VMD-L Mailing List

From: Ibrahim Moustafa (I.moustafa_at_psu.edu)
Date: Wed Jun 11 2008 - 11:27:48 CDT

Hi Peter,

  I'm in the same situation...tried hard to get IED working on MACOSX 10.4
without success. Though, a friend figured out why it does not work?
When untarring the "lib_MACOSX-numpy" file on MAC it gives an error message
at the end. If you look at the contents of the directory you'll see a
directory named "Python", a file with name "python"- (small case) is
supposed to be in the directory as well. However, the MACOSX has a problem
with case sensitivity in naming files in the same directory. I untarred the
successfully on a Linux machine, but when transferring the directory to
MAC...the same problem appeared. So, MAC is in-tolerant to files having the
same name but differ in cases. I tried to google this problem and it seems
reported before for MACOS. Even, the new Leopard showed the same behavior.

   I'll second you in asking help from GEEKS.

  thank,
 Ibrahim 

-- 
Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802
Tel. (814) 863-8703
Fax (814) 865-7927
 
On 6/11/08 3:57 AM, "vmd-l digest" <owner-vmd-l_at_ks.uiuc.edu> wrote:
> 
> vmd-l digest         Wednesday, June 11 2008         Volume 01 : Number 1086
> 
> 
> 
> In this issue:
> 
>     Re: vmd-l: Image rendering using pov-ray
>     Re: vmd-l: Image rendering using pov-ray
>     vmd-l: IED on MacOSX 10.3.9
>     Re: vmd-l: IED on MacOSX 10.3.9
>     vmd-l: Spring quality watches offer
>     vmd-l: problem loading trajectory in VMD under windows XP
>     Re: vmd-l: problem loading trajectory in VMD under windows XP
>     Re: vmd-l: SpaceNavigator
> 
> ----------------------------------------------------------------------
> 
> Date: Mon, 9 Jun 2008 22:30:35 -0400 (EDT)
> From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> Subject: Re: vmd-l: Image rendering using pov-ray
> 
> On Mon, 9 Jun 2008, Dong Xu wrote:
> 
> DX> Hi All,
> 
> dong,
> 
> DX> I was trying to get high quality images using VMD's Pov-Ray rendering on a
> DX> Windows XP computer. I rendered my current VMD window to a *.pov file and
> DX> load it into Pov-Ray 3.6. Then I clicked "Run" in Pov-Ray, Pov-Ray saved
> the
> DX> rendered image to a *.bmp. However, the bmp file quality is quite low.
> Does
> 
> as with all render programs, the quality of the output
> depends on the settings (quality flags, image size) you
> give to the renderer. VMD can do (next to) nothing about it.
> 
> DX> anyone have similar problem? What do I have to do to get high-resolution
> DX> snapshots?
> 
> read the povray documentation?
> 
> cheers,
>    axel.
> 
> DX> 
> DX> Thanks!
> DX> 
> DX> -DX
> DX> 
> 
> - -- 
> =======================================================================
> Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>    Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 
> ------------------------------
> 
> Date: Mon, 9 Jun 2008 22:34:57 -0400 (EDT)
> From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> Subject: Re: vmd-l: Image rendering using pov-ray
> 
> On Mon, 9 Jun 2008, Dong Xu wrote:
> 
> p.s.: for some really stunning images, you may want to check out:
> 
>  http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/
> 
> i recently did some images using the AO feature and my
> colleagues were quite impressed. ;-)
> 
> a.
> 
> DX> Hi All,
> DX> 
> DX> I was trying to get high quality images using VMD's Pov-Ray rendering on a
> DX> Windows XP computer. I rendered my current VMD window to a *.pov file and
> DX> load it into Pov-Ray 3.6. Then I clicked "Run" in Pov-Ray, Pov-Ray saved
> the
> DX> rendered image to a *.bmp. However, the bmp file quality is quite low.
> Does
> DX> anyone have similar problem? What do I have to do to get high-resolution
> DX> snapshots?
> DX> 
