Re: [Jmol-users] Jmol -- two major advances

On 04/09/2010 07:22 PM, Robert Hanson wrote: We could try that. set repaintWaitMs 1000 12.0.RC4 I havn't tried it with PDB entry 1M4X yet, but I have tried it with entry 2NOX to solve the similar problem discussed in jmol-Bugs-2971384 (Large image export problem - 11.8.20/11.9.24) in Jmol

Re: [Jmol-users] Jmol -- two major advances

wow! On Mon, Apr 19, 2010 at 10:07 AM, Rolf Huehne rhue...@fli-leibniz.dewrote: On 04/09/2010 07:22 PM, Robert Hanson wrote: We could try that. set repaintWaitMs 1000 12.0.RC4 I havn't tried it with PDB entry 1M4X yet, but I have tried it with entry 2NOX to solve the similar

Re: [Jmol-users] Jmol -- two major advances

On 04/07/2010 03:12 PM, Robert Hanson wrote: Rolf, I think what's happening is that the image is too complex. There is a 2-second timeout on the refreshing request, and that is done right before the image is created. So in general, displays take less than 2 seconds, and we have no problem.

Re: [Jmol-users] Jmol -- two major advances

We could try that. set repaintWaitMs 1000 12.0.RC4 On Fri, Apr 9, 2010 at 10:12 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 04/07/2010 03:12 PM, Robert Hanson wrote: Rolf, I think what's happening is that the image is too complex. There is a 2-second timeout on the refreshing

Re: [Jmol-users] Jmol -- two major advances

On 04/05/2010 06:50 PM, Robert Hanson wrote: Thanks, Peter. Yes, that's a killer. Definitely not ready to read 16,000,000 atoms! But I have added a new option that lets you load some smaller number of biomolecule transformations. Looks like we'll have to let Rolf open that one for us ;)

Re: [Jmol-users] Jmol -- two major advances

Wow, thanks, Rolf. I thought perhaps you could do that! Oh, so close! First, write PNG just sends the image to your clipboard as an actual system-dependent image since you didn't specify a file name. So it was trying to create that when the error occurred. I'm guessing that happened not because

Re: [Jmol-users] Jmol -- two major advances

On 04/07/2010 02:10 PM, Robert Hanson wrote: Wow, thanks, Rolf. I thought perhaps you could do that! Oh, so close! First, write PNG just sends the image to your clipboard as an actual system-dependent image since you didn't specify a file name. So it was trying to create that when the

Re: [Jmol-users] Jmol -- two major advances

Rolf, I think what's happening is that the image is too complex. There is a 2-second timeout on the refreshing request, and that is done right before the image is created. So in general, displays take less than 2 seconds, and we have no problem. But if a display takes more than 2 seconds, Jmol

Re: [Jmol-users] Jmol -- two major advances

--- Original Message - From: Robert Hanson To: jmol-users@lists.sourceforge.net Sent: Wednesday, April 07, 2010 8:10 AM Subject: Re: [Jmol-users] Jmol -- two major advances Wow, thanks, Rolf. I thought perhaps you could do that! Oh, so close! First, write PNG just sends

Re: [Jmol-users] Jmol -- two major advances

On 04/07/2010 03:26 PM, Charles Shubert wrote: I'm confused by the 2400% CPU usage claimed below. Does this imply that 24 cores of a multicore machine are running at 100%? Actually there are 36 cores running at pulsating rates with a total average of 2400%. Unfortunately only until all the

Re: [Jmol-users] Jmol -- two major advances

:* Re: [Jmol-users] Jmol -- two major advances Wow, thanks, Rolf. I thought perhaps you could do that! Oh, so close! First, write PNG just sends the image to your clipboard as an actual system-dependent image since you didn't specify a file name. So it was trying to create that when the error

Re: [Jmol-users] Jmol -- two major advances

- From: Robert Hanson To: Charles Shubert ; jmol-users@lists.sourceforge.net Sent: Wednesday, April 07, 2010 11:37 AM Subject: Re: [Jmol-users] Jmol -- two major advances On Wed, Apr 7, 2010 at 8:26 AM, Charles Shubert cshub...@mit.edu wrote: I'm confused by the 2400% CPU usage

