[Proteopedia] Difficulty making scenes

Oberholser, Karl oberhols at messiah.edu
Sat Apr 28 14:54:18 EDT 2012


Jaim & Eric,

I know you attention is focus on other things this weekend, but I will bring you up to date with my latest findings.  I finally realized that in all the scenes that I was attempting to make, except the opening scene of collagen, I was using this series of commands: select protein; calculate structure; cartoon; color structure; calculate hbonds structure;. While playing with some scenes I saw the following message in the Jmol console:

script compiler ERROR: missing END for data
----line 263 command 25 of /wili/scripts/User:Karl_Oberholser/Sandbox_1/initial/1.spt
         data "connect <<<<

Link to the script is http://proteopedia.org/scripts/User:Karl_Oberholser/Sandbox_1/Initial/1.spt.

When you have the time I would also like your input on why my attempts to make an opening scene for Collagen produce a script which contains only exit;.  These are my three attempts http://proteopedia.org/scripts/Collagen/Initial/1.spt, proteopedia.org/scripts/Collagen/Opening/1.spt, and proteopedia.org/scripts/Collagen/Opening/2.spt.  I started with this script http://proteopedia.org/scripts/Collagen/Fiber_segment/2.spt because when I attempt to load 4clp.pdb I only obtain a single atom.  This scene has the five tropocollagens colored differently, and I simply try to color all of them cpk.  This color change occurs in the SAT, but the only thing that is saved is exit;.  I just tried making the scene again with the same result.

Have a productive weekend,
Karl




________________________________________
From: proteopedialist-for-users-bounces at bioinformatics.org [proteopedialist-for-users-bounces at bioinformatics.org] on behalf of Oberholser, Karl [oberhols at messiah.edu]
Sent: Wednesday, April 25, 2012 11:26 AM
To: Proteopedialist-for-users at bioinformatics.org
Subject: [Proteopedia] Difficulty making scenes

Hi All,

Am I the only one having difficulty making scenes since the upgrade of Jmol?  One scene I made since then worked intermittently for a week or two and now is working consistently.   All others have failed to function.  I give some examples below.

I tried to make an opening scene for Collagen starting with proteopedia.org/scripts/Collagen/Fiber_segment/2.spt.  I have made three attempts and with all three the scripts only contain exit:, http://proteopedia.org/scripts/Collagen/Initial/1.spt, proteopedia.org/scripts/Collagen/Opening/1.spt, and proteopedia.org/scripts/Collagen/Opening/2.spt.

The opening scene of Calculate Structure is the one that worked intermittently but now works consistently.  proteopedia.org/scripts/Calculate_structure/Turn_110/2.spt is a a script that I wanted to update with commands now available in 12.3.  Scripts http://proteopedia.org/scripts/Calculate_structure/Turn_110/3.spt, http://proteopedia.org/scripts/Calculate_structure/Turn_110/4.spt, and http://proteopedia.org/scripts/Calculate_structure/Turn_110/5.spt are my attempts to do that.  With my level of understanding I do not see anything in these scripts that would be causing a problem.

I tried to upgrade the opening scene, http://proteopedia.org/scripts/Secondary_structure/1dtg_ss/1.spt, of Secondary structure with the new commands of 12.3, and these were my two attempts http://proteopedia.org/scripts/Secondary_structure/1dtg_ss/2.spt and http://proteopedia.org/scripts/Secondary_structure/1dtg_ss/3.spt.  Again with my level of understanding I do not see anything that would cause a problem.

I am completely dumbfounded!

Karl


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