[PyMOL] (almost) using APBS within PyMOL

2004-09-07 Thread Michael Bovee
Okay, I think I'm getting real close to having this working (Mac G4 AlBook, OSX 10.3.5, Apple X11, X11PyMOL 0.97) Here's my simple-minded approach so far, to get electrostatics in PyMOL instead of the Honig Lab's online GRASS setup (which is also good). 1) maloc and apbs have been

Re: [PyMOL] installing APBS on PBG4

2004-09-02 Thread Michael Bovee
On Sep 2, 2004, at 2:03 PM, Alex W. Smith wrote: Michael: I followed the directions for installing from source and used Bill Scott's tweak (both links below). Everything seems to be running fine. I am a bit short of memory using my Al G4PB, but everything configured and complied with no

[PyMOL] color individual residues on a surface?

2004-07-23 Thread Michael Bovee
. Is this currently possible in PyMOL to do what is pictured in the link above? Thanks, --Michael Bovee, Ph.D. Dept. of Biochemistry University of Vermont

[PyMOL] problem with dist

2004-05-17 Thread Michael Bovee
Hi,I'm running MacPyMOL 0.95 on a G3 Lombard/BronzeKeyboard Powerbook, OSX 10.2.8. The ref manual says to measure distances you can ctrl-shift left, and then right click to select the positions to measure. I can ctrl-shift left click to select the first atom, but ctrl-shift right click doesnt

Re: [PyMOL] question on differential coloring of protein chains

2004-02-18 Thread Michael Bovee
On Tuesday, February 17, 2004, at 02:57 PM, ALEX DAJKOVIC wrote: hello- i am new to pymol and am trying to figure out how to differentially color different chains (i.e. different proteins) in the structure i am viewing. the structure i am working with is actually a structure of two proteins

[PyMOL] cannot print most of user manual pdf

2003-12-16 Thread Michael Bovee
Hi there, Trying to make myself a desk copy of the user manual is proving to be a pain. I can print the text of the table of contents, but anything with screen shot graphics never prints from our new HP2300 (48MB of memory). The refman pdf printed fine, but this userman pdf file seems

[PyMOL] assign secondary structure?

2003-12-11 Thread Michael Bovee
, --Michael Bovee

[PyMOL] cannot 'fit' a particular pdb file

2003-12-02 Thread Michael Bovee
Hi, I have loaded 3 pdb files of homologous forms of an enzyme. The 'fit' command works for superimposing/aligning two of them, but the third file always gives a No Atoms Selected error. Is there something in the pdb file I can fix? As a general rule now, I Hide Everything at first and then

[PyMOL] aa residues disconnected from 'fancy helices'?

2003-11-07 Thread Michael Bovee
that reside on 'strand' regions appear to float in midair and do not connect to the strand backbone. Anyone else seen this behaviour? Thanks! --Michael Bovee University of Vermont

Re: [PyMOL] aa residues disconnected from 'fancy helices'?

2003-11-07 Thread Michael Bovee
Friday, November 7, 2003, 8:50:13 AM, you wrote: MB ...I built a model of my protein of interest using 'set cartoon_fancy_helices,1'...but sidechains of MBamino acids that reside on 'strand' regions appear to float in midair and do not connect to the strand MBbackbone... On Friday, November