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek)
Date: Sat, 04 Nov 2006 09:44:33 -0600
Subject: [Chimera-users] font change in v1.2303+
In-Reply-To: <Pine.OSF.4.63.0611032213210.1881375@guanine.cgl.ucsf.edu>
References: <454BD811.3010905@vanderbilt.edu>
	<Pine.OSF.4.63.0611032213210.1881375@guanine.cgl.ucsf.edu>
Message-ID: <454CB561.2000507@vanderbilt.edu>

Hi,

> It's actually the same font but drawn with a different technique.  The 
> new technique is much faster, so you can have many more labels 
> interactively displayed, and works on more graphics cards.  With the new 
> technique, labels are roughly the same size as before in the middle of 
> the scene, smaller in the back and larger in the front.  In some cases 
> of extreme depth, you can see pixelation in the labels in the front.  
> You can change the size and type of font in the Background preferences.

> Please email why you want the old technique back and maybe I can fix the 
> new technique to address your concerns.

No that's ok. I was mainly just wondering if the font changes were 
cosmetic or functional, but you seem to have answered that question.

Thanks,
Sabuj



From sabuj.pattanayek at vanderbilt.edu  Sat Nov  4 12:09:06 2006
From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek)
Date: Sat, 04 Nov 2006 14:09:06 -0600
Subject: [Chimera-users] font change in v1.2303+
In-Reply-To: <EC67483F-B8E4-4E05-A3D7-1578E475DAF1@cgl.ucsf.edu>
References: <454BD811.3010905@vanderbilt.edu>
	<EC67483F-B8E4-4E05-A3D7-1578E475DAF1@cgl.ucsf.edu>
Message-ID: <454CF362.1030001@vanderbilt.edu>

Hi,

Yes, now that you mention it I think we have confused each other. I am 
talking about the fonts in the widgets and dialogs and not the 
annotation fonts in the linux version.

I will grab an old install from 
http://www.cgl.ucsf.edu/chimera/olddownload.html, and make a screenshot 
comparing that with the latest 1.2304. I don't think I saw this change 
in the WinXP version, but I'll check that too.

Thanks,
Sabuj

Elaine Meng wrote:
> Hi Sabuj,
> It seems like Greg's response was about the labels on the structures, 
> whereas you said "gui" which I interpret as the widgets and dialogs.  
> Were you asking about these?  I noticed that the font for the "Really 
> Exit?" dialog is now different, but I haven't seen differences in other 
> dialogs.
> Elaine


From papai at titus.u-strasbg.fr  Tue Nov  7 00:25:43 2006
From: papai at titus.u-strasbg.fr (Gabor Papai)
Date: Tue, 07 Nov 2006 09:25:43 +0100
Subject: [Chimera-users] fitting map into map
Message-ID: <45504307.1090204@igbmc.u-strasbg.fr>

Hi,

Does anybody know if there is a way to calculate fitting of EM density 
map into another EM density map? I know how it goes with PDBs, but 
couldn't figure out how I can do it with maps.
Thanks for help in advance,
Gabor

-- 
Gabor Papai
IGBMC
Department of Structural Biology and Genomics
1, rue Laurent Fries, BP 10142
67404 Illkirch, France
phone  +33-3-90244796
Fax +33-3-88653201
E-mail: papai at igbmc.u-strasbg.fr




From goddard at cgl.ucsf.edu  Tue Nov  7 09:22:52 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 7 Nov 2006 09:22:52 -0800 (PST)
Subject: [Chimera-users] fitting map into map
In-Reply-To: <45504307.1090204@igbmc.u-strasbg.fr> (message from Gabor Papai
	on Tue, 07 Nov 2006 09:25:43 +0100)
References: <45504307.1090204@igbmc.u-strasbg.fr>
Message-ID: <200611071722.kA7HMqrZ1894579@guanine.cgl.ucsf.edu>

Hi Gabor,

  Chimera currently has no way to fit one EM map into another EM map
other than placing the map by hand.

  We plan on adding a local optimization capability for fitting one
map in another-- it is almost the same code as the "fit models in
maps" tool only the map-map correlation is optimized.  This is
probably less than a day's work to make the code changes but I am
working on a grant right now and will not be able to look at it until
next Thursday.  If you can wait, I might be able to provide some code
to test out at the end of next week.

	Tom


From ksgodin at u.washington.edu  Tue Nov  7 10:15:54 2006
From: ksgodin at u.washington.edu (ksgodin at u.washington.edu)
Date: Tue, 7 Nov 2006 10:15:54 -0800 (PST)
Subject: [Chimera-users] sparky-chimera error
Message-ID: <Pine.LNX.4.43.0611071015540.21487@hymn09.u.washington.edu>

Hi all,

I having been trying to open an ensemble of NMR structures with the 'km' feature of Sparky.  Everything opens fine, but the Model Panel does not open properly.  The error log sites

Program Files\Sparky\python\lib-tk\Tix.py, line 477, in_init_ self.stylename=self.tk.call ('tixDisplayStyle', itemtype,

TclError: invalid command name "tixDisplayStyle"

Does anyone know how to fix this?  It comes up with Sparky 3.111 and Chimera 1.2065 or 1.1195.

Thanks,
Kate

~~~~~~~~~~~~~~~~~~~~~~
Kate Godin
UW Chemistry Dept
Varani Group
BAG 63
~~~~~~~~~~~~~~~~~~~~~~









From goddard at cgl.ucsf.edu  Tue Nov  7 15:17:56 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 7 Nov 2006 15:17:56 -0800 (PST)
Subject: [Chimera-users] sparky-chimera error
In-Reply-To: <Pine.LNX.4.43.0611071015540.21487@hymn09.u.washington.edu>
	(ksgodin@u.washington.edu)
References: <Pine.LNX.4.43.0611071015540.21487@hymn09.u.washington.edu>
Message-ID: <200611072317.kA7NHuto2002781@guanine.cgl.ucsf.edu>

Hi Kate,

  I tested on Linux and observed the same error you report with Sparky
3.110 and Chimera 1.2065.  I tried a few changes and was not able to
make it work.

  I also tested on Linux Sparky versino 3.112 and Chimera version
1.2154 (as recommended in the Sparky manual) and Model Panel did work.
So you could update your versions if it is worth your trouble.
Otherwise the best suggestion I can offer is to not use Model Panel.

  I believe the problem is because a library called Tix is not being
properly initialized by another library called Tcl.  Tix is needed by
Chimera but not by Sparky.  There are lines in the Sparky startup
script (sparky/bin/sparky) that set variables TIX_LIBRARY and
TCLLIBPATH that are supposed to allow Tix to initialize correctly.
The only different in the Sparky startup script between 3.110 and 3.112
is that Python 2.4 is used instead of Python 2.3.  Chimera may have
changed the way it initializes the Tix library.

  The error occurs in a Sparky file Tix.py that is also included in
Chimera.  But the Chimera and Sparky versions of Tix.py are identical.

  The missing tixDisplayStyle command is supposed to be initialized
by libtix8.2.so (or on Windows libtix8.2.dll) that is included in
Chimera (in chimera/lib).

	Tom


From gregc at cgl.ucsf.edu  Tue Nov  7 16:10:54 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Tue, 7 Nov 2006 16:10:54 -0800 (PST)
Subject: [Chimera-users] font change in v1.2303+
In-Reply-To: <454CF362.1030001@vanderbilt.edu>
References: <454BD811.3010905@vanderbilt.edu>
	<EC67483F-B8E4-4E05-A3D7-1578E475DAF1@cgl.ucsf.edu>
	<454CF362.1030001@vanderbilt.edu>
Message-ID: <Pine.OSF.4.63.0611061055460.1930045@guanine.cgl.ucsf.edu>

On Sat, 4 Nov 2006, Sabuj Pattanayek wrote:

> Yes, now that you mention it I think we have confused each other. I am
> talking about the fonts in the widgets and dialogs and not the
> annotation fonts in the linux version.

Ah ha, yes, those fonts may or may not have changed depending on which 
window manager you're using and what you have in your ~/.Xdefaults file.
The old chimera picked it's own font (12 pixel high Helvetica) unless you 
had a specific font set in your .Xdefaults.  The new chimera tries to 
figure out which window manager you're using and use its fonts, or 
fallback to screen-size depdendent defaults.  Unfortunately, it was 
missing support for the gnome2 desktop that ships by default in Red Hat. 
That will be fixed in the next snapshot (probably tommorrow).

 	- Greg


From papai at titus.u-strasbg.fr  Wed Nov  8 00:45:08 2006
From: papai at titus.u-strasbg.fr (Gabor Papai)
Date: Wed, 08 Nov 2006 09:45:08 +0100
Subject: [Chimera-users] fitting map into map
In-Reply-To: <200611071722.kA7HMqrZ1894579@guanine.cgl.ucsf.edu>
References: <45504307.1090204@igbmc.u-strasbg.fr>
	<200611071722.kA7HMqrZ1894579@guanine.cgl.ucsf.edu>
Message-ID: <45519914.3090901@igbmc.u-strasbg.fr>

Dear Tom,

Thank you for your help! I am working with EM maps, and I certainly 
would like to try the code for fitting maps in map.
Sincerely,
Gabor

-- 
Gabor Papai
IGBMC
Department of Structural Biology and Genomics
1, rue Laurent Fries, BP 10142
67404 Illkirch, France
phone  +33-3-90244796
Fax +33-3-88653201
E-mail: papai at igbmc.u-strasbg.fr




From engelhar at medi.mappi.helsinki.fi  Thu Nov  9 01:01:37 2006
From: engelhar at medi.mappi.helsinki.fi (Peter Engelhardt)
Date: Thu, 9 Nov 2006 12:01:37 +0300
Subject: [Chimera-users] Fwd: Chimera crashes with MacPro show solid
Message-ID: <p06230937c17899e7aff4@[84.230.97.6]>

In our Mac Pro Quad-Core 2.66GHz CTO
Processor: 2.66 GHz Quad Xeon
RAM 4G and NVIDIA Quadro FX 4500 512MB SDRAM, using Crystal Eyes Stereo

Stereo works with iso surface and mesh but:
CRASHES  with show solid?

Peter

PS Following errors were reported and fwd to apple.

