[PyMOL] PyMOL 1.2r1 error report

2009-07-16 Thread Stuart Ballard
Hello all, Warren,


With the new PyMOL version, myself and others at the lab have found an issue
with ray tracing of mesh representations causing memory utilization errors.

With parameters identical to those used in previous versions of PyMOL, 1.2r1
has crashed when ray tracing isomesh generated isosurface meshes. A memory
allocation error is given, but a lack of memory does not appear to be the
real issue, as PyMOL crashes long before all RAM is consumed, and the same
error is given when we attempt to run this process on a machine with 12GB of
RAM.

There have also been a few minor issues with the fetch command. Namely,
we've seen intermitent inexplicable failure of the fetch command, while
simultaneously using it in another version of PyMOL with no issue.

Also, some older scripts now need more specific import statements to utilize
certain build-in PyMOL functionality. For example, I did not need to state
from pymol import selector to use the selector.process() function in other
versions of PyMOL, but this is not the case with the new version. Does this
reflect changes in the cmd API setup?


Regards,
Stuart Ballard





 --

 Message: 1
 Date: Thu, 9 Jul 2009 13:34:53 -0700
 From: Warren DeLano war...@delsci.com
 Subject: [PyMOL] PyMOL 1.2r1 Released
 To: pymol-users@lists.sourceforge.net
 Message-ID:
896b75251ba19745a529b1b867893fa50eb...@planet.delsci.local
 Content-Type: text/plain; charset=us-ascii

 Greetings,



 Mac, Windows, and Linux builds for 1.2r1 were posted early this morning.
 Current subscribers can download them via



 Direct download: http://delsci.com/ip/12  or via online docs:
 http://delsci.info/dsc/ip



 As usual, I recommend caution with upgrading.  Please don't upgrade
 right before a major talk or presentation, unless you have time to test
 everything thoroughly beforehand.  There were many last-minute changes
 made after the last beta, so some glitches are to be expected.



 Please try loading your important PyMOL session and show files into the
 new version and report any serious problems.  At least one additional
 revision of the 1.2 release is anticipated before the end of the summer.



 Enabling information about the new capabilities of 1.2 will be
 forthcoming over the next month, and will likely consist of a series of
 screencast demonstrations and tutorials.  There is a lot of new stuff to
 communicate!



 Cheers,

 Warren





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Re: [PyMOL] PyMOL 1.2r1 error report

2009-07-16 Thread Warren DeLano
Stuart,

 

Thank you for the reports, and sorry to hear you're having trouble.
Please allow me to draw your attention to the Bug Reporter link on the
PyMOL main page (www.pymol.org http://www.pymol.org/ ).  The direct
link is:

 

http://sourceforge.net/tracker/?atid=104546group_id=4546func=browse

 

One advantage of using the bug reporter system is that you can submit
accompanying script or data files which reproduce the problem.  

 

With respect to meshes, rendering of meshes is not generally broken in
1.2r1, so there must be something specific about your input which is
triggering the crash.  We may need an example file, or at least a PDB
code with associated commands, to reproduce the problem.  Likewise,
fetch is known not to be generally broken, so we may need more
information about reproducing the problem.

 

[For what it's worth, I just confirmed that:

 

fetch 1fjf, async=0

 

show mesh

 

ray

 

runs fine with 1.2r1].

 

As for selector, it is not a supported part of the supported Python
cmd API, but rather, an internal module.  In other words, you should
not ever need to be importing it.  Operationally speaking, the Python
cmd. api is defined by the file modules/pymol/api.py, and virtually
all public symbols should be accessed as methods or submethods of this
module.

 

Cheers,

Warren

 



From: Stuart Ballard [mailto:srball...@wisc.edu] 
Sent: Thursday, July 16, 2009 2:14 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] PyMOL 1.2r1 error report

 

Hello all, Warren,


With the new PyMOL version, myself and others at the lab have found an
issue with ray tracing of mesh representations causing memory
utilization errors.