> DX> Thanks!
> DX> 
> DX> -DX
> DX> 
> 
> - -- 
> =======================================================================
> Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>    Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 
> ------------------------------
> 
> Date: Tue, 10 Jun 2008 20:54:54 +1000
> From: Peter Jones <p.m.jones_at_optusnet.com.au>
> Subject: vmd-l: IED on MacOSX 10.3.9
> 
> - --Apple-Mail-14-712376568
> Content-Transfer-Encoding: 7bit
> Content-Type: text/plain;
> charset=US-ASCII;
> format=flowed
> 
> Hi all,
> 
> 
> I am trying to get IED going on MacOSX 10.3.9. I have downloaded and
> unpacked the relevant pylib.macosx.tar.gz, set the $PYTHONHOME
> environment variable to the path to the lib_MACOSX-numpy directory and
> installed VMD 1.8.3. However I still get the error-
> 
> 
> vmd > gopython
> Info) Starting Python...
> Numeric Python module _numpy not found; vmdnumpy module not available.
> ImportError: Failure linking new module
> Info) Text interpreter now Python
> Traceback (most recent call last):
>    File "<string>", line 1, in ?
>    File "/Applications/VMD
> 1.8.3.app/Contents/vmd/scripts/python/Tkinter.py", line 59, in ?
>      import _tkinter # If this fails your Python may not be configured
> for Tk
> ImportError: No module named _tkinter
> 
> 
> I have tried quite a few times to get IED going on Linux boxes and Macs
> but never succeeded, so any help would be greatly appreciated,
> 
> 
> thankyou,
> 
> 
> Peter Jones
> - --Apple-Mail-14-712376568
> Content-Transfer-Encoding: 7bit
> Content-Type: text/enriched;
> charset=US-ASCII
> 
> Hi all,
> 
> 
> 
> I am trying to get IED going on MacOSX 10.3.9. I have downloaded and
> unpacked the relevant
> <fontfamily><param>Lucida Grande</param>pylib.macosx.tar.gz, set the
> $PYTHONHOME environment variable to the path to the lib_MACOSX-numpy
> directory and installed VMD 1.8.3. However I still get the error-</fontfamily>
> 
> 
> 
> vmd > gopython
> 
> Info) Starting Python...
> 
> Numeric Python module _numpy not found; vmdnumpy module not available.
> 
> ImportError: Failure linking new module
> 
> Info) Text interpreter now Python
> 
> Traceback (most recent call last):
> 
>   File "<<string>", line 1, in ?
> 
>   File "/Applications/VMD
> 1.8.3.app/Contents/vmd/scripts/python/Tkinter.py", line 59, in ?
> 
>     import _tkinter # If this fails your Python may not be configured
> for Tk
> 
> ImportError: No module named _tkinter
> 
> 
> 
> I have tried quite a few times to get IED going on Linux boxes and
> Macs but never succeeded, so any help would be greatly appreciated,
> 
> 
> 
> thankyou,
> 
> 
> 
> Peter Jones
> - --Apple-Mail-14-712376568--
> 
> ------------------------------
> 
> Date: Tue, 10 Jun 2008 08:03:30 -0400 (EDT)
> From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> Subject: Re: vmd-l: IED on MacOSX 10.3.9
> 
> On Tue, 10 Jun 2008, Peter Jones wrote:
> 
> PJ> Hi all,
> PJ> 
> PJ> 
> PJ> I am trying to get IED going on MacOSX 10.3.9. I have downloaded and
> PJ> unpacked the relevant pylib.macosx.tar.gz, set the $PYTHONHOME environment
> PJ> variable to the path to the lib_MACOSX-numpy directory and installed VMD
> PJ> 1.8.3. However I still get the error-
> 
> 
> why VMD 1.8.3???
> 
> PJ> 
> PJ> vmd > gopython
> PJ> Info) Starting Python...
> PJ> Numeric Python module _numpy not found; vmdnumpy module not available.
> PJ> ImportError: Failure linking new module
> PJ> Info) Text interpreter now Python
> PJ> Traceback (most recent call last):
> PJ>   File "<string>", line 1, in ?
> PJ>   File "/Applications/VMD
> PJ> 1.8.3.app/Contents/vmd/scripts/python/Tkinter.py", line 59, in ?
> PJ>     import _tkinter # If this fails your Python may not be configured for
> Tk
> PJ> ImportError: No module named _tkinter
> PJ> 