>Date/Time:      2006-11-07 17:17:49.047 +0200
>OS Version:     10.4.8 (Build 8L2127)
>Report Version: 4
>
>Command: python2.4
>Path:    /Applications/Chimera.app/Contents/Resources/bin/python2.4
>Parent:  WindowServer [55]
>
>Version: 1.2303 (1.2303)
>
>PID:    457
>Thread: 0
>
>Exception:  EXC_BAD_ACCESS (0x0001)
>Codes:      KERN_PROTECTION_FAILURE (0x0002) at 0x000000a4
>
>Thread 0 Crashed:
>0   libGLImage.dylib           	0x940a3fc4 glgProcessColor(GLDPixelMode
>const*, GLGOperation const*, unsigned long) + 46870
>1   libGLImage.dylib           	0x940972aa glgProcessPixels + 296
>2   com.apple.GeForceFXGLDriver	0x028b4f1e gldGetTextureLevel + 10243
>3   GLEngine                   	0x02732062 glTexSubImage2D_Exec + 1633
>4   libGL.dylib                	0x92b0edaa glTexSubImage2D + 139
>5   _volume.so                 	0x037fb30f Texture_2d::fill(unsigned
>short*) + 147
>6   _volume.so                  
>	0x037fb424 Texture_Plane::fill_texture()
>+ 76
>7   _volume.so                 	0x037fb627
>Volume_Renderer_2DT::update_colormap_textures(int) + 159
>8   _volume.so                 	0x037fd865
>Volume_Renderer_2DT::update_texture_planes(int) + 567
>9   _volume.so                  
>	0x037fd9d8 Volume_Renderer_2DT::draw() +
>122
>10  _chimera.dylib              
>	0x0101c5f8 chimera::LensModel::xformDraw
>(chimera::LensViewer const*, chimera::LensViewer::DrawPass) const + 572
>11  _chimera.dylib             	0x010190e1 chimera::Lens::draw
>(chimera::LensViewer const*, chimera::LensViewer::DrawPass, int const*) +
>241
>12  _chimera.dylib             	0x01020e98
>chimera::LensViewer::drawScreenBoxes(otf::Array<int, (unsigned long)4>
>const&, __gnu_cxx::__normal_iterator<chimera::ScreenBox*,
>std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >,
>__gnu_cxx::__normal_iterator<chimera::ScreenBox*,
>std::vector<chimera::ScreenBox, std::allocator<chimera::ScreenBox> > >)
>const + 1024
>13  _chimera.dylib             	0x01022674 chimera::LensViewer::draw
>(bool) const + 460
>14  _chimera.dylib              
>	0x0101dd34 chimera::LensViewer::displayCB
>(_object*) + 90
>15  _chimera.dylib             	0x01095323 LensViewer_displayCB + 43
>16  python2.4                  	0x00006549 PyObject_Call + 45
>(abstract.c:1795)
>17  python2.4                   
>	0x0005d0ee PyEval_CallObjectWithKeywords
>+ 112 (ceval.c:3430)
>18  python2.4                  	0x000b89dc builtin_apply + 201
>(bltinmodule.c:100)
>19  python2.4                  	0x0006359e PyEval_EvalFrame + 22313
>(ceval.c:3563)
>20  python2.4                  	0x000642ca PyEval_EvalCodeEx + 1774
>(ceval.c:2736)
>21  python2.4                  	0x000b6570 function_call + 320
>(funcobject.c:548)
>22  python2.4                  	0x00006549 PyObject_Call + 45
>(abstract.c:1795)
>23  python2.4                  	0x0000c662 instancemethod_call + 401
>(classobject.c:2447)
>24  python2.4                  	0x00006549 PyObject_Call + 45
>(abstract.c:1795)
>25  python2.4                   
>	0x0005d0ee PyEval_CallObjectWithKeywords
>+ 112 (ceval.c:3430)
>26  _tkinter.so                	0x016efea4 PythonCmd + 220 (_tkinter.c:
>2001)
>27  libtcl8.4.dylib            	0x0a00d10f TclInvokeStringCommand + 121
>28  libtcl8.4.dylib            	0x0a00fa41 TclEvalObjvInternal + 769
>29  libtcl8.4.dylib            	0x0a010694 Tcl_EvalObjv + 232
>30  libTogl2.0.dylib           	0x0255d047 Togl_CallCallback + 144
>31  libTogl2.0.dylib           	0x0255d235 Togl_Render + 46
>32  libtcl8.4.dylib            	0x0a0648a9 TclServiceIdle + 65
>33  libtcl8.4.dylib            	0x0a055661 Tcl_DoOneEvent + 380
>34  libtk8.4.dylib             	0x0b00ae3a Tk_UpdateObjCmd + 44
>35  libtcl8.4.dylib            	0x0a00fa41 TclEvalObjvInternal + 769
>36  libtcl8.4.dylib            	0x0a010694 Tcl_EvalObjv + 232
>37  _tkinter.so                 
>	0x016f18ad Tkapp_Call + 199 (_tkinter.c:
>1314)
>38  python2.4                  	0x0006359e PyEval_EvalFrame + 22313
>(ceval.c:3563)
>39  python2.4                  	0x000638b1 PyEval_EvalFrame + 23100
>(ceval.c:3645)
>40  python2.4                  	0x000642ca PyEval_EvalCodeEx + 1774
>(ceval.c:2736)
>41  python2.4                  	0x0006370c PyEval_EvalFrame + 22679
>(ceval.c:3656)
>42  python2.4                  	0x000642ca PyEval_EvalCodeEx + 1774
>(ceval.c:2736)
>43  python2.4                  	0x000b6570 function_call + 320
>(funcobject.c:548)
>44  python2.4                  	0x00006549 PyObject_Call + 45
>(abstract.c:1795)
>45  python2.4                  	0x000617c2 PyEval_EvalFrame + 14669
>(ceval.c:3840)
>46  python2.4                  	0x000642ca PyEval_EvalCodeEx + 1774
>(ceval.c:2736)
>47  python2.4                  	0x000b6570 function_call + 320
>(funcobject.c:548)
>48  python2.4                  	0x00006549 PyObject_Call + 45
>(abstract.c:1795)
>49  python2.4                   
>	0x0005d0ee PyEval_CallObjectWithKeywords
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>
>Thread 1:
>0   libSystem.B.dylib          	0x90019d3c select + 12
>1   libSystem.B.dylib          	0x90023d87 _pthread_body + 84
>
>Thread 0 crashed with X86 Thread State (32-bit):
>   eax: 0x00000002    ebx: 0x940988bf ecx: 0x00000000 edx: 0x00000001
>   edi: 0x00000000    esi: 0x608d1000 ebp: 0xbfffba68 esp: 0xbfffb720
>    ss: 0x0000001f    efl: 0x00010246 eip: 0x940a3fc4  cs: 0x00000017
>    ds: 0x0000001f     es: 0x0000001f  fs: 0x00000000  gs: 0x00000037
>
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>	/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/
>Print.framework/Versions/A/Print
>0x92cbd000 - 0x92d20fff com.apple.htmlrendering 66.1 (1.1.3)
>	/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/
>HTMLRendering.framework/Versions/A/HTMLRendering
>0x92d47000 - 0x92d88fff com.apple.NavigationServices 3.4.4 (3.4.3)
>	/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/
>NavigationServices.framework/Versions/A/NavigationServices
>0x92daf000 - 0x92dbdfff com.apple.audio.SoundManager 3.9.1
>	/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/
>CarbonSound.framework/Versions/A/CarbonSound
>0x92dc4000 - 0x92dc9fff com.apple.CommonPanels 1.2.3 (73)
>	/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/
>CommonPanels.framework/Versions/A/CommonPanels
>0x92dce000 - 0x930c2fff com.apple.HIToolbox 1.4.8 (???)
>	/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/
>HIToolbox.framework/Versions/A/HIToolbox
>0x931c8000 - 0x931d3fff com.apple.opengl 1.4.12
>	/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
>0x94096000 - 0x940d0fff libGLImage.dylib	/System/Library/Frameworks/
>OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
>0x9492b000 - 0x94950fff libssl.0.9.7.dylib
>	/usr/lib/libssl.0.9.7.dylib
>0x96451000 - 0x96451fff com.apple.vecLib 3.3.1 (vecLib 3.3.1)
>	/System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
>0x969cb000 - 0x96a99fff libGLProgrammability.dylib
>	/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/
>libGLProgrammability.dylib
>0x96ab4000 - 0x96ab5fff libGLSystem.dylib
>	/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/
>libGLSystem.dylib
>0x99756000 - 0x99762fff libXplugin.1.dylib
>	/usr/lib/libXplugin.1.dylib
>
>Model: MacPro1,1, BootROM MP11.005C.B01, 4 processors, Dual-Core Intel Xeon,
>2.66 GHz, 5 GB
>Graphics: NVIDIA Quadro FX 4500, NVIDIA Quadro FX 4500, PCIe, 512 MB
>Memory Module: DIMM Riser A/DIMM 1, 512 MB, DDR2 FB-DIMM, 667 MHz
>Memory Module: DIMM Riser A/DIMM 2, 512 MB, DDR2 FB-DIMM, 667 MHz
>Memory Module: DIMM Riser B/DIMM 1, 1 GB, DDR2 FB-DIMM, 667 MHz
>Memory Module: DIMM Riser B/DIMM 2, 1 GB, DDR2 FB-DIMM, 667 MHz
>Memory Module: DIMM Riser A/DIMM 3, 1 GB, DDR2 FB-DIMM, 667 MHz
>Memory Module: DIMM Riser A/DIMM 4, 1 GB, DDR2 FB-DIMM, 667 MHz
>Network Service: Built-in Ethernet 1, Ethernet, en0
>PCI Card: NVIDIA Quadro FX 4500, Display, Slot-1
>Serial ATA Device: ST3250824AS  P, 232.89 GB
>Parallel ATA Device: SONY    DVD RW DW-D150A
>USB Device: Hub in Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec,
>500 mA
>USB Device: Apple Optical USB Mouse, Primax Electronics, Up to 1.5 Mb/sec,
>100 mA
>USB Device: Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, 250 mA
>FireWire Device: built-in_hub, unknown_value, Unknown
>
>
>___________________________________________________________
>Peter Engelhardt, PhD, docent
>Assistant Professor in Molecular Genetics
>Unit of Molecular Electron Tomography
>Department of Pathology and Virology
>Haartman Institute
>P.O.Box 21, FIN-00014 Univ. of Helsinki, Finland
>Visiting Address: Haartmaninkatu 3, Helsinki
>Office Tel: (+358-9)-19126431 (direct)
>Laboratory Tel: (+358-9)-19126441
>EM-facilities, Tel: (+358-9)-19126885
>Digiroom: Tel: (+358-9)-1912886
>Fax: (+358-9)-19126491
>FIN-00014 Univ. of Helsinki, Helsinki, Finland
>
>LCE, Laboratory of Computational Engineering,
>Research Center for Computational Science and Engineering
>Helsinki University of Technology (HUT),
>P.O.Box 9203, FIN-02015 HUT, FINLAND
>Visiting Address: Innopolis2, Tekniikantie 14, Espoo
>
>Home address:
>  Lindstedstv?gen 1 B 7
>  FIN-02700 Grankulla,
>  Finland
>Tel: (+358-9)-5091381
>
>  Mobil Phone: +358 (0)415610171
>  Email: Peter.Engelhardt at Helsinki.Fi
>  URL: http://www.lce.hut.fi/~engelhar/


-- 
___________________________________________________________
Peter Engelhardt, PhD, docent
Assistant Professor in Molecular Genetics
Unit of Molecular Electron Tomography
Department of Pathology and Virology
Haartman Institute
P.O.Box 21, FI-00014 Univ. of Helsinki, Finland
Visiting Address: Haartmaninkatu 3, Helsinki

Office Tel: (+358-9)-19126431 (direct)
Laboratory Tel: (+358-9)-19126729, 19126442   
EM-facilities, Tel: (+358-9)-19126885
Fax: (+358-9)-19126700

Laboratory of Computational Engineering,
Research Center for Computational Science and Engineering
Helsinki University of Technology (HUT),
P.O.Box 9203, FI-02015 HUT, FINLAND  
Visiting Address: Innopolis2, Tekniikantie 14, Espoo
Office Tel: (+358-9)-4514843 (direct)  

Home address:
Lindstedstv?gen 1 B 7
FIN-02700 Grankulla,
Finland
Home Tel: (+358-9)-5091381

Mobile Phone: +358-(0)41 561 0171

Email: Peter.Engelhardt at Helsinki.Fi
URL: http://www.lce.hut.fi/~engelhar/
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From bala at igib.res.in  Thu Nov  9 08:32:03 2006
From: bala at igib.res.in (bala)
Date: Thu, 9 Nov 2006 22:02:03 +0530
Subject: [Chimera-users] queries on making image
Message-ID: <1D011717865DAE46B56AA1455F02CAC54B1159@n1ex>


Hello chimera users,

1) I hve to show two molecules in the same figure side by side. When i am
displaying, i have a problem that both molecules are not coming at same plane.
Is there any option to adjust this.

2) I labelled both these molecules. The labels are coming fine in the screen.
But when i create an image (i save it as tif file), some labels are getting
hided below my molecular surface. Which option i should use to rectify that.

3) How one can add text on the screen/near a particular spot on the molecule ?

4) Someone kindly Suggest me on best settings (i mean values) of the
resolution based on your experience of making figures using chimera or which
you normally use.

Thanks in advance,
Bala
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From meng at cgl.ucsf.edu  Thu Nov  9 09:22:00 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 9 Nov 2006 09:22:00 -0800
Subject: [Chimera-users] queries on making image
In-Reply-To: <1D011717865DAE46B56AA1455F02CAC54B1159@n1ex>
References: <1D011717865DAE46B56AA1455F02CAC54B1159@n1ex>
Message-ID: <BB358751-0DAE-4C40-B103-0251DC21665E@cgl.ucsf.edu>


On Nov 9, 2006, at 8:32 AM, bala wrote:

>
> Hello chimera users,
>
> 1) I hve to show two molecules in the same figure side by side.  
> When i am
> displaying, i have a problem that both molecules are not coming at  
> same plane.
> Is there any option to adjust this.
>
You can move models in the Z dimension (closer/farther) using the mouse:

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html

First, you'd want to make one model unmovable so that only the other  
one would move.   Models can be made unmovable by unchecking "Active"  
in the Model Panel (under Favorites in the menu).  You can see where  
the models are in the Z dimension by looking at the Side View (also  
under Favorites).  Another approach is to first match the two  
structures and then only move them apart  in the X and/or Y  
directions.   Of course, if you rotate the whole view, that will  
again make one molecule farther back than the other if they are side  
by side.  You can make each model rotate around its own center with  
the command "set independent."

> 2) I labelled both these molecules. The labels are coming fine in  
> the screen.
> But when i create an image (i save it as tif file), some labels are  
> getting
> hided below my molecular surface. Which option i should use to  
> rectify that.
For figures, I recommend 2D Labels (see #3 below) and not the usual  
labels that move with the structure.  The labels that move with the  
structure are mainly good for interactive viewing.
>
> 3) How one can add text on the screen/near a particular spot on the  
> molecule ?
Use 2D Labels (Tools... Utilities... 2D Labels, or the command  
2dlabels).  These are arbitrary labels in
the plane of the screen that will not move when the structure is  
moved.  Thus, you need to position the molecule how you want it in  
the figure first, then add the 2D Labels.  Manual pages:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ 
2dlabels.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html
>
> 4) Someone kindly Suggest me on best settings (i mean values) of the
> resolution based on your experience of making figures using chimera  
> or which
> you normally use.
If it's for a paper to be published, usually the journal has  
instructions on the necessary resolution.  Sometimes it is 300 dpi.    
If so, you'd measure the final size of the picture and multiply to  
give the number of pixels.  If the column is 3 inches wide, for  
example, you would want an image in that column to be at least 900  
pixels wide.  Generally 300 dpi is pretty high resolution, 600 dpi  
really high resolution.  For the web, I usually just go by how it  
looks to me, and end up with 300-1000 pixels wide depending on how  
large the image should be.

For other settings relating to saved images, see the Image Tips and  
the "Images for Publication" tutorial:

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
frameimages.html

> Thanks in advance,
> Bala
>

You're welcome.  I hope this helps!

-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




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From goddard at cgl.ucsf.edu  Thu Nov  9 09:59:00 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 9 Nov 2006 09:59:00 -0800 (PST)
Subject: [Chimera-users] Fwd: Chimera crashes with MacPro show solid
In-Reply-To: <p06230937c17899e7aff4@[84.230.97.6]> (message from Peter
	Engelhardt on Thu, 9 Nov 2006 12:01:37 +0300)
References: <p06230937c17899e7aff4@[84.230.97.6]>
Message-ID: <200611091759.kA9Hx0nc1674157@guanine.cgl.ucsf.edu>

Hi Peter,

  The crash with solid rendering is almost surely a graphics driver bug.
The solid rendering code works correctly on many different graphics cards
and there is nothing in that code that works differently for stereo
rendering.

  Does the crash occur for solid rendering without stereo?

  Does the size of the data set matter?

  There are two solid rendering options that may avoid this crash.
These are shown in the volume dialog using the Features / Solid Rendering
Options menu entry.  From the back trace you sent I see the crash occurs
when pushing the data to the graphics card and mapping the colors using
a colormap.  If you turn off the option "Use colormap of size X for solids"
then different code will be used -- colors will be computed on the CPU
instead of on the graphics card.  A second change that may avoid the
crash is turning off "Solids using 2D textures".  This makes Chimera use
3 dimensional textures instead of 2 dimensional textures.

	Tom


From goddard at cgl.ucsf.edu  Thu Nov  9 14:41:09 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 9 Nov 2006 14:41:09 -0800 (PST)
Subject: [Chimera-users] longbond and session restore problems
Message-ID: <200611092241.kA9Mf9W31733568@guanine.cgl.ucsf.edu>

Here are two problems reported by Jean-Francois Menetret in Chimera
2304 and 2306.

------- Start of forwarded message -------
Date: Thu, 9 Nov 2006 16:38:58 -0500 (EST)
From: jean-francois menetret <menetret at bu.edu>
To: Thomas Goddard <goddard at cgl.ucsf.edu>
Subject: problems report

Hi Thomas,

I have two problems to report

1) the longbond command doesn't seem to work (with chimera 2304 or 2306)

2) I saved a session under chimera 2304 but couldn't open it after=20
upgrading to 2306

Jean-Francois


Jean-Fran=E7ois M=E9n=E9tret,  PhD
Boston University School of Medicine
Physiology and Biophysics Department
700 Albany Street  W315
Boston, MA 02118
Email: menetret at bu.edu
Mailing address: 715 Albany Street
------- End of forwarded message -------


From goddard at cgl.ucsf.edu  Thu Nov  9 14:45:09 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 9 Nov 2006 14:45:09 -0800 (PST)
Subject: [Chimera-users] Fwd: Chimera crashes with MacPro show solid
Message-ID: <200611092245.kA9Mj9VN1767919@guanine.cgl.ucsf.edu>


Peter EngelHardt replies about solid rendering crash on Mac.

