Herbert, 1. I believe the coloring problems are a known issue which was mentioned during the 2.7.2 release, though I am unable to find this documented right now. I'm running linux with 32bit rasmol. In 2.7.2 if I load an image, and use "color temperature" everything is fine, but if I then zap the image and load a second one, color temperature no longer works. 2. We are using a sequence of commands as follows: load xyz somefile.xyz rotate y -90 color temperature zoom 440 slab 46 set ambient 100 write someoutputfile.ppm zap the .xyz files are like the following: 1310720 1 32 32 160 0.114102400000E+03 0.114102400000E+03 0.570512000000E+03 90.0000000 90.0000000 90.0000000 Time(ps)= 4.0000 C -5.6590E+01 -5.6606E+01 -2.9792E+02 -3.248E+00 0.000E+00 1 0 .... more atoms.... .... etc... I usually only run 2-3 copies of rasmol. Running fewer or more makes no real difference, and I begin to see failures at around 500-700 loads. The workstation I use is an AMD sempron 1800+ with 1.5gb of RAM (Centos 4.4 ). Thanks for your help. Keith McLaughlin On 4/13/07, Herbert J. Bernstein <yaya at bernstein-plus-sons.com> wrote: > > Dear Keith, > > Thank you for bringing this to my attention. We would like to fix > it. You have raised two problems that clearly need to be fixed in > the latest version: > > 1. You have described "coloring problems when loading images one > after the other." Could you clarify and provide an example? > It sounds like the color maps are not getting reset properly. > Are you using a 32-bit, 16-bit or 8-bit version of RasMol? > > 2. You say that after about "500 images rasmol gives an error and > is unable to load any new images, saying that the file is not found". > Could you be more specific about the sequence of commands and data files > used, so we can reproduce this error and fix it. it sounds like a > memory leak. > > Are you running one copy of RasMol and loading and zapping multiple images > or are you running multiple copies of RasMol. In the former case the > problem need to be addressed primarily directly in RasMol. In the > later case, the problem needs to be adressed more at the operating > system level. In either case, we would like to solve it. > > Please specify the hardware platform and operating system you use, so > we can try to work in a similar environment. > > In the meantime, I would agree with your guess that adding more memory > would help, but if you are keeping 500 copies of RasMol open and are > in a unix environment, you probably need to increase process limits > as well. If you are in an MS windows environment, there may not be > any easy answer. > > Regards, > Herbert > > > At 7:28 PM -0400 4/12/07, Keith McLaughlin wrote: > >Hello all; > > > >My research involves 4 million atom MD simulations and we've decided to > use > >rasmol for visualization. From my experiences, I have two questions and > am > >hoping that someone here may be able to help. > > > >1. Currently I'm using version 2.7.1 because it doesn't have the coloring > >problems when loading images one after another. Unfortunately, after > about > >500 images rasmol gives an error and is unable to load any new images > saying > >that the file is not found, or something to that effect. Does anyone have > >experience with handling this? > > > >2. We are planning on some upgrades, and are kind of curious as to which > >components will help the most with increasing the speed in which these > files > >are loaded: memory or video memory, or perhaps processor. We mostly > suspect > >that adding more memory would be the best choice, but I'd like to hear > other > >opinions. > > > >Thanks! > >-- > >Keith McLaughlin > >University of South Florida > >Physics Dept. PHY225 > >4202 E. Fowler Ave > >Tampa, FL 33620 > > > >-- > >Keith McLaughlin > >University of South Florida > >Physics Dept. PHY225 > >4202 E. Fowler Ave > >Tampa, FL 33620 > >_______________________________________________ > >Molvis-list mailing list > >Molvis-list at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/molvis-list > > > -- > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 121 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya at dowling.edu > ===================================================== > _______________________________________________ > Molvis-list mailing list > Molvis-list at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/molvis-list > -- Keith McLaughlin University of South Florida Physics Dept. PHY225 4202 E. Fowler Ave Tampa, FL 33620