> PJ> 
> PJ> I have tried quite a few times to get IED going on Linux boxes and Macs
> but
> PJ> never succeeded, so any help would be greatly appreciated,
> 
> i don't know much about macs, but on linux i've been having the
> best experiences with self-compiled vmd and everything using
> the "native" packages (with dynamic linking). that renders the
> resulting executable rather non-portable between distributions
> and releases, so to have a widely compatible distribution of VMD,
> the provided binaries cannot link dynamically, but due to its
> wrapping of dynamical objects python implicitly re-introduces
> this non-portability. IED not only uses python but through python
> also Tk, which VMD uses itself, so you have to make sure that
> _everything_ is in sync. if you have a fedora linux box, you
> may want to try out the rpms that i deposited into the biocore
> (not fully up-to-date i have to confess).
> 
> i suspect that on different mac os versions there are similar
> issues and perhaps there are some additional dynamic linkers
> issues that you are running in.
> 
> cheers,
>     axel.
> 
> PJ> 
> PJ> 
> PJ> thankyou,
> PJ> 
> PJ> 
> PJ> Peter Jones
> PJ> 
> 
> - -- 
> =======================================================================
> Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>    Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 
> ------------------------------
> 
> Date: Tue, 10 Jun 2008 18:50:16 -0500
> From: "Estela Gibbs" <villa_at_ks.uiuc.edu>
> Subject: vmd-l: Spring quality watches offer
> 
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> 
> ------------------------------
> 
> Date: Wed, 11 Jun 2008 09:41:24 +1000
> From: <Aaron.Oakley_at_csiro.au>
> Subject: vmd-l: problem loading trajectory in VMD under windows XP
> 
> Hi Folks,
>  
> I have a PC (AMD Phenom X4, 4GB memory) running
> Windows XP at home. For some reason, VMD 1.8.6 crashes when memory use
> exceedes
> 2GB. I don't think it is memory its self to blame because I can have
> two instances of VMD running simultaneously with <= 2GB of memory usage.
> Is this because the windows version is 32 bit but the architecture is 64
> bit?
> 
> Any ideas about the cause/remedy?
> 
> Thanks,
> 
> Aaron++
>  
> - ----------------------------------------------------------------
> CSIRO Molecular and Health Technologies
> 343 Royal Parade
> Parkville
> VIC 3052
> Australia
> Phone (+61) 3 9662 7262
> - ----------------------------------------------------------------
> 
> ------------------------------
> 
> Date: Tue, 10 Jun 2008 21:21:24 -0400 (EDT)
> From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> Subject: Re: vmd-l: problem loading trajectory in VMD under windows XP
> 
> On Wed, 11 Jun 2008, Aaron.Oakley_at_csiro.au wrote:
> 
> AO> Hi Folks,
> AO>  
> AO> I have a PC (AMD Phenom X4, 4GB memory) running
> AO> Windows XP at home. For some reason, VMD 1.8.6 crashes when memory use
> AO> exceedes
> AO> 2GB. I don't think it is memory its self to blame because I can have
> AO> two instances of VMD running simultaneously with <= 2GB of memory usage.
> AO> Is this because the windows version is 32 bit but the architecture is 64
> AO> bit?
> 
> yes. under windows xp the maximum address space is limited to
> 2GB per process. also the fact that you have a 64-bit capable
> cpu does not mean you are running a 64-bit OS.
> 
> AO> 
> AO> Any ideas about the cause/remedy?
> 
> install BSD or Linux?
> 
> cheers,
>    axel.
> 
> AO> 
> AO> Thanks,
> AO> 
> AO> Aaron++
> AO>  
> AO> ----------------------------------------------------------------
> AO> CSIRO Molecular and Health Technologies
> AO> 343 Royal Parade
> AO> Parkville
> AO> VIC 3052
> AO> Australia
> AO> Phone (+61) 3 9662 7262
> AO> ----------------------------------------------------------------