------- Start of forwarded message -------
Date: Thu, 9 Nov 2006 22:42:41 +0300
To: Thomas Goddard <goddard at cgl.ucsf.edu>
From: Peter Engelhardt <engelhar at medi.mappi.helsinki.fi>
Subject: Re: [Chimera-users] Fwd: Chimera crashes with MacPro show solid

Dear Tom,

Thanks,   I did what you told and it all worked out very fine

Though a bit buggy - volumes disappear and appear 
suddenly - but under certain control anyhow.

Cheers and thanks again

Peter


>   The crash with solid rendering is almost surely a graphics driver bug.
>The solid rendering code works correctly on many different graphics cards
>and there is nothing in that code that works differently for stereo
>rendering.
>
>   Does the crash occur for solid rendering without stereo?

yes instantly

>
>   Does the size of the data set matter?

not tested

>
>   There are two solid rendering options that may avoid this crash.
>These are shown in the volume dialog using the Features / Solid Rendering
>Options menu entry.  From the back trace you sent I see the crash occurs
>when pushing the data to the graphics card and mapping the colors using
>a colormap.  If you turn off the option "Use colormap of size X for solids"
>then different code will be used -- colors will be computed on the CPU
>instead of on the graphics card.  A second change that may avoid the
>crash is turning off "Solids using 2D textures".  This makes Chimera use
>3 dimensional textures instead of 2 dimensional textures.
>
>	Tom


- -- 
___________________________________________________________
Peter Engelhardt, PhD, docent
Assistant Professor in Molecular Genetics
Unit of Molecular Electron Tomography
Department of Pathology and Virology
Haartman Institute
P.O.Box 21, FI-00014 Univ. of Helsinki, Finland
Visiting Address: Haartmaninkatu 3, Helsinki

------- End of forwarded message -------


From pett at cgl.ucsf.edu  Thu Nov  9 15:16:01 2006
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 9 Nov 2006 15:16:01 -0800
Subject: [Chimera-users] longbond and session restore problems
In-Reply-To: <200611092241.kA9Mf9W31733568@guanine.cgl.ucsf.edu>
References: <200611092241.kA9Mf9W31733568@guanine.cgl.ucsf.edu>
Message-ID: <36B9501C-8AF6-4821-8185-7123DE31661E@cgl.ucsf.edu>

On Nov 9, 2006, at 2:41 PM, Thomas Goddard wrote:

> Here are two problems reported by Jean-Francois Menetret in Chimera
> 2304 and 2306.
>
> ------- Start of forwarded message -------
> Date: Thu, 9 Nov 2006 16:38:58 -0500 (EST)
> From: jean-francois menetret <menetret at bu.edu>
> To: Thomas Goddard <goddard at cgl.ucsf.edu>
> Subject: problems report
>
> Hi Thomas,
>
> I have two problems to report
>
> 1) the longbond command doesn't seem to work (with chimera 2304 or  
> 2306)

As per the release notes, the longbond command was changed in the  
1.2304 release because the way that missing connectivity is handled  
was changed.  Starting with 1.2304, the long bond is automatically  
hidden (but not broken) and a dashed pseudobond is displayed in its  
place.  To hide these pseudobonds, you use "~longbond"; to show them  
again you use "longbond".  This change is noted in red text in the  
status line if you try to use "longbond" the old way.

> 2) I saved a session under chimera 2304 but couldn't open it after=20
> upgrading to 2306

I have no trouble restoring a 1.2304 session in 1.2306.  We would  
need the session he's having trouble with to track this down.

--Eric

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




From mv.krier at googlemail.com  Fri Nov 10 08:22:59 2006
From: mv.krier at googlemail.com (Mireille Krier)
Date: Fri, 10 Nov 2006 17:22:59 +0100
Subject: [Chimera-users] MultiAlign viewer
Message-ID: <b5d009790611100822r31a87680m82fc71e8a0f6ed38@mail.gmail.com>

Dear all,

I want to add to the header of a sequence alignment graphical
representations such as cylinders and thick arrows to symbolize
stretches of helix and strand.
Is this possible? Should one annotate this in the Stockholm format
file (and if yes could you provide me an example file) ?

Cheers,

Mireille


From xiaobinfan at tju.edu.cn  Mon Nov 13 17:27:02 2006
From: xiaobinfan at tju.edu.cn (xiaobinfan at tju.edu.cn)
Date: Tue, 14 Nov 2006 09:27:02 +0800
Subject: [Chimera-users] About electrostatic potentials
Message-ID: <363467622.12437@tju.edu.cn>

Dear Sir/Madam:
  Thank you for reading. I am a new Chimera's user in China. I wonder whether the
surface of a virus opened by Chimera could be colored by its electrostatic
potentials calculated by the DelPhiController. I can color the surface of a small
protein on Linux platform now. However, the surface of a whole virus (PDB 1ny7)
opened by the Multiscale Models could not. Does it possible to do that? Thank you
for your support. Best wishes!

Sincerely,

Xiaobin Fan

---------------------------   




From meng at cgl.ucsf.edu  Tue Nov 14 11:06:26 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 14 Nov 2006 11:06:26 -0800
Subject: [Chimera-users] Fwd:  longbond and session restore problems
References: <6559EEA5-8536-4F72-9461-FE66CFD38ABA@cgl.ucsf.edu>
Message-ID: <3EEF98AF-1E1D-481B-A1F9-58FD51EBDAEE@cgl.ucsf.edu>



Begin forwarded message:

> From: Elaine Meng <meng at cgl.ucsf.edu>
> Date: November 14, 2006 10:36:35 AM PST
> To: jean-francois menetret <menetret at bu.edu>
> Cc: Eric Pettersen <pett at cgl.ucsf.edu>, Thomas Goddard  
> <goddard at cgl.ucsf.edu>, Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] longbond and session restore problems
>
> Hi Jean-Francois,
> In my tests I didn't have this problem; showing Pipes-and-Planks  
> should not change which atoms and bonds are shown.
>
> However, I might understand what is happening:  when you show the  
> "chain trace" of CA atoms only, a connection across the missing  
> part is shown even after you use "~longbond".  This CA connection  
> line is different than the "missing segments" pseudobonds:
>
> -CA-CA-------CA-CA-
> is the chain trace, not affected by ~longbond
>
> -N-CA-C- - - -N-CA-C-
> is the backbone showing "real bonds" except for the pseudobond,  
> which is affected by ~longbond
>
> If you are showing just the CA atoms and you don't want the  
> connection, here are some possibilities:
> (1) just hide all the CA atoms (for example, command: ~disp @ca)
> OR
> (2) change from "chain trace" (the CA atoms) to "backbone  
> only" (N,CA,C) - if you used ~longbond the connection will be gone
> OR
> (3) if you really wanted to keep showing just the CA atoms, you can  
> select each long CA-CA bond (which is also a pseudobond, although  
> not shown with a dashed line) with Ctrl-click, and use the  
> Selection Inspector to undisplay it.  This tool is opened by  
> clicking the button on the lower right of the Chimera window.  In  
> the Inspector, change to Inspect [Pseudobond] and change the  
> "displayed" attribute to "false."
>
> I hope this helps,
> Elaine
>
> On Nov 14, 2006, at 6:51 AM, jean-francois menetret wrote:
>
>> Hi Elaine,
>>
>> thank you for your message
>> I still have one problem with the long bonds, though : there  
>> reappear in pipes-and-plancks.
>> About restoring a session, I agree, it was not an issue with the  
>> chimera version but with the speed/memory of my PC. Although  
>> chimera could save the session, it couldn't reopen it on my PC but  
>> it did on a faster one.
>>
>> Best wishes
>>
>> Jean-Fran?ois M?n?tret,  PhD
>> Boston University School of Medicine
>> Physiology and Biophysics Department
>> 700 Albany Street  W315
>> Boston, MA 02118
>> Email: menetret at bu.edu
>> Mailing address: 715 Albany Street
>
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html
>




From goddard at cgl.ucsf.edu  Tue Nov 14 16:11:46 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 14 Nov 2006 16:11:46 -0800 (PST)
Subject: [Chimera-users] About electrostatic potentials
In-Reply-To: <363467622.12437@tju.edu.cn> (xiaobinfan@tju.edu.cn)
References: <363467622.12437@tju.edu.cn>
Message-ID: <200611150011.kAF0Bkcq1629563@guanine.cgl.ucsf.edu>

Hi Xiaobin,

  In theory you could compute the electrostatic potential for the
entire virus capsid and then display it in Chimera.  But that is a big
calculation.  I tried calculating the electrostatic potential for just
the asymmetric unit of 1ny7 using a program called APBS (equivalent to
Delphi).  The 1.5 Gbytes of memory on my machine was not enough (grid
spacing ~0.7A).  For the full capsid with 60 copies the volume I think
it would be about 4 times larger in each dimension requiring 64
(4x4x4) times more memory.  So you would probably need a machine with
about 128 Gbytes of physical memory.  Maybe other software can break
down the calculation and use less memory.

  So the straight-forward approach seems quite difficult.  Here is a
simple approach you could use in Chimera on a normal computer.  You
can simply color the residues by charge (positive blue, negative red)
then map those colors onto the virus surface.  Of course that is not
as accurate as an electrostatics calculation.  Here is how you would
do this simple display in Chimera.  Open 1ny7.  The PDB version of
1ny7 only has the symmetry matrices to produce a pentamer.  So I
suggest using the version from the Virus Particle Explorer (VIPERdb)
web site:

	http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1ny7

Note that the VIPERdb 1ny7 has 3 chains (A,B,C) while the PDB 1ny7 has
only 2 chains (1,2).  I think the VIPERdb version is more useful in
general.  The structure 1ny7 comes from Jack Johnson's lab which
created the VIPERdb web site.

  So open 1ny7.vdb.  With the ".vdb" suffix Chimera will recognize this
as a VIPERdb file and use the Chimera Multiscale tool to show the whole
virus capsid.  Now color the charged residues.  First show the atomic
model by pressing the select "with loaded atoms" button on the Multiscale
dialog, then choose the Style Show... / Wire option in the Multiscale dialog.
To do the coloring use Chimera menu entry

	Select / Residue / amino acid category / positive

then menu entry

	Actions / Color / blue

then

	Select / Residue / amino acid category / negative

and

	Actions / Color / red

  Now to use the atom coloring to color the multiscale surfaces you need
the Multiscale Coloring command tool that is not distributed with Chimera.
Get it from the Chimera experimental features page

	http://www.cgl.ucsf.edu/chimera/experimental/experimental.html

and install it according to the instructions given there.  You have to
restart Chimera after installing it so you should do this before the steps
I described above.

  Now to color the capsid surface using the atom colors use the Chimera
command

	msc #1 #0 5

which says to color Chimera model #1 (the multiscale surfaces) using atoms
from model #0 (1ny7.vdb) within a range of 5 angstroms.  To display the
Chimera command-line where you type this command use Chimera menu entry

	Favorites / Command line

  Now you probably want a higher resolution virus surface.  To get that
press the Select All button on the multiscale dialog.  Then change the
resolution value in the middle of that dialog from 8 angstroms to 3
and press the Enter key or the Resurface button.  You'll then have to
rerun the "msc" command to get the red/blue coloring by charge.

  Here's an image I made for 1ny7.vdb showing what this looks like:

	http://www.cgl.ucsf.edu/home/goddard/temp/1ny7-charges.png

I used some more tricks to make this image.  I decided the red/blue
coloring over the whole capsid was too confusing to look at all at
once, so I selected one copy of chains B and C with the mouse, then
pressed the Select Copies button in the multiscale dialog, then
changed their resolution to 8 angstroms which erased their red/blue
coloring for those chains.  Also I used resolution equal to 0 for
chain A.  That makes a solvent excluded molecular surface which is
higher quality and resolution than the multiscale surfaces made with
resolution > 0.  I did run into a problem that 1ny7 vdb failed to
create solvent excluded surfaces for chain C because two atoms (number
1481 and 1485 in the file) have identical coordinates.  I deleted atom
1481 from the file when I was experimenting with this model to
circumvent that error in the data.

  This is kind of a complex process.  Here's some more info on the
multiscale tool, the msc command, and electrostatic coloring.

	http://www.cgl.ucsf.edu/chimera/tutorials/virus-howto/showvirus.html

	http://www.cgl.ucsf.edu/chimera/experimental/multiscale_color/msc.html

	http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/07-VolumeData/tutorial/chaperonin.html

	http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html


   Tom


From pett at cgl.ucsf.edu  Tue Nov 14 16:28:47 2006
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 14 Nov 2006 16:28:47 -0800
Subject: [Chimera-users] MultiAlign viewer
In-Reply-To: <b5d009790611100822r31a87680m82fc71e8a0f6ed38@mail.gmail.com>
References: <b5d009790611100822r31a87680m82fc71e8a0f6ed38@mail.gmail.com>
Message-ID: <FB98656A-F91D-4562-9469-5CA1207B45FC@cgl.ucsf.edu>

On Nov 10, 2006, at 8:22 AM, Mireille Krier wrote:

> Dear all,
>
> I want to add to the header of a sequence alignment graphical
> representations such as cylinders and thick arrows to symbolize
> stretches of helix and strand.
> Is this possible? Should one annotate this in the Stockholm format
> file (and if yes could you provide me an example file) ?

	Sorry for the slow response, but Friday was a holiday here and  
Monday was very busy (the NIH was site-visiting us).  The shortest  
answer is no, Multalign Viewer can't yet depict graphics in its  
header lines (except for histograms).  Assuming you are trying to  
develop a figure for a paper, some alternatives are ALSCRIPT (http:// 
www.compbio.dundee.ac.uk/Software/Alscript/alscript.html) and ESPript  
(http://espript.ibcp.fr//ESPript/ESPript/).  Perhaps others on the  
list can suggest more.
	That said, one of my highest development priorities for Multalign  
Viewer is to make such graphical headers available (the other being  
dendrogram support).  Nonetheless, it will take months to implement  
and deploy that feature, so you should use something else until then.
	If you aren't doing this for a paper, you can already insert your  
own alphanumeric or histogram headers if that's good enough.  That's  
described here:  http://www.cgl.ucsf.edu/chimera/docs/ 
ContributedSoftware/multalignviewer/defineheader.html#headerformat
	Also, GC markups in Stockholm files are displayed as headers.
	I'm glad you spoke up since although I get a good amount of feedback  
from users here at UCSF, I don't get as much opportunity to hear the  
needs of other users.  Feel free to mention other things you'd like  
to see implemented.