With parameters identical to those used in previous versions of PyMOL,
1.2r1 has crashed when ray tracing isomesh generated isosurface meshes.
A memory allocation error is given, but a lack of memory does not appear
to be the real issue, as PyMOL crashes long before all RAM is consumed,
and the same error is given when we attempt to run this process on a
machine with 12GB of RAM.

There have also been a few minor issues with the fetch command. Namely,
we've seen intermitent inexplicable failure of the fetch command, while
simultaneously using it in another version of PyMOL with no issue.

Also, some older scripts now need more specific import statements to
utilize certain build-in PyMOL functionality. For example, I did not
need to state from pymol import selector to use the selector.process()
function in other versions of PyMOL, but this is not the case with the
new version. Does this reflect changes in the cmd API setup?


Regards,
Stuart Ballard

 





--

Message: 1
Date: Thu, 9 Jul 2009 13:34:53 -0700
From: Warren DeLano war...@delsci.com
Subject: [PyMOL] PyMOL 1.2r1 Released
To: pymol-users@lists.sourceforge.net
Message-ID:

896b75251ba19745a529b1b867893fa50eb...@planet.delsci.local
Content-Type: text/plain; charset=us-ascii

Greetings,



Mac, Windows, and Linux builds for 1.2r1 were posted early this
morning.
Current subscribers can download them via



Direct download: http://delsci.com/ip/12  or via online docs:
http://delsci.info/dsc/ip



As usual, I recommend caution with upgrading.  Please don't
upgrade
right before a major talk or presentation, unless you have time
to test
everything thoroughly beforehand.  There were many last-minute
changes
made after the last beta, so some glitches are to be expected.



Please try loading your important PyMOL session and show files
into the
new version and report any serious problems.  At least one
additional
revision of the 1.2 release is anticipated before the end of the
summer.



Enabling information about the new capabilities of 1.2 will be
forthcoming over the next month, and will likely consist of a
series of
screencast demonstrations and tutorials.  There is a lot of new
stuff to
communicate!



Cheers,

Warren





 

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Info Page: 

[PyMOL] 3D visualization and Samsung SyncMaster 2233RZ/Nvidia GeForce 3D Vision Kit

2009-07-16 Thread Valentina Corradi
Dear PyMOL users,

my research group is interested in using 3D stereo visualization with PyMOL.
We have a Windows Vista/Linux (Fedora 11) 64 bit system, with Nvidia GeForce
GTX 295 Graphic card and Nvidia GeForce 3D Vision Kit (Samsung SyncMaster
2233RZ 120Hz monitor).

Dr. Delano's post, dated June 22 (
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07014.html),
says that only Zalman monitor can be used with PyMOL for 3D stereo
visualization.

I installed the latest Nvidia 3D Vision drivers (released on June 22)
officially supporting our monitor and I read on PyMOL home page that on June
30, PyMOL 1.2r0 version supports stereo 3D for Samsung display.
I am wondering if now it is possible to use this PyMOL version or the latest
one (1.2r1) for 3D stereo visualization together with the OS and Nvidia kit
we have.

Thank you in advance for your help,

Valentina Corradi,
University of Calgary
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[PyMOL] 3D visualization and Samsung SyncMaster 2233RZ/Nvidia GeForce 3D Vision Kit

2009-07-16 Thread Valentina Corradi
Dear PyMOL users,

my research group is interested in using 3D stereo visualization with PyMOL.
We have a Windows Vista/Linux (Fedora 11) 64 bit system, with Nvidia GeForce
GTX 295 Graphic card and Nvidia GeForce 3D Vision Kit (Samsung SyncMaster
2233RZ 120Hz monitor).

Dr. Delano's post, dated June 22 (
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07014.html),
says that only Zalman monitor can be used with PyMOL for 3D stereo
visualization.

I installed the latest Nvidia 3D Vision drivers (released on June 22)
officially supporting our monitor and I read on PyMOL home page that on June
30, PyMOL 1.2r0 version supports stereo 3D for Samsung display.
I am wondering if now it is possible to use this PyMOL version or the latest
one (1.2r1) for 3D stereo visualization together with the OS and Nvidia kit
we have.

