RE: [PyMOL] long loading times as the number of existing objects increases

On Tue, 7 Sep 2004, Warren DeLano wrote: > In relation to this, I just noticed something very important: > > If you "set auto_zoom, off" before loading a series of structures, you'll > boost PyMOL's loading performance dramatically: by 10X at least...perhaps > much more. Just zoom once manually

RE: [PyMOL] long loading times as the number of existing objects increases

In relation to this, I just noticed something very important: If you "set auto_zoom, off" before loading a series of structures, you'll boost PyMOL's loading performance dramatically: by 10X at least...perhaps much more. Just zoom once manually after everything is loaded in. cmd.set("zoom","off

[PyMOL] light source inside a molecule??

Hi, I was wodering if it is possible to change the light source to a ligand inside a protein, so it creates a glowing effect? Anton Vila

Re: [PyMOL] long loading times as the number of existing objects increases

Warren- Thanks for your prompt response! Given the fundamental issues you mentioned, I think I will change my script so that it loads files only when they are needed and deletes the associated objects when they are no longer being displayed. Initially, I rejected this solution as less efficien

Re: [PyMOL] (almost) using APBS within PyMOL

On Sep 7, 2004, at 3:07 PM, Michael George Lerner wrote: Fine so far. The Visualization tab is for visualizing an electrostatic potential, so it won't make sense until after you've loaded a molecule (your pdb file) and a map (most likely the electrostatic potential map that APBS generates). Oh

Re: [PyMOL] (almost) using APBS within PyMOL

> 1) maloc and apbs have been successfully compiled from source and > installed in /usr/local > > 2) M. Lerner's APBS Tools plugin 'About' tab says to load a structure; > the 'Visualization' tab says to load a "molecule and a map" So, I just > loaded a pdb file like I usually do, and displayed as

RE: [PyMOL] long loading times as the number of existing objects increases

Ben, Thanks for the great benchmarks! PyMOL is definitely showing non-linear behavior when it comes to loading a lot of objects...I don't know why this is exactly, but I can tell you that I didn't originally envision (and thus optimize PYMOL for) loading of so many objects. As it currently stan

RE: [PyMOL] Fast Coloring

> I have almost got the coloring working fast, but I have > one last problem. I am just loading a pdb, then I am wanting > to go through and set the 'q' variable for each atom to the > value I am wanting to color on. How do I get a chempy handle > on the molecule being displayed? > 'ge

[PyMOL] long loading times as the number of existing objects increases

I have a situation in which I need to load a large number of separate pdb files into a single pymol session. In this case, the number is ~150, but it could potentially be more. However, the amount of time required to load a file appears to be strongly dependent on the number of files already

[PyMOL] (almost) using APBS within PyMOL

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 successfull

[PyMOL] questions about PQR visualization

Hi, guys: I have a confusion about PQR file visualization. Since my computer is Mac G4, I think I may not be able to use the new version of mac pymol 0.97 for the APBS plugin. I converted my pdb file to PQR from the serve: https://gridport.npaci.edu/apbs/. However, when I want to visualize the