--Eric

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




From ndebroy at gmail.com  Wed Nov 15 00:14:00 2006
From: ndebroy at gmail.com (Nihshanka Debroy)
Date: Wed, 15 Nov 2006 03:14:00 -0500
Subject: [Chimera-users] Question about molecular surface generation
Message-ID: <561eeeda0611150014s3b6bc6b9qd212dab57f4de9b5@mail.gmail.com>

Hi Chimera users,
                            I have been generating molecular surfaces for
several proteins and am hoping to perform some matrix calculations on the
points where the surfaces are being calculated. So I was wondering if there
is a way to reduce the # points where the surface is calculated/plotted, as
that would really reduce the dimensions of my matrices!
                            I am using the Delphi Controller to generate
electrostatic potentials. My understanding of Delphi is that it finds finite
difference solutions to the Poisson Boltzmann equation by mapping the system
onto a grid of points. After the potentials are calculated at those grid
points, when generating the potentials on the molecular surface,
interpolation is used to calculate the potentials for locations on the
molecular surface that are between points on the grid used in Delphi. So I
don't think its the grid size for Delphi that I need to be reducing, but the
# points where the actual molecular surface is calculated. Is it possible to
reduce this number somewhere in the code files?

Thanks a lot!
Sincerely,
Nihshanka
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From goddard at cgl.ucsf.edu  Wed Nov 15 09:10:30 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 15 Nov 2006 09:10:30 -0800 (PST)
Subject: [Chimera-users] Question about molecular surface generation
In-Reply-To: <561eeeda0611150014s3b6bc6b9qd212dab57f4de9b5@mail.gmail.com>
	(ndebroy@gmail.com)
References: <561eeeda0611150014s3b6bc6b9qd212dab57f4de9b5@mail.gmail.com>
Message-ID: <200611151710.kAFHAUsw1765688@guanine.cgl.ucsf.edu>

Hi Nihshanka,

  There is a parameter called "vertex density" that can be adjusted when
computing a molecular surface in Chimera.  Open a PDB model, use menu
entry Actions / Surface / show, open Model Panel with menu entry
Favorites / Model Panel, double click on the MSMS surface listed in
Model Panel to get the surface attributes dialog.  Then change the
vertex density value (default 2) and press the Enter key to recalculate
the surface.  To see how many points you are getting change the
"representation" setting in the attributes dialog to "mesh".  I believe
the vertex density means points per square angstrom.

  This method can reduce the number of surface points to a few per
atom at the surface.  If you want fewer points than that then other
techniques would be needed involving writing Python code to sample the
mesh of points more coarsely.

	Tom


From wencryo at yahoo.com  Wed Nov 15 17:14:07 2006
From: wencryo at yahoo.com (wendy ochoa)
Date: Wed, 15 Nov 2006 17:14:07 -0800 (PST)
Subject: [Chimera-users] deleting model memories
Message-ID: <20061116011407.71966.qmail@web37304.mail.mud.yahoo.com>

Is there a way to delete model memories in the emanimator option?
thanks a lot

wendy



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From goddard at cgl.ucsf.edu  Wed Nov 15 20:58:48 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 15 Nov 2006 20:58:48 -0800 (PST)
Subject: [Chimera-users] deleting model memories
In-Reply-To: <20061116011407.71966.qmail@web37304.mail.mud.yahoo.com> (message
	from wendy ochoa on Wed, 15 Nov 2006 17:14:07 -0800 (PST))
References: <20061116011407.71966.qmail@web37304.mail.mud.yahoo.com>
Message-ID: <200611160458.kAG4wmef2074445@guanine.cgl.ucsf.edu>

Hi Wendy,

  I looked at the emanimator code (today's build) and see nothing that
allows deleting model memories.  That would be useful.  Steve Ludtke
is the author of emanimator and I have forwarded your message to him.

	Tom


> Date: Wed, 15 Nov 2006 17:14:07 -0800 (PST)
> From: wendy ochoa <wencryo at yahoo.com>
> To: chimera-users at cgl.ucsf.edu
> 
> Is there a way to delete model memories in the emanimator option?
> thanks a lot
> 
> wendy



From sludtke at bcm.edu  Wed Nov 15 21:48:34 2006
From: sludtke at bcm.edu (Steve Ludtke)
Date: Wed, 15 Nov 2006 23:48:34 -0600 (CST)
Subject: [Chimera-users] deleting model memories
In-Reply-To: <200611160458.kAG4wmef2074445@guanine.cgl.ucsf.edu>
References: <20061116011407.71966.qmail@web37304.mail.mud.yahoo.com>
	<200611160458.kAG4wmef2074445@guanine.cgl.ucsf.edu>
Message-ID: <Pine.LNX.4.58.0611152345070.8626@id.grid.bcm.edu>

There is no way to delete model memories, and in addition, you cannot load new
models into chimera after creating a memory. However, you can replace a current
memory with a new set of values using the right mouse button.  The emanimator
system is quite limited in a number of different ways, and is not actively
developed much, beyond insuring that it continues to work with new chimera
versions.

----------------------------------------------------------------------------
Steven Ludtke, PhD              |        Baylor College of Medicine
sludtke at bcm.tmc.edu             |       Asst. Professor & Co-Director
stevel at alumni.caltech.edu       | National Center For Macromolecular Imaging
V: (713)798-9020                |    Dept of Biochemistry and Mol. Biol.
F: (713)798-1625                |
instant messenger: sludtke42    |             Those who Do, Are
http://ncmi.bcm.tmc.edu/~stevel |         The converse also applies

On Wed, 15 Nov 2006, Thomas Goddard wrote:

> Hi Wendy,
>
>   I looked at the emanimator code (today's build) and see nothing that
> allows deleting model memories.  That would be useful.  Steve Ludtke
> is the author of emanimator and I have forwarded your message to him.
>
> 	Tom
>
>
> > Date: Wed, 15 Nov 2006 17:14:07 -0800 (PST)
> > From: wendy ochoa <wencryo at yahoo.com>
> > To: chimera-users at cgl.ucsf.edu
> >
> > Is there a way to delete model memories in the emanimator option?
> > thanks a lot
> >
> > wendy
>
>


From baucom at msg.ucsf.edu  Thu Nov 16 15:46:31 2006
From: baucom at msg.ucsf.edu (Albion Baucom)
Date: Thu, 16 Nov 2006 15:46:31 -0800
Subject: [Chimera-users] Duplicate Atom Serial Numbers
Message-ID: <2817EE0D-1045-463A-96BC-1BF5EA90EC6F@msg.ucsf.edu>

When I generate a PDB file, and generate symmetry related biological  
units, I frequently replicate the single structure. When I do this  
the atoms numbers get duplicated and when I open the structure in  
Chimera it prints to the screen

warning: duplicate atom serial number found: NNNN

where NNNN is the duplicate number.

The problem with this is it slows down opening the file by a huge  
factor. I assume that the print statement to the terminal is adding a  
lot of time to the file reading process.

Is there any way around this, or a way to simply turn this off? I am  
not concerned with the specifics of the duplicate atom numbers. A  
single error message to alert me the fact that there are duplicate  
atoms would be enough.

Once Chimera is done reading the structure it works fine. Rotations  
are smooth. Displaying ribbons is quick, etc. This doesn't appear to  
be a slow down due to atom limitations, but simply the overhead of  
printing that error message over and over to the console.

Of course I am aware that there are BIOMT records to generate  
symmetry related molecules using a single repeating unit, or I could  
generate separate PDB files for each repeating unit, but this is a  
lot more work and bookkeeping when I can use some existing simple  
programs to simply rotate and translate a single set of coordinates.

Thanks

Albion


From goddard at cgl.ucsf.edu  Thu Nov 16 18:59:31 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 16 Nov 2006 18:59:31 -0800 (PST)
Subject: [Chimera-users] Duplicate Atom Serial Numbers
In-Reply-To: <2817EE0D-1045-463A-96BC-1BF5EA90EC6F@msg.ucsf.edu> (message from
	Albion Baucom on Thu, 16 Nov 2006 15:46:31 -0800)
References: <2817EE0D-1045-463A-96BC-1BF5EA90EC6F@msg.ucsf.edu>
Message-ID: <200611170259.kAH2xVai1675265@guanine.cgl.ucsf.edu>

Hi Albion,

  If you are on linux you might try starting chimera with output
redirected to /dev/null:

	% chimera >& /dev/null &

Maybe that will be faster since time for the large number of warning
messages is probably taken drawing text and scrolling the shell window.

  We will look into reducing the warning messages, like only reporting
the first 3 duplicate serial numbers and then a line saying how many
additional ones were encountered.

	Tom


From goddard at cgl.ucsf.edu  Thu Nov 16 19:24:43 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Thu, 16 Nov 2006 19:24:43 -0800 (PST)
Subject: [Chimera-users] suggestion
In-Reply-To: <6638778774B9F14997D316BCC99504CE8C6F94@hermes.mcb.ucdavis.edu>
	(dmorgan@ucdavis.edu)
References: <6638778774B9F14997D316BCC99504CE8C6F94@hermes.mcb.ucdavis.edu>
Message-ID: <200611170324.kAH3OhAs2006598@guanine.cgl.ucsf.edu>

Hi David,

  Thanks for your suggestion to add coloring of isosurfaces based on
gradient magnitude to Chimera.  I think I can add this to the Surface
Color tool in an hour or two since the gradient calculation code is
already in Chimera (for fitting atomic models in maps).  I'll try to
put it in soon and send you the code to test.

Description of coloring from article:

    "OpenDX (www.opendx.org) module MAKROVIS was implemented to create
     masks of different shapes and to analyze disorder in the
     reconstructions (Figure 1B). For this, isosurface rendering of a
     given voxel was colored as a function of the maximum density
     difference between the voxel and its neighbors."

	Tom

> From: "David G. Morgan" <dmorgan at ucdavis.edu>
> To: goddard at cgl.ucsf.edu
> Subject: suggestion
> Date: Thu, 16 Nov 2006 19:03:50 -0800
> 
> Tom,
> 
> I have a suggestion for the developers "list of ideas to implement," if
> you think there would be enough interest from users and that it is
> something that chimera should do.  I realize that you get lots of
> suggestions, and that some of them are simply outside the realm of what
> the chimera developers think chimera is intended to do.  But since you
> do ask for suggestions, here's my most recent one.
> 
> I'm attaching a recent journal article where the authors used a color
> coding scheme to display "order/disorder" regions of an EM
> reconstruction.  The images are in Fig 1 B and the rather sparse
> description of the "algorithm" is a single sentence in the "Image
> Processing 3D Reconstruction" section (p 1046).  The idea of color
> coding some estimate of the better defined regions of a density map is
> very nice (and clever), and would be extremely helpful in lots of
> situations (my plug for wanting you guys to implement something
> similar...).
> 
> The idea behind this is that for any given region of iso-surface, the
> density gradient normal to that surface should be a reasonable measure
> of how well defined the density is.  In other words, a very steep
> gradient (e.g., a fast transition between protein and solvent) means
> very well defined density and a flat gradient means weakly defined
> density (disordered regions, partial occupancy, etc.).  The authors
> don't do such a complicated calculation, but it seems that what they
> implemented at least captures most of this sort of character.
> 
> I think the key to this is that the gradient is calculated "locally."
> I've looked at gradients as a function of resolution with the idea of
> using it to help chose a proper iso-surface.  While it works well with
> model data, real reconstructions aren't nearly so well behaved.  I
> hadn't thought about this in a while, but I think what the authors have
> done both helps explain the behavior of my real data (the gradient is
> simply too varied) and is a quite useful visualization tool.
> 
> So please think about implementing something like this in the volume
> handling tools of chimera.
> 
>                     David Gene Morgan
>              Advanced Microscopy & Proteomics
>                 Molecular & Cellular Biology
>              University of California at Davis
>                     530 752 2693 (lab)
>                     530 752 3085 (FAX)
> ----
> removed PDF for 
> 
> Huiskonen JT, de Haas F, Bubeck D, Bamford DH, Fuller SD, Butcher SJ.
> Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging.
> Structure. 2006 Jun;14(6):1039-48. 


From meng at cgl.ucsf.edu  Fri Nov 17 08:14:39 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 17 Nov 2006 08:14:39 -0800
Subject: [Chimera-users] Duplicate Atom Serial Numbers
In-Reply-To: <2817EE0D-1045-463A-96BC-1BF5EA90EC6F@msg.ucsf.edu>
References: <2817EE0D-1045-463A-96BC-1BF5EA90EC6F@msg.ucsf.edu>
Message-ID: <7242813974239fa61b032349cfd5788a@cgl.ucsf.edu>

Hi Albion,
If you bracket each set of coordinates with the PDB records MODEL and 
ENDMDL (see NMR structures in the PDB, e.g. 1plx), Chimera will treat 
each set as a separate model and won't complain.

Another possibility is to use different chain IDs for each set, but 
that is a little more work.
Best,
Elaine

On Nov 16, 2006, at 3:46 PM, Albion Baucom wrote:

> When I generate a PDB file, and generate symmetry related biological
> units, I frequently replicate the single structure. When I do this
> the atoms numbers get duplicated and when I open the structure in
> Chimera it prints to the screen
>
> warning: duplicate atom serial number found: NNNN
>
> where NNNN is the duplicate number.
>
> The problem with this is it slows down opening the file by a huge
> factor. I assume that the print statement to the terminal is adding a
> lot of time to the file reading process.
>
> Is there any way around this, or a way to simply turn this off? I am
> not concerned with the specifics of the duplicate atom numbers. A
> single error message to alert me the fact that there are duplicate
> atoms would be enough.
>
> Once Chimera is done reading the structure it works fine. Rotations
> are smooth. Displaying ribbons is quick, etc. This doesn't appear to
> be a slow down due to atom limitations, but simply the overhead of
> printing that error message over and over to the console.
>
> Of course I am aware that there are BIOMT records to generate
> symmetry related molecules using a single repeating unit, or I could
> generate separate PDB files for each repeating unit, but this is a
> lot more work and bookkeeping when I can use some existing simple
> programs to simply rotate and translate a single set of coordinates.
>
> Thanks
>
> Albion
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




From meng at cgl.ucsf.edu  Fri Nov 17 08:19:58 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 17 Nov 2006 08:19:58 -0800
Subject: [Chimera-users] Duplicate Atom Serial Numbers
In-Reply-To: <7242813974239fa61b032349cfd5788a@cgl.ucsf.edu>
References: <2817EE0D-1045-463A-96BC-1BF5EA90EC6F@msg.ucsf.edu>
	<7242813974239fa61b032349cfd5788a@cgl.ucsf.edu>
Message-ID: <54da20c7ad9cfa24c6f7596cd7931059@cgl.ucsf.edu>

Whoops, my second suggestion (below) wouldn't work - ignore that one, 
sorry.

