Re: [PyMOL] Install of Pymol 0.88 from Fink?

[Hanspeter Niederstrasser]

On Thu, 5 Jun 2003, Kelley Moremen wrote:

> I am having problems getting access to the updated (0.88) version of Pymol
> from Fink.  After updating Fink and Pymol, my Fink still seems to think that
> the 0.86 version is the most up-to-date version.  Am I missing something?

Pymol 0.88 is only in the unstable Fink tree right now. See
 for getting hold
of unstable (this means that the package has not been heavily tested, NOT
that it will crash every 2 minutes) packages.

Hanspeter

-- 
Science is like sex: sure, it may give some practical results, but
that's not why we do it.
-Richard Feynman

[PyMOL] dial boxes on SGI

[Hanspeter Niederstrasser]

Do dialboxes that are sold with SGIs work for moving molecules around in
PyMOL?  They don't seem to do anything out of the box.

Hanspeter

-- 
Hanspeter Niederstrasser   Nogales Lab
nie...@ocf.berkeley.eduhttp://cryoem.berkeley.edu/~nieder/

[PyMOL] creating objects from pdb w/out chain id

[Hanspeter Niederstrasser]

I'm trying to create an object of a protein from a PDB file that doesn't
give a chain ID (pdb is 1BG2).

I normally do something like:

create atub=(/1jff//a/)

to pull a specific chain out of a PDB file, but 1BG2 doesn't have a chain
name.  And if i use "create kin=(/1BG2)", the object kin gets ALL the
elements from 1BG2, including the waters, nucleotide, and ions, which is
exactly what I'm trying to not do.

How can I create an object out from a nameless chain?

Hanspeter

[PyMOL] bug with APBS plugin and OSX/X11 hybrid pymol environment?

[Hanspeter Niederstrasser]

I've been using the APBS plugin the last couple days and have noticed a 
bug in the behavior of the plugin.  This is using the hybrid X11 version 
of PyMOL 0.97 on OSX 10.3.5 and Apple's X11.


After starting X11, I click the PyMOLX11Hybrid icon and select the APBS 
plugin from the tcl GUI.  Looking at the tab "APBS Location", the location 
for the apbs binary is not filled in (the binary is at 
/usr/local/bin/apbs).  I can fill that in manually and everything works 
ok.


However, the apbs location is not saved.  Setting APBS_BINARY in either 
~/.bash_profile, ~/.bashrc, or /etc/bashrc does not help.  While both 
Terminal.app and xterms show that APBS_BINARY is set, PyMOL is not seeing 
this as being set.


However, if I open PyMOL by typing "open 
~/Applications/PyMOLX11Hybrid.app" in either an xterm or Terminal.app, 
then PyMOL does automatically see the location of apbs.


This seems to me the result of PyMOL using X11.app's environment and not 
the environment of a normal shell when run by clicking the icon.  Is this 
a reasonable assumption?  Could someone with XDarwin and apbs try this? 
I no longer have a Mac with XDarwin, but with other stuff, XDarwin always 
read the environment normally.


If this is a problem with Apple's X11 and PyMOL, can PyMOL be modified to 
work around this?  The issue is not critical in this case and there's a 
simple workaround, but I could see it causing problems for other things 
that expect a normal environment.


Hanspeter

--
And when the last last law was down, and the Devil turned round on 
you - where would you hide, Roper, the laws all being flat?

  --Robert Bolt, "A Man For All Seasons"

Re: [PyMOL] OS-X question

[Hanspeter Niederstrasser]

Joel Tyndall wrote:

I have recently installed pymol on a friends ibook and it all works 
fine...but there seems to be no external GUI (as seen on PC and Linux 
versions). Is it missing on OSX or is my install flawed? It does make it 
a little easier to use for the novice.


Did you install the PyMOLX11 hybrid version?  If so, then you need to 
start up X11.app (or XDarwin if that's what they have) first in order to 
get the full GUI.


Hanspeter

--
Hanspeter Niederstrasser, Ph.D.Dept. of Cell Biology
hniederstrasser at cellbiology.wustl.edu   Campus Box 8228
Cooper Lab 660 South Euclid Avenue
Washington University in St. Louis St. Louis, MO 63110