Thank you in advance for your help,

Valentina Corradi,
University of Calgary
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This is your chance to win up to $100,000 in prizes! For a limited time, 
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[PyMOL] Color By RMSD -- New Script

2009-07-16 Thread Shiven Shandilya
Hello List,

A new PyMol script for coloring two objects by mutual RMS Deviation is
now available on the PyMol wiki:

http://pymolwiki.org/index.php/ColorByRMSD

Hope some of you will find it useful...

Many thanks to Jason Vertrees for help with turning the initial
proof-of-principle into useful code!!

Best,
Shiven



Shivender Shandilya,
Graduate Student,
Schiffer Lab,
Dept. of Biochemistry  Molecular Pharmacology,
University of Massachusetts Medical School,
Worcester, MA 01604.

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Re: [PyMOL] 3D visualization and Samsung SyncMaster 2233RZ/Nvidia GeForce 3D Vision Kit

2009-07-16 Thread Warren DeLano
Valentina,

 

PyMOL has been known to work great with the Samsung 2233rz for quite
some time, but nVidia had not publicly released any of the required
190-series drivers until today.  

 

Note that, officially speaking, you will need a Quadro graphics card in
order to do OpenGL-based stereo 3D.  nVidia does not support OpenGL
stereo 3D on GeForce cards, and the required control panel options for
configuring OpenGL stereo 3D will be absent.

 

More details about today's release will be posted soon...

 

Cheers,

Warren

 



From: Valentina Corradi [mailto:valentina.corr...@gmail.com] 
Sent: Thursday, July 16, 2009 4:25 PM
To: pymol-users@lists.sourceforge.net
Subject: 3D visualization and Samsung SyncMaster 2233RZ/Nvidia GeForce
3D Vision Kit

 

Dear PyMOL users,

my research group is interested in using 3D stereo visualization with
PyMOL.
We have a Windows Vista/Linux (Fedora 11) 64 bit system, with Nvidia
GeForce GTX 295 Graphic card and Nvidia GeForce 3D Vision Kit (Samsung
SyncMaster 2233RZ 120Hz monitor).

Dr. Delano's post, dated June 22 (
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07014.h
tml ), says that only Zalman monitor can be used with PyMOL for 3D
stereo visualization.

I installed the latest Nvidia 3D Vision drivers (released on June 22)
officially supporting our monitor and I read on PyMOL home page that on
June 30, PyMOL 1.2r0 version supports stereo 3D for Samsung display.
I am wondering if now it is possible to use this PyMOL version or the
latest one (1.2r1) for 3D stereo visualization together with the OS and
Nvidia kit we have.

Thank you in advance for your help,

Valentina Corradi,
University of Calgary

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[PyMOL] Here at last: PyMOL in Stereo 3D on 120 Hz LCDs (Vista info)!

2009-07-16 Thread Warren DeLano
Today nVidia issued their first public beta release of their 190-series
driver.  Although this release is officially for GeForce hardware, it
seems to work fine for Quadro cards as well.  So, if you have the
following hardware setup, then you can at last now use PyMOL in Stereo
3D at full 1680x1050 resolution on a 120 Hz LCD.  Here is what you need:

 

- A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm

 

- A recent Quadro series graphics card such as an FX 380 or 570.

 

- A GeForce 3D Vision hardware kit (an emitter with 3D shutter glasses).

 

- Windows Vista 32 bit or 64 bit

 

- The driver download (warning ~230 MB ZIP file):

 

http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.htm
l
http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.ht
ml 

 

I personally confirmed today that this download enables PyMOL to run in
Stereo 3D on a 2233RZ with a Quadro 570 graphics card and GeForce 3D
Vision hardware under Windows Vista 32 bit.  Instructions:

 

1. Uninstall the existing display drivers, disconnect the USB emitter,
and reboot.

 

2. Extract the contents of the downloaded ZIP file.

 

3. Run the enclosed Launch.exe, click the first option to install the
graphics driver, and then reboot when prompted (essential!).