On Nov 17, 2006, at 8:14 AM, Elaine Meng wrote:

> Another possibility is to use different chain IDs for each set, but 
> that is a little more work.
>
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




From baucom at msg.ucsf.edu  Fri Nov 17 11:26:40 2006
From: baucom at msg.ucsf.edu (Albion Baucom)
Date: Fri, 17 Nov 2006 11:26:40 -0800
Subject: [Chimera-users] Duplicate Atom Serial Numbers
In-Reply-To: <54da20c7ad9cfa24c6f7596cd7931059@cgl.ucsf.edu>
References: <2817EE0D-1045-463A-96BC-1BF5EA90EC6F@msg.ucsf.edu>
	<7242813974239fa61b032349cfd5788a@cgl.ucsf.edu>
	<54da20c7ad9cfa24c6f7596cd7931059@cgl.ucsf.edu>
Message-ID: <BE931921-5E7A-4A44-9F3F-6F4F5E86B049@msg.ucsf.edu>

Thanks Elaine, Tom.

This is of course for "quick and dirty" helical structures where I  
want to take a single chain and replicate it dozens of times while  
imposing symmetry to create a short segment of a fiber. The MODEL and  
ENDMDL are good suggestions, as well as the /dev/null redirect.

I suppose there are scenarios when one would want to know about  
duplicate atoms, but in my case there are just so many that it is  
pointless to print them all out. The ultimate solution here is really  
for me to not to be so lazy ;)

As an aside, I typically use the program pdbsymm which is included  
with the SITUS package to impose the symmetry to generate an  
arbitrary number of symmetry mates along a helical axis (using polar  
coordinates). It simply replicates the original PDB file while  
updating the coordinates, thus I have the duplicate numbering problem.

But your suggestions should do the trick in the meantime.

Thanks again.

Albion


From goddard at cgl.ucsf.edu  Mon Nov 20 11:28:59 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 20 Nov 2006 11:28:59 -0800 (PST)
Subject: [Chimera-users] Gradient coloring
In-Reply-To: <200611170324.kAH3OhAs2006598@guanine.cgl.ucsf.edu> (message from
	Thomas Goddard on Thu, 16 Nov 2006 19:24:43 -0800 (PST))
References: <6638778774B9F14997D316BCC99504CE8C6F94@hermes.mcb.ucdavis.edu>
	<200611170324.kAH3OhAs2006598@guanine.cgl.ucsf.edu>
Message-ID: <200611201928.kAKJSxhA1588887@guanine.cgl.ucsf.edu>

Hi David,

  I added the coloring of surfaces based on the norm of the volume
data gradient.  You use the Surface Color tool.  If you would like to
try it out here is the code:

	https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/gradientcolor.zip

This zip archive contains a SurfaceColor and a VolumeViewer directory that
replace the existing ones in your chimera/share directory.  It should work
with Chimera version 1.2304 and newer.

  Open a volume data set, then show the Surface Color dialog (menu entry
Tools / Volume Data / Surface Color), select using "mymap.mrc gradient norm",
press the "Set full range colormap values" and press the Color button.

  Let me know if this proves of any use.

	Tom



From goddard at cgl.ucsf.edu  Mon Nov 20 13:35:25 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 20 Nov 2006 13:35:25 -0800 (PST)
Subject: [Chimera-users] Get angles in degree out of Rotation matrix
In-Reply-To: <4A2AB4CC01998D46807D8032B06CDBDA04D75239@EXCHANGE01.zdv.Uni-Mainz.DE>
	(stohr@uni-mainz.de)
References: <4A2AB4CC01998D46807D8032B06CDBDA04D75239@EXCHANGE01.zdv.Uni-Mainz.DE>
Message-ID: <200611202135.kAKLZP9w1723085@guanine.cgl.ucsf.edu>

Hi Michael,

  It is not very common to specify a 3-dimensional rotation in terms
of a x-axis rotation, y-axis rotation and z-axis rotation because this
decomposition depends on the order of the x, y, and z rotations.
If you rotate 90 degrees about the x-axis, then 90 about the y-axis
you get a different orientation than if you do the y-axis rotation
first followed by the x-axis rotation.

  Chimera has a routine to produce the rotation axis (a unit vector in
3-dimensions) and rotation angle about that vector corresponding to a
3x3 rotation matrix.  You could use that in Chimera with some Python code.
If you just want the rotation angle and don't need the axis then the
formula is simple

	Tr(R) = 1 + 2*cos(theta)

where
	Tr(R) = sum of rotation matrix diagonal elements

so the rotation angle

	theta = arccos((Tr(R) - 1)/2)

  Below I give the Chimera C++ code that also computes the axis.  There
are corner cases handled by this code for 0 degree and 180 degree rotations.

	Tom


void Xform::getRotation(Vector *axis, Real *angle) const
{
	Real cosTheta = (rot[0][0] + rot[1][1] + rot[2][2] - 1) / 2;
	if (fuzzyEqual(cosTheta, 1)) {
		*angle = 0;
		(*axis)[0] = (*axis)[1] = 0;
		(*axis)[2] = 1;
		return;
	}
	if (!fuzzyEqual(cosTheta, -1)) {
		*angle = degrees(acos(cosTheta));
		Real sinTheta = sqrt(1 - cosTheta * cosTheta);
		(*axis)[0] = (rot[2][1] - rot[1][2]) / 2 / sinTheta;
		(*axis)[1] = (rot[0][2] - rot[2][0]) / 2 / sinTheta;
		(*axis)[2] = (rot[1][0] - rot[0][1]) / 2 / sinTheta;
		return;
	}
	*angle = 180;
	if (rot[0][0] >= rot[1][1]) {
		if (rot[0][0] >= rot[2][2]) {
			// rot00 is maximal diagonal term
			(*axis)[0] = sqrt(rot[0][0] - rot[1][1] - rot[2][2]
					  			+ 1.0f) / 2;
			Real halfInverse = 1 / (2 * (*axis)[0]);
			(*axis)[1] = halfInverse * rot[0][1];
			(*axis)[2] = halfInverse * rot[0][2];
		} else {
			// rot22 is maximal diagonal term
			(*axis)[2] = sqrt(rot[2][2] - rot[0][0] - rot[1][1]
					  			+ 1.0f) / 2;
			Real halfInverse = 1 / (2 * (*axis)[2]);
			(*axis)[0] = halfInverse * rot[0][2];
			(*axis)[1] = halfInverse * rot[1][2];
		}
	} else {
		if (rot[1][1] >= rot[2][2]) {
			// rot11 is maximal diagonal term
			(*axis)[1] = sqrt(rot[1][1] - rot[0][0] - rot[2][2]
					  			+ 1.0f) / 2;
			Real halfInverse = 1 / (2 * (*axis)[1]);
			(*axis)[0] = halfInverse * rot[0][1];
			(*axis)[2] = halfInverse * rot[1][2];
		} else {
			// rot22 is maximal diagonal term
			(*axis)[2] = sqrt(rot[2][2] - rot[0][0] - rot[1][1]
					  			+ 1.0f) / 2;
			Real halfInverse = 1 / (2 * (*axis)[2]);
			(*axis)[0] = halfInverse * rot[0][2];
			(*axis)[1] = halfInverse * rot[1][2];
		}
	}
}


From goddard at cgl.ucsf.edu  Wed Nov 22 12:14:09 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 22 Nov 2006 12:14:09 -0800 (PST)
Subject: [Chimera-users] fitting map into map
In-Reply-To: <45519914.3090901@igbmc.u-strasbg.fr> (message from Gabor Papai
	on Wed, 08 Nov 2006 09:45:08 +0100)
References: <45504307.1090204@igbmc.u-strasbg.fr>
	<200611071722.kA7HMqrZ1894579@guanine.cgl.ucsf.edu>
	<45519914.3090901@igbmc.u-strasbg.fr>
Message-ID: <200611222014.kAMKE9a01627128@guanine.cgl.ucsf.edu>

Hi Gabor,

  I added a dialog to Chimera for fitting one density map in another density
map.  Here is the code

	https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/fitmapinmap.zip

The fitmapinmap.zip archive contains two directories FitMap and VolumeViewer
that replace those in your Chimera distribution in chimera/share.  I've
tested this code with Chimera version 1.2309 (most recent snapshot).

  Installing the above code will create a new menu entry

	Tools / Volume Data / Fit Map in Map

that shows the new dialog.  You open the two maps using Chimera menu entry
File / Open, then choose these maps in the fit map dialog and press the Fit
button.  This code does oly a local optimization so you have to position one
map at approximately the right position in the other map before you optimize.
It is very similar to the "Fit Models in Maps" tool distributed with
Chimera that fits atomic models into maps.  Use the Model Panel (menu entry
Favorites / Model Panel) to freeze (switch active button off) one map and
move the other map with the mouse.  After pressing the Fit button
the first map is rotated and shifted to increase the "overlap".
The overlap is defined as the sum over the pointwise product of the two
maps with given relative orientation.  By default the sum is carried out
over the grid points in the first map that are above the displayed contour
level.  The correlation of the two maps is the overlap divided by two
normalization factors, the squareroot of the sum of squares of map values
at the grid points for each map.  If the values of the two maps at the
grid points are represented as vectors u and v then in mathematical terms

	overlap = (u,v)
	correlation = (u,v)/|u||v|  (= cosine of angle between vectors)

where (u,v) means inner-product of vectors u,v and |u| means norm of u.
The correlation is always in the range [-1,1] while the range of overlap
values depends on the scaling of the maps.  Optimizing the overlap is not
the same as optimizing the correlation.  I may add an option in the future
to optimize correlation.

  The resulting position of one map in the other is given in the Reply Log
(menu entry Favorites / Reply Log) as a 3 by 4 matrix (3x3 rotation matrix
and the last column is a translation).  Also the size of the shift and
rotation angle is listed so you can get an idea about convergence.

  If you turn off the switch "Use only data above contour level from first
map" then the set of grid points used includes all grid points of the first
map having non-zero data values.  The contour level is ignored.  But points
with data value = 0 (probably masked out in processing the map) are not used
for the fit.

  By pressing the Correlation button (instead of the Fit) button you can
get the correlation and overlap for the current map positions without moving
either map.

  I encountered a bug in the Chimera gradient calculation code when
interpolating values near the boundary of a map.  It caused Chimera to
crash when fitting a map in an identical copy of itself.  I have fixed
this bug, but the fix is in C++ code and is not included in the above zip
archive.  I don't think you will hit this bug when fitting a map in
another map of differing size.  This fit map in map tool and the bug fix
will be in the next Chimera snapshot.

  I observed that sometimes I need to press the Fit button a second or
third time to get convergence to the best fit.  The fitting will make
at most 100 gradient descent steps, but sometimes it decides it has
converged even before then even though it is not yet at a locally optimal
solution.  The dialog does not give control over the convergence criteria
(which is the same as the Fit Models in Maps tool) although in the future
I may add access to these settings.  Set the Fit Models in Maps documentation
in the Chimera User's Guide for details on the method.

	http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodels.html

Documentation for this Fit Map in Map tool is not yet available other than
this description.

  Suggestions welcome!  I'll be off for Thanksgiving until Monday.

	Tom



From davidng at mail.nih.gov  Wed Nov 22 10:57:34 2006
From: davidng at mail.nih.gov (Ng, David (NIH/NCI) [E])
Date: Wed, 22 Nov 2006 13:57:34 -0500
Subject: [Chimera-users] question about using swapaa in Chimera
Message-ID: <5ED58A706B5CE84281BDBB960A842BCA0159B6DF@NIHCESMLBX11.nih.gov>

Hi,

 

I'm currently learning to use Chimera. I wish to look at specific amino
acid mutations in CDKN2A for effects in conformational changes and
changes in protein interactions with known partners.

 

When I type the command "swapaa P #0:24" in chimera to mutate arginine
24 to proline in CDKN2A, I get an error message that says "Value error:
No connectivity template for residue P" 

 

Can you help me with this issue? Thanks.

 

 

David Ng, M.D.

Staff Clinician

 

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From meng at cgl.ucsf.edu  Wed Nov 22 14:34:51 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 22 Nov 2006 14:34:51 -0800
Subject: [Chimera-users] question about using swapaa in Chimera
In-Reply-To: <5ED58A706B5CE84281BDBB960A842BCA0159B6DF@NIHCESMLBX11.nih.gov>
References: <5ED58A706B5CE84281BDBB960A842BCA0159B6DF@NIHCESMLBX11.nih.gov>
Message-ID: <528116DF-FAC7-4905-8845-6667E7BB0DE2@cgl.ucsf.edu>

Hi David,
The swapaa command needs the 3-letter residue name, for example

swapaa pro #0:24

It should be noted, however, that swapaa is a fairly crude way of  
looking at mutations.  It will not adjust the positions of atoms in  
other residues, and the coordinates of the one you just "swapped" are  
not necessarily reasonable.  Situations where I would use "swapaa"  
are when I plan to rotate the sidechain of the new residue myself.

In the future, we plan to have Chimera know about reasonable  
conformations of amino acid side chains (rotamers) and possibly try  
to use a conformation that does not clash with the other atoms.  For  
now, you can look at clashes with the Find Contacts/Clashes tool  
(under Tools... Structure Analysis).

