VMD-L Mailing List

From: Oliver Beckstein (orbeckst_at_jhmi.edu)
Date: Thu Dec 20 2007 - 15:50:10 CST

John,

> I've posted two Linux builds with 64 bonds per atom in the alpha
> directory in the VMD Public project on BioCoRE:
> http://www.ks.uiuc.edu/Research/vmd/alpha/

thanks for the Linux builds. I only tested the 32bit one
(vmd-1.8.7a14extrabonds.bin.LINUX.opengl). It works in principle. In
particular, I get all my 'bonds' displayed.

I'm having a few stability issues. Although they won't prevent me from
using the build I'll mention them nevertheless.

For testing, I ran Linux-VMD remotely (bad, I know) through X11 on my
PowerBook laptop:

VMD: 1.8.7a14extrabonds (December 19, 2007)

remote:
Linux: CentOs 4.2 (Rocks 4.1)
Linux 2.6.9-22.ELsmp #1 SMP Sat Oct 8 19:11:43 CDT 2005 i686 i686 i386
GNU/Linux

local:
Mac OS X 10.3.9, Apple's X11

VMD's startup output:
Info) ATI Linux driver detected, limiting features to avoid driver bugs.
Info) Set the environment variable VMDDISABLEATILINUXWORKAROUND
Info) to enable full functionality on a known-safe driver version.
Info) OpenGL renderer: ATI Radeon 9600 XT OpenGL Engine
Info) Features: STENCIL MDE MTX
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (2048x2048), Multitexture (8)

The following operations crashed VMD:
* Render -> Tachyon Internal
   (Tachyon external works)
* Trying to load any pdb file on its own (psf + pdb works)
* Trying to load a pdb from the web

(Also, when I resize the VMD OpenGL window with a molecule present my
local MacOS X freezes (either hangs or the display becomes brighter and
brighter while hanging until the user panics and hits the power-off
button...). This happens with both 1.8.5 and 1.8.7a14extrabonds running
remotely on Linux (and it doesn't matter if I do 'export
VMDDISABLEATILINUXWORKAROUND=1' ). --- I suspect that's more a problem
with my ancient version of MacOS X than with VMD per se, though; native
MacOS X ppc VMD 1.8.6 has no problems.)
>
> Give those a spin and let me know if all is well. I can do a MacOS
> build
> for you tomorrow if the Linux builds work for you.

I'd like to test the OS X build as well, please (hoping that it works
around the OpenGL problems and so that I can run VMD locally).

Many thanks,
Oliver

>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Dec 18, 2007 at 05:05:02PM -0500, Oliver Beckstein wrote:
>> Hello John,
>>
>>> I can make you special builds with larger max bond counts.
>>
>> I appreciate this very much.
>>
>>> Will 30 be adequate? I can make it any number you like
>>> up to 255, but the larger the number the more memory VMD will use
>>> on a per-atom basis.
>>
>> To be on the safe side let's choose 64 – more are really not going to
>> come up in my problems.
>>
>> Thank you,
>> Oliver
>>
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>>
>>> On Mon, Dec 17, 2007 at 02:37:42PM -0500, Oliver Beckstein wrote:
>>>> Hello,
>>>>
>>>> is there a way to obtain binaries for Mac OS X and Linux i686 that
>>>> have
>>>> MAXATOMBONDS increased to, say, 30? I am (ab)using VMD for graph
>>>> plotting and some of my nodes simply don't behave like atoms
>>>> although
>>>> I'd like to keep using atom-like representations instead of drawing
>>>> bonds as graphics objects because it makes it so much easier to
>>>> change
>>>> colors, materials etc.
>>>>
>>>> As I understand it, MAXATOMBONDS is defined to be 12 in Atom.h:
>>>> http://www.ks.uiuc.edu/Research/vmd/doxygen/Atom_8h.html
>>>>
>>>> I don't have the VMD source and as I understand it, it can be a bit
>>>> complicated compiling it, though I'd give it a shot if this is too
>>>> much
>>>> work for the developers (which I would certainly understand).
>>>>
>>>> Thanks,
>>>> Oliver
>>>>
> 

--
Oliver Beckstein * orbeckst_at_jhmi.edu
Johns Hopkins University, School of Medicine
Dept. of Physiology, Biophysics 206
725 N. Wolfe St
Baltimore, MD 21205, USA
Tel.: +1 (410) 614-4435