Hi: Thanks for the advice. I'll have to determine some reasonable way to communicate this to my class. I do have another problem though! I have a rather long script that involves some VRML and it is also misbehaving. The script to follow has the same behaviour and is much simpler: import chimera from chimera import runCommand import CGLutil from CGLutil import vrml def vr_plot(): wrl = vrml.Transform() for ii in range(10): for jj in range(10): translateBaseCube = vrml.Transform(translation = tuple([jj, ii, 0])) base = vrml.Box(size = (.1, .1, .1), color = (1.,1.,.5)) translateBaseCube.addChild(base) wrl.addChild(translateBaseCube) return vrml.vrml(wrl) vvrr = vr_plot() vrlmModel = chimera.openModels.open(vvrr, type = 'VRML')[0] chimera.viewer.viewAll() This VRML snippet gives me an array of 100 little cubes. Here's the catch: On last year's version of Chimera (1.5.3) the script generates the scene almost instantaneously. With the current version of Chimera (the January release or the Feb. 04 release) the execution is extremely slow. I am running Windows 7 on a machine with 12 GB of RAM and an Intel i7 CPU 3.2GHz so I am not lacking for computing power. One of my students also tried this script and reports a similar slow down. I am also noticing that the latest version seems to launch more slowly and takes more time to display BIG scenes (consider PDB ID = 1FFK). Is there some way to improve this situation or do I have to give up on using VRML? Cheers, Forbes On Tue, 7 Feb 2012, Eric Pettersen wrote:
Hi Forbes, The trick is that, unlike a Chimera command file, there is no implicit "wait 1" (i.e. show a new frame) at the end of commands executed with the Python runCommand call. Therefore with this sequence of runCommands:
runCommand("color red") runCommand("color green") runCommand("color blue")
the display will never show the models colored red or green, just blue. So, with the print command removed from your script the modeldisp/~modeldisp commands are executed "back to back" and you never see anything. Though due to the arcane minutiae of how the print command works, you do wind up getting a frame redraw after a print which is why it works with the print in there. Also, Chimera does not execute at all (including frame redraws) during your time.sleep(0.1). To get the script to work the way you want your options are:
1) add "; wait 1" to the end of the modeldisp commands 2) change time.sleep(0.1) to runCommand("wait 3") [3 frames at 30 frames/second] 3) both
Sorry for the inscrutableness of all this.
--Eric
On Feb 6, 2012, at 7:10 PM, Forbes J. Burkowski wrote:
Hi:
I have given my students a little problem that involves producing an "animation" with each step in the animation being a PDB model within an NMR generated file. The solution to the problem is more complicated than what is shown in the script below involving as it does the calculation of RMSDs to get smoother transitions between successive displays of the models.
My answer script is not working as expected due to an issue that I have recreated in a shorter script that follows next:
import chimera from chimera import runCommand import time
numCycles = 10
# ID's to try: 1BMR, 1DW5, 1QDP, 1D1H, 1N4N, 1IJC, 1PFD, 2LI3, 1AH1 prot_L = chimera.openModels.open("1AH1", type="PDB") numModels = len(prot_L)
runCommand("~modeldisp")
for ic in range(numCycles): for aix in range(numModels): subIDstr = str(prot_L[aix].subid) command = "modeldisp #0" + "." + subIDstr runCommand(command) time.sleep(0.1) command = "~modeldisp #0" + "." + subIDstr # The following print command seems to be necessary to get # the animation! print command runCommand(command)
This script runs just fine and does exactly what I wanted it to do. Here is the problem: If I remove the print statement, initially there for debugging, the script does not work! It seems weird that printing the argument for the runCommand would have any effect on the execution of the runCommand statement. Am I missing some vital point here????
I am running the latest version of Chimera: (version 1.6 build 35398) under Windows 7 Professional. Prior to each run I have being doing
File... Close Session
to eliminate any models that were brought in on a previous run.
Cheers, Forbes Burkowski
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