Apart from Chimera, you might want to take a look at the program  
SCWRL.  I believe it is free for noncommercial use from the Dunbrack  
group:

http://dunbrack.fccc.edu/SCWRL3.php

SCWRL isn't graphical, but you could view the output in Chimera.
Elaine

On Nov 22, 2006, at 10:57 AM, Ng, David ((NIH/NCI)) [E] wrote:

> Hi,
>
>
>
> I?m currently learning to use Chimera. I wish to look at specific  
> amino acid mutations in CDKN2A for effects in conformational  
> changes and changes in protein interactions with known partners.
>
>
>
> When I type the command ?swapaa P #0:24? in chimera to mutate  
> arginine 24 to proline in CDKN2A, I get an error message that says  
> ?Value error: No connectivity template for residue P?
>
>
>
> Can you help me with this issue? Thanks.
>
>
>
>
>
> David Ng, M.D.
>
> Staff Clinician
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




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From meng at cgl.ucsf.edu  Wed Nov 22 14:49:32 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 22 Nov 2006 14:49:32 -0800
Subject: [Chimera-users] question about using swapaa in Chimera
In-Reply-To: <528116DF-FAC7-4905-8845-6667E7BB0DE2@cgl.ucsf.edu>
References: <5ED58A706B5CE84281BDBB960A842BCA0159B6DF@NIHCESMLBX11.nih.gov>
	<528116DF-FAC7-4905-8845-6667E7BB0DE2@cgl.ucsf.edu>
Message-ID: <300791B8-F1D0-4A57-A1B5-449FE791F9DA@cgl.ucsf.edu>

Hi David,
I forgot to mention that swapaa and SCWRL do not move the backbone.   
Further modeling approaches would be needed if you intend to examine  
conformational changes in the backbone.
Elaine

On Nov 22, 2006, at 2:34 PM, Elaine Meng wrote:

> Hi David,
> The swapaa command needs the 3-letter residue name, for example
>
> swapaa pro #0:24
>
> It should be noted, however, that swapaa is a fairly crude way of  
> looking at mutations.  It will not adjust the positions of atoms in  
> other residues, and the coordinates of the one you just "swapped"  
> are not necessarily reasonable.  Situations where I would use  
> "swapaa" are when I plan to rotate the sidechain of the new residue  
> myself.
>
> In the future, we plan to have Chimera know about reasonable  
> conformations of amino acid side chains (rotamers) and possibly try  
> to use a conformation that does not clash with the other atoms.   
> For now, you can look at clashes with the Find Contacts/Clashes  
> tool (under Tools... Structure Analysis).
>
> Apart from Chimera, you might want to take a look at the program  
> SCWRL.  I believe it is free for noncommercial use from the  
> Dunbrack group:
>
> http://dunbrack.fccc.edu/SCWRL3.php
>
> SCWRL isn't graphical, but you could view the output in Chimera.
> Elaine
>
> On Nov 22, 2006, at 10:57 AM, Ng, David ((NIH/NCI)) [E] wrote:
>
>> Hi,
>>
>>
>>
>> I?m currently learning to use Chimera. I wish to look at specific  
>> amino acid mutations in CDKN2A for effects in conformational  
>> changes and changes in protein interactions with known partners.
>>
>>
>>
>> When I type the command ?swapaa P #0:24? in chimera to mutate  
>> arginine 24 to proline in CDKN2A, I get an error message that says  
>> ?Value error: No connectivity template for residue P?
>>
>>
>>
>> Can you help me with this issue? Thanks.
>>
>>
>>
>>
>>
>> David Ng, M.D.
>>
>> Staff Clinician
>>
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html
>
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




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From stefano.ciurli at unibo.it  Fri Nov 24 12:05:30 2006
From: stefano.ciurli at unibo.it (Stefano Ciurli)
Date: Fri, 24 Nov 2006 21:05:30 +0100
Subject: [Chimera-users] DelPhi
Message-ID: <a0624080bc18d00bcfc2a@[192.168.1.5]>

Hello,

does anyone know how to implement the DelPhi algorithm into Chimera? 
I am using a Powerbook G4.
Thanks a lot
Stefano
-- 
____________________________________________

Stefano Ciurli
Professor of Chemistry
Laboratory of Bioinorganic Chemistry
Department of Agro-Environmental Science and Technology
University of Bologna
Viale Giuseppe Fanin, 40
I-40127 Bologna
Italy
Phone:	+39-051-209-6204
Fax: 	+39-051-209-6203

"Fatti non foste a viver come bruti,
ma per seguir virtute e canoscenza"
Dante Alighieri - Inferno - Canto XXVI

"Ihr seid bestimmt, nicht Tieren gleich zu leben,
Nein, Tugend zu erringen und Erkenntnis"
"Ye were not form'd to live the life of brutes,
But virtue to pursue and knowledge high"


From meng at cgl.ucsf.edu  Fri Nov 24 12:58:05 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 24 Nov 2006 12:58:05 -0800
Subject: [Chimera-users] DelPhi
In-Reply-To: <a0624080bc18d00bcfc2a@[192.168.1.5]>
References: <a0624080bc18d00bcfc2a@[192.168.1.5]>
Message-ID: <b63aaf07a41614237a7f8eeb4a99cbec@cgl.ucsf.edu>

Hello Stefano,
Did you already get the DelPhi program?  It is not included with 
Chimera, but is available for download (including executable for Mac) 
from the Honig lab at Columbia, see this page:

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi

Chimera can also read electrostatic potential maps from other similar 
programs (GRASP, APBS, UHBD) although I'm guessing DelPhi will be most 
convenient for you because of the Mac executable available from the 
Honig group, and the DelPhiController tool in Chimera.
Best,
Elaine

On Nov 24, 2006, at 12:05 PM, Stefano Ciurli wrote:

> Hello,
>
> does anyone know how to implement the DelPhi algorithm into Chimera?
> I am using a Powerbook G4.
> Thanks a lot
> Stefano
> -- 
> ____________________________________________
>
> Stefano Ciurli
> Professor of Chemistry
> Laboratory of Bioinorganic Chemistry
> Department of Agro-Environmental Science and Technology
> University of Bologna
> Viale Giuseppe Fanin, 40
> I-40127 Bologna
> Italy
> Phone:	+39-051-209-6204
> Fax: 	+39-051-209-6203
>
> "Fatti non foste a viver come bruti,
> ma per seguir virtute e canoscenza"
> Dante Alighieri - Inferno - Canto XXVI
>
> "Ihr seid bestimmt, nicht Tieren gleich zu leben,
> Nein, Tugend zu erringen und Erkenntnis"
> "Ye were not form'd to live the life of brutes,
> But virtue to pursue and knowledge high"
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




From meng at cgl.ucsf.edu  Fri Nov 24 14:08:00 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 24 Nov 2006 14:08:00 -0800
Subject: [Chimera-users] DelPhi
In-Reply-To: <a0624080fc18d1111d00c@[192.168.1.5]>
References: <a0624080bc18d00bcfc2a@[192.168.1.5]>
	<b63aaf07a41614237a7f8eeb4a99cbec@cgl.ucsf.edu>
	<a0624080fc18d1111d00c@[192.168.1.5]>
Message-ID: <99bbd7904f67c91f3bb4ecb36804c3d7@cgl.ucsf.edu>

Hi Stefano,
Oh I see - it appears to be a problem with the Mac DelPhi download.  I 
tried getting this myself, and could not run the executable, with this 
error message (probably the same problem you had):

meng% /Users/meng/Desktop/release1.1/exe/delphiMacOSX; exit
dyld: /Users/meng/Desktop/release1.1/exe/delphiMacOSX can't open 
library: /opt/ibmcmp/lib/libxlf90.dylib  (No such file or directory, 
errno = 2)
Trace/BPT trap
logout
[Process completed]

I'm not an expert at understanding these messages, but it looks like 
the executable is looking for some code library that is not there.

If you could run the executable successfully, the next step would be to 
put it in your "path," so that just typing the name of the executable 
in a Mac Terminal window would run the program.  That would allow 
DelPhiController to connect properly.  You would also want to download 
the DelPhi "sample data"

http://luna.bioc.columbia.edu/honiglab/software/DelPhi/data.tar.gz

which has charge and radius parameter files that can be used with the 
program. Sadly, in our current situation, we cannot use the program. I 
do not have the programming expertise to fix this library problem, but 
if any of us figures it out, we will definitely let you know.

If you do get a fix from the Honig lab, it would be great if you could 
let me (or chimera-users) know - probably several of us would like to 
use this software on a Mac.  Sorry about the trouble,
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




From agrosdidier_phd at yahoo.fr  Fri Nov 24 23:25:06 2006
From: agrosdidier_phd at yahoo.fr (Aurelien Grosdidier)
Date: Sat, 25 Nov 2006 08:25:06 +0100
Subject: [Chimera-users] DelPhi
In-Reply-To: <99bbd7904f67c91f3bb4ecb36804c3d7@cgl.ucsf.edu>
References: <a0624080bc18d00bcfc2a@[192.168.1.5]>
	<a0624080fc18d1111d00c@[192.168.1.5]>
	<99bbd7904f67c91f3bb4ecb36804c3d7@cgl.ucsf.edu>
Message-ID: <200611250825.06540.agrosdidier_phd@yahoo.fr>

On Friday 24 November 2006 23:08, Elaine Meng wrote:
> meng% /Users/meng/Desktop/release1.1/exe/delphiMacOSX; exit
> dyld: /Users/meng/Desktop/release1.1/exe/delphiMacOSX can't open
> library: /opt/ibmcmp/lib/libxlf90.dylib  (No such file or directory,
> errno = 2)
> Trace/BPT trap
> logout
> [Process completed]

Dear all,

The error message indicates that the IBM XLF compiler runtime library is not 
installed on the mac, altough required by Delphi. You can get it for free 
from the IBM website : 
http://www-1.ibm.com/support/dlsearch.wss?rs=43&lang=en&loc=en_US&r=10&cs=utf-8&rankfile=0&cc=&spc=&stc=&apar=include&q1=&dc=D400&atrn=SWPlatform&atrv=Mac+OS+X&atrn1=SWVersion&atrv1=all&Go.x=7&Go.y=17&tc=SSCVSB3 . 
If the link does not work because of the session management on ibm.com, you 
can find it indirectly from 
http://www-306.ibm.com/software/awdtools/fortran/xlfortran/support/, "View 
all downloads", the select "Mac OS X" in the "plateform/OS" scrolling list, 
the "Go", then "RTE" in "Product category", then "Go" again.

The webpage says that you need a 10.2 or 10.3 Max OS X. In fact, it runs 
pretty well on Tiger, even though it might be broken one day by OS updates.

Good luck !

Aur?lien.



From meng at cgl.ucsf.edu  Sat Nov 25 10:53:16 2006
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 25 Nov 2006 10:53:16 -0800
Subject: [Chimera-users] DelPhi
In-Reply-To: <200611250825.06540.agrosdidier_phd@yahoo.fr>
References: <a0624080bc18d00bcfc2a@[192.168.1.5]>
	<a0624080fc18d1111d00c@[192.168.1.5]>
	<99bbd7904f67c91f3bb4ecb36804c3d7@cgl.ucsf.edu>
	<200611250825.06540.agrosdidier_phd@yahoo.fr>
Message-ID: <0399ec856c83780acd10ce19f94c4b2e@cgl.ucsf.edu>

Hello,
The runtime library obtained as described below includes files with  
slightly different names than the Mac DelPhi executable requires.

The Mac delphi executable wants:
/opt/ibmcmp/lib/libxlf90.dylib (compatibility version 1.0.0, current  
version 1.0.0)
/opt/ibmcmp/lib/libxlomp_ser.dylib (compatibility version 0.0.0,  
current version 0.0.0)
  /opt/ibmcmp/lib/libxlfmath.dylib (compatibility version 1.0.0, current  
version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current  
version 71.0.0)

The runtime library downloaded as described below includes:
libxlf90.A.dylib        libxlf90_t.A.dylib
libxlf90_r.A.dylib      libxlfmath.A.dylib

Even if we assume the slight name differences are not important and  
rename the f90 and math files from the download, there does not seem to  
be any equivalent to libxlomp_ser.dylib ... and I couldn't find a  
download that includes such a file.  Suggestions welcome!  Thanks,
Elaine

On Nov 24, 2006, at 11:25 PM, Aurelien Grosdidier wrote:

> On Friday 24 November 2006 23:08, Elaine Meng wrote:
>> meng% /Users/meng/Desktop/release1.1/exe/delphiMacOSX; exit
>> dyld: /Users/meng/Desktop/release1.1/exe/delphiMacOSX can't open
>> library: /opt/ibmcmp/lib/libxlf90.dylib  (No such file or directory,
>> errno = 2)
>> Trace/BPT trap
>> logout
>> [Process completed]
>
> Dear all,
>
> The error message indicates that the IBM XLF compiler runtime library  
> is not
> installed on the mac, altough required by Delphi. You can get it for  
> free
> from the IBM website :
> http://www-1.ibm.com/support/dlsearch.wss? 
> rs=43&lang=en&loc=en_US&r=10&cs=utf 
> -8&rankfile=0&cc=&spc=&stc=&apar=include&q1=&dc=D400&atrn=SWPlatform&at 
> rv=Mac+OS+X&atrn1=SWVersion&atrv1=all&Go.x=7&Go.y=17&tc=SSCVSB3 .
> If the link does not work because of the session management on  
> ibm.com, you
> can find it indirectly from
> http://www-306.ibm.com/software/awdtools/fortran/xlfortran/support/,  
> "View
> all downloads", the select "Mac OS X" in the "plateform/OS" scrolling  
> list,
> the "Go", then "RTE" in "Product category", then "Go" again.
>
> The webpage says that you need a 10.2 or 10.3 Max OS X. In fact, it  
> runs
> pretty well on Tiger, even though it might be broken one day by OS  
> updates.
>
> Good luck !
>
> Aur?lien.
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html





From tuhin at iitk.ac.in  Mon Nov 27 06:56:50 2006
From: tuhin at iitk.ac.in (tuhin at iitk.ac.in)
Date: Mon, 27 Nov 2006 20:26:50 +0530 (IST)
Subject: [Chimera-users] Increase/decrease the sphere
Message-ID: <3050.172.28.124.123.1164639410.squirrel@newwebmail.iitk.ac.in>

Dear Chimera users,

Could anybody tell me whether there is a way in chimera to
increase/decrease the size of the spheres/ball-and-stick in atom display
(Action-->Atoms/Bonds-->sphere...). The wireframe has an option in "wire
width", is there something like that for the above two options ??

Waiting for yours suggestions.
Thanks in advance.