> AO> 
> AO> 
> 
> - -- 
> =======================================================================
> Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>    Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 
> ------------------------------
> 
> Date: Wed, 11 Jun 2008 02:53:39 -0500
> From: John Stone <johns_at_ks.uiuc.edu>
> Subject: Re: vmd-l: SpaceNavigator
> 
> Dear VMD-L,
>   I wanted to let people know that all of the new test versions of
> VMD 1.8.7 now incorporate built-in support for the new 3DConnexion
> "SpaceNavigator" Spaceball-like input devices.  The Windows versions
> of VMD have always worked with these devices when using the 3DConnexion
> driver, but I have now added support in all of the Unix/Linux
> versions of VMD as well.  The new code also supports the open source
> "spacenavd" driver in addition to 3DConnexion's commercial drivers.
> Soon I plan add support in the MacOS X builds as well, but that requires
> entirely different interface code.
> 
> I invite interested users to send me an email and I'll provide
> the test builds and preliminary instructions on how to use the devices
> within VMD.  I've added many new capabilities to the Spaceball interfaces
> in VMD, so they can now be used to controller a much more diverse range
> of functionality within the program.  The new versions also retain
> direct serial I/O support for the old Spaceball 2003/3003/4000FLX
> devices, which also benefit from the user interfaces and programmability.
> I'm interested in getting feedback from the users on the new code
> to further tweak and improve it so that the final release of
> VMD 1.8.7 has excellent Spaceball support all around.
> 
> Cheers,
>   John Stone
>   vmd_at_ks.uiuc.edu
> 
> 
> On Thu, Nov 29, 2007 at 06:23:01PM +0100, Carsten Olbrich wrote:
>> Dear all,
>> 
>> we bought a SpaceNavigator (PE) (3DConnexion) and I still try to get
>> this device working in Linux (SuseLinux 10.1).
>> It works fine in Windows with the corresponding driver and I don't
>> need to configure anything corresponding to VMD.
>> In Linux it looks different:
>>    - I managed to install the driver and all example programs, which
>> are distributed with the driver, work fine but not VMD.
>>      Therefor I added following to .vmdsensors:    device spacenav
>> sballtracker://local//proc/bus/usb/005/036
>>      But VMD doesn't respond on moving the device.
>>    - I also tried to use VRPN (Version 7.14) with this configuration:
>>     vrpn_3DConnexion_Navigator device0
>>      The client "vrpn_print_devices" program can connect to the
>> vrpn_server and prints for instance
>> 
>>       Analog device0_at_localhost:
>>           0.09,  0.07, -0.47,  0.19, -0.17,  0.16 (6 chans)
>>       Analog device0_at_localhost:
>>           0.01,  0.07, -0.47,  0.19, -0.17,  0.16 (6 chans)
>>       Analog device0_at_localhost:
>>           0.01,  0.07, -0.07,  0.19, -0.17,  0.16 (6 chans)
>> 
>>       if I move the device.
>>       Then I added following to .vmdsensors:
>>          device spacenavtracker  vrpntracker://exciton/device0
>>          device spacenavbuttons  vrpnbuttons://exciton/device0
>>       The chose the tracker and the buttons in the TOOLS menu but
>> nothing happens except the message:
>> 
>> vrpn: Connection request received: 127.0.0.2 45092
>> vrpn_Connection: VRPN Note: minor version number doesn't match:
>> (prefer 'vrpn: ver. 07.14', got 'vrpn: ver. 07.03  0').  This is not
>> normally a problem.
>> 
>> I hope someone might help me to get our SpaceNavigator working.
>> 
>> Regards,
>> Carsten
> 
> - -- 
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>   WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
> 
> ------------------------------
> 
> End of vmd-l digest V1 #1086
> ****************************
> 
>