 

5. Again run Launch.exe, click the second option to install the 3D
Vision Software, and connect the USB emitter when prompted. Confirm that
the stereo 3D tests work as expected, then exit the wizard by clicking
Finish.

 

6. Open the NVIDIA Control Panel, and increase the display refresh rate
to 120 Hz using the display resolution tab.  Then go to the 3D Settings
tab and set the Stereo display mode to Generic active stereo (with
NVIDIA IR Emitter), click Apply, and then set Stereo - enable mode to
on, click Apply, and then close the NVIDIA control panel.

 

7. Reboot (again, essential -- OpenGL stereo 3D will not actually work
until after you reboot.)

 

8. Launch PyMOL 1.2r1 for Windows.  You should get the message: OpenGL
quad-buffer stereo 3D detected and enabled.

 

9. Now load a PDB file and issue stereo on.  The emitter should light
up and the glasses should activate.  

 

Congratulations -- you should now be able to view PyMOL molecular
structures in stereo 3D on a 120 Hz LCD!  

 

Cheers,

Warren

 

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[PyMOL] Here at last: PyMOL in Stereo 3D on 120 Hz LCDs (WinXP info)!

2009-07-16 Thread Warren DeLano
Continuing coverage...

 

Although GeForce 3D Vision is not officially supported for Windows XP, I
managed to get it to work with PyMOL.   Assuming you have the following
setup:

 

- A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm

 

- A recent Quadro series graphics card such as an FX 380 or 570.

 

- A GeForce 3D Vision hardware kit (an emitter with 3D shutter glasses).

 

- Windows XP 32 bit 

 

You need the 190-series graphics driver for Windows XP:

 

http://www.nvidia.com/object/winxp_190.38_beta.html

 

and the 190-series 3D Vision driver for Windows Vista:

 

http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_190.38.html

 

Instructions:

 

1. Uninstall the existing display drivers, disconnect the USB emitter,
and reboot.

 

2. Run the Window XP graphics driver installer and reboot.

 

3. Launch the Vista 3D Vision driver in order to extract the files you
need, but do not yet click Next on the Welcome page...just leave it open
for now...do not close the installer.

 

4. Plug in the USB emitter.  Windows should throw up the Found New
Hardware Wizard**. Choose No, not this time and go to the Next page.
Select install from a list or specific location and click Next to
continue.  Choose Search for the best driver, include this specific
location..., and click Browse.  Now comes the hard part: you must
select the folder which contains the file nvstusb.inf.  On my system,
that file was unpacked into c:\Documents and
Settings\Warren~1~000\Locals~1\Temp\pft16~tmp - your copy may be in a
similar location.  You may need to use Windows Search to find the file.
Once you've chosen the correct folder, click Ok and then Next.  You may
then be asked to locate nvstusb.sys, which should be in the same
folder.  Click Ok once you've found the file, and then Finish.  This
should complete installation of the USB driver.

 

**If Windows doesn't throw up the Found New Hardware Wizard, use the
Device Manager to locate the device and then update the driver for the
device using the same process described above.

 

5. Now allow the 3D Vision Installer to continue.  Since your on XP, not
Vista, it will complain and throw up one warning and one error message,
but it should still complete.  Reboot when prompted.  The rest of the
instructions are basically the same as for Vista:

 

6. Open the NVIDIA Control Panel, and increase the display refresh rate
to 120 Hz using the display resolution tab.  Then go to the 3D Settings
tab and set the Stereo display mode to Generic active stereo (with
NVIDIA IR Emitter), click Apply, and then set Stereo - enable mode to
on, click Apply, and then close the NVIDIA control panel.

 

7. Launch PyMOL 1.2r1 for Windows.  You should get the message: OpenGL
quad-buffer stereo 3D detected and enabled.

 

8. Now load a PDB file and issue stereo on.  The emitter should light
up and the glasses should activate.  

 

Congratulations -- you should now be able to view PyMOL molecular
structures in stereo 3D on a 120 Hz LCD using Windows XP!  

 

Cheers,

Warren

 

 

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