Best,
TKP


From papai at titus.u-strasbg.fr  Fri Nov 24 07:44:19 2006
From: papai at titus.u-strasbg.fr (Gabor Papai)
Date: Fri, 24 Nov 2006 16:44:19 +0100
Subject: [Chimera-users] fitting map into map
In-Reply-To: <200611222014.kAMKE9a01627128@guanine.cgl.ucsf.edu>
References: <45504307.1090204@igbmc.u-strasbg.fr>
	<200611071722.kA7HMqrZ1894579@guanine.cgl.ucsf.edu>
	<45519914.3090901@igbmc.u-strasbg.fr>
	<200611222014.kAMKE9a01627128@guanine.cgl.ucsf.edu>
Message-ID: <45671353.2080804@igbmc.u-strasbg.fr>

Hi Tom,

Thank you very much, it works very well!
Gabor

-- 
Gabor Papai
IGBMC
Department of Structural Biology and Genomics
1, rue Laurent Fries, BP 10142
67404 Illkirch, France
phone  +33-3-90244796
Fax +33-3-88653201
E-mail: papai at igbmc.u-strasbg.fr




From aurelien.grosdidier at gmail.com  Fri Nov 24 23:22:26 2006
From: aurelien.grosdidier at gmail.com (Aurelien Grosdidier)
Date: Sat, 25 Nov 2006 08:22:26 +0100
Subject: [Chimera-users] DelPhi
In-Reply-To: <99bbd7904f67c91f3bb4ecb36804c3d7@cgl.ucsf.edu>
References: <a0624080bc18d00bcfc2a@[192.168.1.5]>
	<a0624080fc18d1111d00c@[192.168.1.5]>
	<99bbd7904f67c91f3bb4ecb36804c3d7@cgl.ucsf.edu>
Message-ID: <200611250822.27136.aurelien.grosdidier@gmail.com>

On Friday 24 November 2006 23:08, Elaine Meng wrote:
> meng% /Users/meng/Desktop/release1.1/exe/delphiMacOSX; exit
> dyld: /Users/meng/Desktop/release1.1/exe/delphiMacOSX can't open
> library: /opt/ibmcmp/lib/libxlf90.dylib  (No such file or directory,
> errno = 2)
> Trace/BPT trap
> logout
> [Process completed]
>
> I'm not an expert at understanding these messages, but it looks like
> the executable is looking for some code library that is not there.

Dear all,

The error message indicates that the IBM XLF compiler runtime library is not 
installed on the mac, altough required by Delphi. You can get it for free 
from the IBM website : 
http://www-1.ibm.com/support/dlsearch.wss?rs=43&lang=en&loc=en_US&r=10&cs=utf-8&rankfile=0&cc=&spc=&stc=&apar=include&q1=&dc=D400&atrn=SWPlatform&atrv=Mac+OS+X&atrn1=SWVersion&atrv1=all&Go.x=7&Go.y=17&tc=SSCVSB3 . 
If the link does not work because of the session management on ibm.com, you 
can find it indirectly from 
http://www-306.ibm.com/software/awdtools/fortran/xlfortran/support/, "View 
all downloads", the select "Mac OS X" in the "plateform/OS" scrolling list, 
the "Go", then "RTE" in "Product category", then "Go" again.

The webpage says that you need a 10.2 or 10.3 Max OS X. In fact, it runs 
pretty well on Tiger, even though it might be broken one day by OS updates.

Good luck !

Aur?lien.



From pett at cgl.ucsf.edu  Mon Nov 27 11:31:20 2006
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 27 Nov 2006 11:31:20 -0800
Subject: [Chimera-users] Increase/decrease the sphere
In-Reply-To: <3050.172.28.124.123.1164639410.squirrel@newwebmail.iitk.ac.in>
References: <3050.172.28.124.123.1164639410.squirrel@newwebmail.iitk.ac.in>
Message-ID: <C71F527E-49EC-4287-95A8-C588CC3DF908@cgl.ucsf.edu>

Hi,
	Sphere size is the same as the atom's VDW radius.  You can change  
atom radii with the "vdwdefine" command, or by selecting atoms and  
bringing up the Selection Inspector (click on the button at the lower  
right of the Chimera interface) and typing a new value into the  
"radius:" field.
	Ball and stick size are controlled on a per-model basis.  Use the  
Model Panel (Favorites->Model Panel) and double-click on line with  
the model you want to control.  A dialog listing the attributes of  
that model will come up.  The "ball scale:" field controls the size  
of balls.  It is a fraction that the VDW radius is multiplied by to  
get the ball size (default: 0.25).  The "stick scale:" field controls  
stick size and also a fraction that sticks get multiplied by.  The  
default stick radius is 0.2 angstroms and default stick scale is 1.0,  
so the final default radius is 0.2 angstroms.  The help page for the  
attribute dialog describes why there are two numbers involved if you  
care, and also describes the other attributes if you're interested.

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


On Nov 27, 2006, at 6:56 AM, tuhin at iitk.ac.in wrote:

> Dear Chimera users,
>
> Could anybody tell me whether there is a way in chimera to
> increase/decrease the size of the spheres/ball-and-stick in atom  
> display
> (Action-->Atoms/Bonds-->sphere...). The wireframe has an option in  
> "wire
> width", is there something like that for the above two options ??
>
> Waiting for yours suggestions.
> Thanks in advance.
>
> Best,
> TKP
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From goddard at cgl.ucsf.edu  Mon Nov 27 14:38:31 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 27 Nov 2006 14:38:31 -0800 (PST)
Subject: [Chimera-users] Get angles in degree out of Rotation matrix
In-Reply-To: <4A2AB4CC01998D46807D8032B06CDBDA050A6D0C@EXCHANGE01.zdv.Uni-Mainz.DE>
	(stohr@uni-mainz.de)
References: <4A2AB4CC01998D46807D8032B06CDBDA050A6D0C@EXCHANGE01.zdv.Uni-Mainz.DE>
Message-ID: <200611272238.kARMcV9r1816465@guanine.cgl.ucsf.edu>


Hi Michael,

  Perhaps you can compare the orientation between the exact symmetric
placement of a chain and the actual position by measuring the
translation and rotation angle needed to align the two.  By rotation
angle I mean that any rotation can be represented as a rotation about
a single axis (which depends on the rotation).  I do not understand
what you mean by rotation angles about x, y and z axes.  As I
mentioned that depends on the order of the rotations and therefore is
rarely used.  In the Chimera match command or matchmaker tool the
optimal rotation matrix is computed -- it is *not* decomposed into
separate x, y and z rotations during that calculation.  I suppose if
your system has symmetry about the z axis you could ask what rotation
about z best aligns a chain with the exact symmetric chain location.
In other words, only a z-axis rotation rather then rotation about an
arbitrary axis would be allowed.  Chimera does not have code for that
and I have never heard that number reported.

  If you spell out precisely what angle is needed I can give better
advice on how to get it from Chimera.

	Tom


> From: "Stohr, Michael" <stohr at uni-mainz.de>
> To: "Thomas Goddard" <goddard at cgl.ucsf.edu>
> Date: Mon, 27 Nov 2006 09:51:31 +0100
> Subject: AW: Get angles in degree out of Rotation matrix
> 
> Hi Tom,
> 
> Thanks a lot for your description. It does not fit completely my demand. I will rephrase my question, is there a simple way to determine the three angles between the two 3d-structures of two identical chains? The background is that my molecule is not absolutely symmetrical and I want to quantify the asymmetry. So, I want to be able to say, this angle between this two chains differs from ideal symmetry angle by X degrees for different directions (x, y, z). I thought the rotation matrix would be the way to do so, but it does not seem so. I've found a not very precise method by using the distance tool and trigonometric functions. Therefore, if there is no answer for my question it will be ok at first especially I have to finish my theses very soon. By the way, in which order does for example the tool match or matchmaker rotates a structure or is this not predictable?
> 
> Thanks for your afford,
> Michael


From palat at fzu.cz  Tue Nov 28 01:08:51 2006
From: palat at fzu.cz (Lukas Palatinus)
Date: Tue, 28 Nov 2006 10:08:51 +0100
Subject: [Chimera-users] Control of the volume viewer from the command line
Message-ID: <51A93DC0-89B8-458F-BEE8-6D5F2C90CD9E@fzu.cz>

Hello all,
I am trying to make a movie showing an evolution of an electron  
density map during an iterative optimization. For each optimization  
step I have one density map as volume data in xplor format. I depict  
the maps using the volume viewer, where I can set the number and  
level of the isosurface thresholds as well as their color. However,  
each newly opened map opens with default threshold setting, which is  
not suitable for my purposes. I make the movie using a command file  
of the type:

open density1.xplor
movie record
wait 10
movie stop
close 0
open density2.xplor
movie record
wait 10
movie stop
...

I would need to be able to control the properties of the isosurfaces  
of the newly opened map from the command line or from the script  
file, or find a way to preserve the properties set for the first map  
in all subsequently opened maps. The search in Chimera manual did not  
lead me anywhere. Could anyone give me a hint how to proceed?

With best regards

Lukas


Lukas Palatinus
Laboratoire de Cristallographie
EPFL Lausanne
Tel.: +41 (0)21 693 0639
mailto: palat at fzu.cz



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From anna.feldman-salit at eml-r.villa-bosch.de  Tue Nov 28 03:19:17 2006
From: anna.feldman-salit at eml-r.villa-bosch.de (Anna Feldman-Salit)
Date: Tue, 28 Nov 2006 12:19:17 +0100
Subject: [Chimera-users] Stereo on the 1.2304 version
Message-ID: <456C1B35.2000507@eml-r.villa-bosch.de>

Hello,

Unfortunately, I'm facing with a problem of stereo option on the version 
1.2304.

I can see the stereo when I turn the "stereo" option on, but the quality 
of the picture is not of the best ones.
The main picture is likely screened on background, while it's also 
impossible to focus on the frontal part. I was playing a bit with 
camera-viewing parameters, but nothing worked for me.
Before, working with pymol I used the "swap sides" option, which helped 
a lot.
I tested our stereo glasses with pymol's stereo option again and it 
works smoothly.

Since I definitely prefer to work with chimera, I would appreciate if 
this problem would be solved somehow.
Do you have any suggestions?

Thank you in advance!

Best,

Anna


From goddard at cgl.ucsf.edu  Tue Nov 28 10:45:08 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 28 Nov 2006 10:45:08 -0800 (PST)
Subject: [Chimera-users] Control of the volume viewer from the command
	line
In-Reply-To: <51A93DC0-89B8-458F-BEE8-6D5F2C90CD9E@fzu.cz> (message from Lukas
	Palatinus on Tue, 28 Nov 2006 10:08:51 +0100)
References: <51A93DC0-89B8-458F-BEE8-6D5F2C90CD9E@fzu.cz>
Message-ID: <200611281845.kASIj8Ne1590624@guanine.cgl.ucsf.edu>

Hi Lukas,

  There is no Chimera command to set the volume contour surface threshold
or color.  We plan on adding this command.

  For now, I have four suggestions.  You can use "Volume Series" tool
available on the Chimera Experimental Features web page:

	http://www.cgl.ucsf.edu/chimera/experimental/experimental.html

This page contains plugins that are not yet distributed with Chimera.
You download a zip file and put the new directory in with your existing
Chimera to use it.  The Volume Series tool lets you play a series of
volume data sets perserving thershold level and color settings just as
you want:

	http://www.cgl.ucsf.edu/chimera/experimental/volume_series/volume_series.html

There is no Chimera command for this tool either so to make a movie you
would start Movie recorder (menu entry Tools / Utilities / Movie Recorder
or use Chimera movie command) then press the Play button on the volume series
dialog.

  A second approach is to use the EMANimator animation tool

	http://www.cgl.ucsf.edu/chimera/related/emanimator/emanimator.html

It is a Chimera extension included with the EMAN single particle reconstruction
package.  It provides a time-line user interface for composing animations
and has a specific capability for playing a sequence of volume data sets
just as you want.

  A third approach is to use some Python code in Chimera to script your
movie.  This is a bit more complicated than using just Chimera commands.
But you can easily use all Chimera commands in a Python script and you
additionally can control all of the volume settings.  I include an example
at the bottom of this email.  You simply open the Python file to run the
script.

  A fourth approach is to get the Animation Commands package

	http://www.cgl.ucsf.edu/chimera/experimental/transition/transition.html

from the Chimera experimental features page.  It includes a command
to change the contour level of a volume map from one value to another over
a set number of frames.  You could use it to set the contour level.  But
there is not a command in this package to set the volume color.

	Tom


------------
Example seriesmovie.py Python script follows.  Tested in Chimera 1.2309.

directory = '/usr/local/src/chimera-demos/volume/dna_blur' # Volume file location
files = ['1enn_00.mrc', '1enn_05.nc', '1enn_10.nc', '1enn_15.nc', '1enn_20.nc',
          '1enn_25.nc', '1enn_30.nc', '1enn_35.nc', '1enn_40.nc',
          '1enn_45.nc', '1enn_50.nc']
movie_path = '/usr/local/src/staff/goddard/1enn.mov'
threshold = 0.12
color = (.5, .7, 0)     # red, green, blue
delay = 10              # movie frames per volume

def set_volume_threshold_and_color(threshold, rgb):
    import VolumeViewer
    d = VolumeViewer.volume_dialog()
    r = d.focus_region
    r.set_parameters(surface_levels = [threshold],      # Set threshold level.
                     surface_colors = [color])  # Set color rgb or rgba.
    d.show_region(r, 'surface')


from chimera import runCommand
runCommand('cd %s' % directory)
runCommand('movie record')
for filename in files:
    runCommand('open %s' % filename)
    set_volume_threshold_and_color(threshold, color)
    runCommand('wait %d' % delay)
    runCommand('close #0')
runCommand('movie stop')
runCommand('movie encode mformat mov output %s' % movie_path)


From bd92 at mail.gatech.edu  Tue Nov 28 11:05:55 2006
From: bd92 at mail.gatech.edu (Batsal Devkota)
Date: Tue, 28 Nov 2006 14:05:55 -0500
Subject: [Chimera-users] Multiple Volume Viewer Windows and saving PDB file
Message-ID: <D329EB63-C815-46EB-B92C-AB66992D0D99@mail.gatech.edu>

Hi,

I am just wondering if there is any way that I can have two or more  
volume viewer windows open at the same time. I am comparing two  
density maps and to be able to change the threshold and color for  
both maps, without having to go back and forth in the same window,  
would be much easier and useful.

Also, I recently fitted a pdb crystal structure into a density map  
but was not able to save it with relation to the density map (the  
feature which was available in previous releases). However, if I have  
multiple pdb files open then I can save the pdb file of my interest  
with respect to the map. Is there anyway to save a fitted pdb file  
with respect to a density map without opening other pdb files?

Thank you,

Batsal.
--------------------------------------------------
Batsal Devkota
Graduate Student, School of Biology
GeorgiaInstitute
  ofTechnology
Atlanta, GA   30332-0400



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From pett at cgl.ucsf.edu  Tue Nov 28 11:49:36 2006
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 28 Nov 2006 11:49:36 -0800
Subject: [Chimera-users] Increase/decrease the sphere
In-Reply-To: <33262.172.28.124.123.1164691299.squirrel@newwebmail.iitk.ac.in>
References: <3050.172.28.124.123.1164639410.squirrel@newwebmail.iitk.ac.in>
	<C71F527E-49EC-4287-95A8-C588CC3DF908@cgl.ucsf.edu>
	<33262.172.28.124.123.1164691299.squirrel@newwebmail.iitk.ac.in>
Message-ID: <CBD60F40-4CF0-4DEF-9E81-F2F6116A1229@cgl.ucsf.edu>

I forgot to mention that if you want to control ball/stick size on a  
more permanent basis, you can use the New Molecule preferences  
(Favorites->Preferences) to set them for all new molecules you open.