Re: [Jmol-users] Jmol -- two major advances

On 04/07/2010 05:37 PM, Robert Hanson wrote: On Wed, Apr 7, 2010 at 8:26 AM, Charles Shubert cshub...@mit.edu wrote: I'm confused by the 2400% CPU usage claimed below. Does this imply that 24 cores of a multicore machine are running at 100%? I have not been able to get Jmol to run on more

Re: [Jmol-users] Jmol -- two major advances

the software thread safe. Times seem to be changing, however. --Chuck - Original Message - From: Rolf Huehne rhue...@fli-leibniz.de To: jmol-users@lists.sourceforge.net Sent: Wednesday, April 07, 2010 12:13 PM Subject: Re: [Jmol-users] Jmol -- two major advances On 04/07/2010 05:37 PM, Robert

Re: [Jmol-users] Jmol -- two major advances

Which version of Jmol does creating isosurfaces progressively? I may have a little time next week to take a look at the code. Jmol 11.9 -- aka 12.0.RCx We have a couple of interfaces, and I could give you a quick rundown, but not on the users list, probably. I'll send you a note off-list Bob

Re: [Jmol-users] Jmol -- two major advances

Bob, On Wed, Apr 7, 2010 at 5:37 PM, Robert Hanson hans...@stolaf.edu wrote: I'm sure there is. And if VMD is any example, the use of GPUs would vastly increase performance. It would be a great project for someone to explore. Since I know nothing about parallel processing, I'm not the one to

Re: [Jmol-users] Jmol -- two major advances

On Wed, Apr 7, 2010 at 12:43 PM, Egon Willighagen egon.willigha...@gmail.com wrote: Bob, On Wed, Apr 7, 2010 at 5:37 PM, Robert Hanson hans...@stolaf.edu wrote: I'm sure there is. And if VMD is any example, the use of GPUs would vastly increase performance. It would be a great project

Re: [Jmol-users] Jmol -- two major advances

Robert Hanson schrieb: Question: What's the largest model in the PDB database? The largest asymmetric unit file is pdb1htq.ent.gz (20 MB, 906720 atoms). The largest biological unit file is 1m4x.pdb1.gz (314 MB, 16284240 atoms). The next one is 3k1q.pdb1.gz (99 MB, 6107880 atoms). Regards,

Re: [Jmol-users] Jmol -- two major advances

Thanks, Rolf. So pdb1htq.ent.gz loads, but takes unacceptably long to do so. So that's a great test case for improving load speed. I think I'll pass on 3k1q.pdb1.gz. Question: Does anyone know how to get PyMol to display the full biomolecule? Bob On Mon, Apr 5, 2010 at 7:49 AM, Rolf Huehne

Re: [Jmol-users] Jmol -- two major advances

Thanks, Peter. Yes, that's a killer. Definitely not ready to read 16,000,000 atoms! But I have added a new option that lets you load some smaller number of biomolecule transformations. Looks like we'll have to let Rolf open that one for us ;) On Mon, Apr 5, 2010 at 11:22 AM, Peter Rose

Re: [Jmol-users] Jmol -- two major advances

On Sun, Apr 4, 2010 at 5:59 AM, Robert Hanson hans...@stolaf.edu wrote: I'm aiming for a Jmol 12.0 release for June 1. In the mean time -- test, test, test! I have updated the status of the translations for Jmol, on the

Re: [Jmol-users] Jmol -- two major advances

minor point -- 4rhv (rhinovirus) biomolecule 1 (full capsid, all 392,520 atoms) loads just fine. I was just loading it in the programming environment rather than the applet and thought there was some sort of limitation, but it appears that was not real. HEADERRIBOSOME

[Jmol-users] Jmol -- two major advances

Jmol users and RCSB/PDB aficionados, Something for everybody here http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip contains a version of Jmol -- 12.0.RC3_dev -- that some of you may be interested in, and I'm very much interested in your testing. 1) Mega-size PDB files 2) true