--Eric

On Nov 27, 2006, at 9:21 PM, tuhin at iitk.ac.in wrote:

> Thanks for your helpful suggestion, Eric.
>
> Regards,
> TKP
>
>> Hi,
>> 	Sphere size is the same as the atom's VDW radius.  You can change
>> atom radii with the "vdwdefine" command, or by selecting atoms and
>> bringing up the Selection Inspector (click on the button at the lower
>> right of the Chimera interface) and typing a new value into the
>> "radius:" field.
>> 	Ball and stick size are controlled on a per-model basis.  Use the
>> Model Panel (Favorites->Model Panel) and double-click on line with
>> the model you want to control.  A dialog listing the attributes of
>> that model will come up.  The "ball scale:" field controls the size
>> of balls.  It is a fraction that the VDW radius is multiplied by to
>> get the ball size (default: 0.25).  The "stick scale:" field controls
>> stick size and also a fraction that sticks get multiplied by.  The
>> default stick radius is 0.2 angstroms and default stick scale is 1.0,
>> so the final default radius is 0.2 angstroms.  The help page for the
>> attribute dialog describes why there are two numbers involved if you
>> care, and also describes the other attributes if you're interested.
>>
>> --Eric
>>                          Eric Pettersen
>>                          UCSF Computer Graphics Lab
>>                          pett at cgl.ucsf.edu
>>                          http://www.cgl.ucsf.edu
>>
>>
>> On Nov 27, 2006, at 6:56 AM, tuhin at iitk.ac.in wrote:
>>
>>> Dear Chimera users,
>>>
>>> Could anybody tell me whether there is a way in chimera to
>>> increase/decrease the size of the spheres/ball-and-stick in atom
>>> display
>>> (Action-->Atoms/Bonds-->sphere...). The wireframe has an option in
>>> "wire
>>> width", is there something like that for the above two options ??
>>>
>>> Waiting for yours suggestions.
>>> Thanks in advance.
>>>
>>> Best,
>>> TKP
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>



From goddard at cgl.ucsf.edu  Tue Nov 28 12:04:20 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Tue, 28 Nov 2006 12:04:20 -0800 (PST)
Subject: [Chimera-users] Multiple Volume Viewer Windows and saving PDB
	file
In-Reply-To: <D329EB63-C815-46EB-B92C-AB66992D0D99@mail.gatech.edu> (message
	from Batsal Devkota on Tue, 28 Nov 2006 14:05:55 -0500)
References: <D329EB63-C815-46EB-B92C-AB66992D0D99@mail.gatech.edu>
Message-ID: <200611282004.kASK4KS41883848@guanine.cgl.ucsf.edu>

Hi Batsal,

  It isn't possible to have more than one volume viewer dialog.  I
agree this would be very helpful and I've added it to my list of
projects.  There is a problem that some Chimera tools like volume
eraser or volume path tracer act on the volume shown in the unique
volume viewer dialog.  Also I'll have to think about the user
interface details of creating, hiding, and removing extra volume
viewer dialogs.

  For now one small aid to working with multiple volume data sets is
to use the volume dialog Features / Data Set List menu entry.  This
shows a list of the volume data sets and you can click on list entries
to switch between them rather than using the more cumbersome menu of
data sets.  If this is frequently useful you can use Features / Save
Default Dialog Settings so the data set list is shown by default.

  There is a bug in Chimera version 1.2304 when using menu entry File /
Save PDB....  If you have one PDB model and a map open it does not offer
you a choice of saving the PDB coordinates relative to the map.  This
is fixed in Chimera snapshot version 1.2309.  You can work around the
problem in 1.2304 by opening two PDB models.  Then Chimera will give you
the choice to save coordinates relative to the map.  The second PDB model
can be anything (another copy of the first model) and does not need to
be saved.  That's inconvenient and I recommend using Chimera 1.2309 instead.

	Tom



From gregc at cgl.ucsf.edu  Tue Nov 28 12:16:32 2006
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Tue, 28 Nov 2006 12:16:32 -0800 (PST)
Subject: [Chimera-users] Stereo on the 1.2304 version
In-Reply-To: <456C1B35.2000507@eml-r.villa-bosch.de>
References: <456C1B35.2000507@eml-r.villa-bosch.de>
Message-ID: <Pine.OSF.4.63.0611281131260.1592450@guanine.cgl.ucsf.edu>

On Tue, 28 Nov 2006, Anna Feldman-Salit wrote:

> Hello,
>
> Unfortunately, I'm facing with a problem of stereo option on the version
> 1.2304.
>
> I can see the stereo when I turn the "stereo" option on, but the quality 
> of the picture is not of the best ones. The main picture is likely 
> screened on background, while it's also impossible to focus on the 
> frontal part. I was playing a bit with camera-viewing parameters, but 
> nothing worked for me. Before, working with pymol I used the "swap 
> sides" option, which helped a lot. I tested our stereo glasses with 
> pymol's stereo option again and it works smoothly.
>
> Since I definitely prefer to work with chimera, I would appreciate if 
> this problem would be solved somehow. Do you have any suggestions?
>
> Thank you in advance!
>
> Best,
>
> Anna

If you need a "swap eyes" option with PyMol, then you need the same option 
in chimera, but it doesn't exist.  Instead, chimera expects that you to 
configure the stereo graphics driver to do that for all applications. 
For instance, the Windows NVidia Quadro graphics driver has an option to 
"Swap eyes" that is off by default -- it's hard to find, show the 
"Performance & Quality Settings" panel for your graphics card (in the 
Display Properties / Settings / Advanced dialog), and change to the 
"Advanced settings" view, and scroll down to the "Swap Eyes" option.

Right now, the best way to adjust the viewing parameters is to use the 
"View All" button in the Sideview or Actions/Focus on a selection, that 
centers stuff so that the center is on the plane of the screen.  Then 
scale everything up as much as you want.  Since, in stereo, many people 
have problems converging on stuff in front of the screen, you might need 
to translate everything back (ie., +z axis) a little bit.  You should also 
look at 
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-May/000779.html> for 
programming ways to change the stereo viewing parameters.

Adjusting the chimera viewing parameters will become easier in the next 
release.  I've added an advanced mode to the Sideview that converts it to 
a top view so you can see the stereo eyes in relationship to the screen. 
And the plane of the screen, shown as a dotted line, can be moved.  You 
will also be able to change the eye separation and distance to the screen 
with the mouse.

 	Hope this helps,

 	Greg Couch
 	UCSF Computer Graphics Lab


From cathy.lawson at rutgers.edu  Tue Nov 28 14:52:04 2006
From: cathy.lawson at rutgers.edu (Catherine Lawson)
Date: Tue, 28 Nov 2006 17:52:04 -0500
Subject: [Chimera-users] where is the chimera directory on my imac?
In-Reply-To: <200611282004.kASK4KS41883848@guanine.cgl.ucsf.edu>
References: <D329EB63-C815-46EB-B92C-AB66992D0D99@mail.gatech.edu>
	<200611282004.kASK4KS41883848@guanine.cgl.ucsf.edu>
Message-ID: <7831B0D5-3014-4487-9436-49416B079059@rutgers.edu>


Dear Chimera Folks,

I am familiar with adding experimental features to Chimera  
installations on linux and pc.  I'd like to do the same for the  
working installation of Chimera on my new intel dual-core iMac, but I  
cannot find the share folder that I should put them into.

I'm using UCSF Chimera beta version 1 build 2309 (2006/11/08),  
platform: darwin, windowing system:X11.  After I installed the  
software following instructions I moved the icon that was on the  
desktop to the applications folder, as suggested.  When I use the  
finder search I cannot find any folders named chimera or chimera.app.
Yet they must be there somewhere!  But where?

thanks in advance for your help...

Cathy




From jeramia at mac.com  Tue Nov 28 14:56:56 2006
From: jeramia at mac.com (Jeramia Ory)
Date: Tue, 28 Nov 2006 17:56:56 -0500
Subject: [Chimera-users] where is the chimera directory on my imac?
In-Reply-To: <7831B0D5-3014-4487-9436-49416B079059@rutgers.edu>
References: <D329EB63-C815-46EB-B92C-AB66992D0D99@mail.gatech.edu>
	<200611282004.kASK4KS41883848@guanine.cgl.ucsf.edu>
	<7831B0D5-3014-4487-9436-49416B079059@rutgers.edu>
Message-ID: <93FFFECA-2CCA-47F7-8EBE-01C1F1029DBB@mac.com>

Hi Cathy,

In the Finder, right click on the Chimera icon, and choose "Show  
Package Contents," and navigate from there.

Applications in Mac OS X are actually folders called foo.app, you can  
accomplish the same thing in the command line by changing to the / 
Applications/Chimera.app/ directory

Ciao,
Jeramia

On Nov 28, 2006, at 5:52 PM, Catherine Lawson wrote:

>
> Dear Chimera Folks,
>
> I am familiar with adding experimental features to Chimera
> installations on linux and pc.  I'd like to do the same for the
> working installation of Chimera on my new intel dual-core iMac, but I
> cannot find the share folder that I should put them into.
>
> I'm using UCSF Chimera beta version 1 build 2309 (2006/11/08),
> platform: darwin, windowing system:X11.  After I installed the
> software following instructions I moved the icon that was on the
> desktop to the applications folder, as suggested.  When I use the
> finder search I cannot find any folders named chimera or chimera.app.
> Yet they must be there somewhere!  But where?
>
> thanks in advance for your help...
>
> Cathy
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users



From goddard at cgl.ucsf.edu  Wed Nov 29 15:32:47 2006
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 29 Nov 2006 15:32:47 -0800 (PST)
Subject: [Chimera-users] Chimera on x86_64?
In-Reply-To: <21f899e18ce4443c959c40988dc5d7cd@salilab.org> (message from Ben
	Webb on Wed, 29 Nov 2006 12:51:27 -0800)
References: <21f899e18ce4443c959c40988dc5d7cd@salilab.org>
Message-ID: <200611292332.kATNWl4C1584362@guanine.cgl.ucsf.edu>

Hi Ben,

  There's no technical obstacle to us making regular 64-bit linux Chimera
distributions.  The only issue is having time to do it.

  The work involves compiling the ~30 third party libraries that
Chimera uses.  I did this is the past and it took about one day of
fiddling.  Our Chimera build scripts compile all of the third party
libraries automatically and my past hand fiddling to build on 64-bit
linux would have to be put into our scripts.  That could take a 1 to 5
days of work.  We have a 64-bit linux machine to do the work on.

  So it all comes down to when one of the 4 developers (Tom Goddard,
Eric Pettersen, Greg Couch, or Conrad Huang) has time to work on that.
I don't think I will have time until January at the earliest.

  Could you give me a better sense of how much need there is in the
Sali lab?  Are you really saying you would not install 32-bit Linux
system libraries except for Chimera?  I would think there are a fair
number of applications out there with binary distributions only for
32-bit.  The other problem you point out is that 32-bit Chimera Python
cannot use your own 64-bit Python modules.  Are you using additional
C Python modules within Chimera that do not come with Chimera?  That
is interesting -- what are they?

	Tom



> From: Ben Webb <ben at salilab.org>
> To: Eric Pettersen <pett at cgl.ucsf.edu>
> Date: Wed, 29 Nov 2006 12:51:27 -0800
> Subject: Chimera on x86_64?
> 
> I wonder if you could give me a rough idea of when you plan to make 
> regular builds of Chimera on x86_64 (if at all)? All I've been able to 
> glean from the download page and the mailing list archive is that you 
> do make occasional builds, but recommend the 32-bit version.
> 
> Memory isn't so much of an issue for us in particular (although we are 
> increasingly looking at large EM maps) but the requirement to have 
> 32-bit libraries is starting to become a problem. All of our new 
> desktops are x86_64 machines, and it's a pain to require the 32-bit 
> libraries just for Chimera. Additionally, our users want to 
> mix-and-match Python modules (including Modeller, of course) and 
> Chimera is unable to import any module which has a C backend, since 
> they're compiled for x86_64 and the Python interpreter in Chimera is 
> 32-bit. (Of course, we could recompile all of our other Python modules 
> for 32-bit, but that would cause problems with x86_64 apps.)
> 
> If you need people to test x86_64 Chimera builds, we certainly have 
> some demanding users here to break them. ;)
> 
> 	Ben
> -- 
> ben at salilab.org                      http://salilab.org/~ben/
> "It is a capital mistake to theorize before one has data."
> 	- Sir Arthur Conan Doyle


From ben at salilab.org  Wed Nov 29 16:44:56 2006
From: ben at salilab.org (Ben Webb)
Date: Wed, 29 Nov 2006 16:44:56 -0800
Subject: [Chimera-users] Chimera on x86_64?
In-Reply-To: <200611292332.kATNWl4C1584362@guanine.cgl.ucsf.edu>
References: <21f899e18ce4443c959c40988dc5d7cd@salilab.org>
	<200611292332.kATNWl4C1584362@guanine.cgl.ucsf.edu>
Message-ID: <456E2988.2090402@salilab.org>

Thomas Goddard wrote:
>   There's no technical obstacle to us making regular 64-bit linux Chimera
> distributions.  The only issue is having time to do it.
...
>   Could you give me a better sense of how much need there is in the
> Sali lab?  Are you really saying you would not install 32-bit Linux
> system libraries except for Chimera?  I would think there are a fair
> number of applications out there with binary distributions only for
> 32-bit.

Yes, of course there are a handful of other applications (mostly ancient 
and unsupported codes) which require a 32-bit glibc. But it's really 
only Chimera which needs all of the X libraries etc. to get pulled in.

> The other problem you point out is that 32-bit Chimera Python
> cannot use your own 64-bit Python modules.  Are you using additional
> C Python modules within Chimera that do not come with Chimera?  That
> is interesting -- what are they?

We've already discussed using our MODELLER package in combination with 
Chimera. The next public release of MODELLER will primarily be made 
available as a Python module, and we are exploring the options for using 
this directly with Chimera (rather than having it generate input files 
and run a subprocess). This works just fine for 32-bit, but not for 
x86_64 unless we build Modeller as a 32-bit application. Given the large 
performance boost we've seen for our x86_64 builds vs. i386, we are 
rather reluctant to do that.

	Ben
-- 
ben at salilab.org                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle