[Jmol-users] Ramachandran plot of selected residues?

There was a feature in Rasmol that allowed one to display a Ramachandran plot of the selected residues. This was a great tool for teaching protein structure. For example, you could separately display Ramachandran plots for all glycines in a protein, all prolines, or all non-glycine and

[Jmol-users] initial view of molecule

I just noticed something peculiar. With Jmol 13.0.10 the initial view of a molecule depends on the method used to open the file. -- If you open a file using the Open command in the File menu, the initial view is in Cartoon style. -- If you open a file using the Recent Files... command, the

Re: [Jmol-users] initial view of molecule

Bob-- It's not hugely important to have Open and Recent Files... do the same thing, but I think it would be nice. I do prefer the Cartoon style (with ligands in ball-and-stick) as the initial view, especially for students. Jeff

[Jmol-users] multiple molecules in Jmol window

within the last 10 days. Strangely, whenever a student who had this problem reopened the same file in Jmol in a new Jmol session, only one molecule was seen in the image. Any idea what is going on? Jeff Cohlberg -- Dr. Jeffrey Cohlberg Department of Chemistry and Biochemistry California State

[Jmol-users] Studying Protein and Nucleic Acid Structure with Jmol

that uses either the Stryer or Lehninger text should have access to the Launchpad for that course, which includes an online version of the manual. I hope that some of you will find the manual useful, and I welcome your comments and suggestions for improvement. Jeff -- Dr. Jeffrey Cohlberg Department

[Jmol-users] FW: Windows help for an ignorant Mac user

Please ignore this message. I think that the students who had trouble had failed to install Java on their computers. Sorry for wasting your time with this. Jeff On 2/5/15, 4:32 PM, Jeffrey Cohlberg jeffrey.cohlb...@csulb.edu wrote: I downloaded the Jmol 14.2.12 to my Mac and launched

[Jmol-users] Windows help for an ignorant Mac user

I downloaded the Jmol 14.2.12 to my Mac and launched it by double-clicking on the jmol.jar icon, as described in the online instructions and as I have done in the past. This procedure used to work for Windows as well. But now when my students download the Windows version, jmol.jar is not the name

[Jmol-users] problem with MUTATE?

was that the his was changed to tyr on the D chain (very cool!) but not on the B chain. Why not both chains? Jeff -- Dr. Jeffrey Cohlberg Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd Long Beach, CA 90840 562-985-4944FAX 775-248-1263

[Jmol-users] loading gzipped files

I have two fairly trivial but pesky problems, both relating to the standalone version of Jmol, jmol.jar. I’m using a Mac with System 10.11.6. --With Jmol 14.18.1 I could download gzipped versions of files (.pdb.gz) and open them directly in Jmol, using either the Open command from the File

[Jmol-users] Jmol Tutorial Manual now online and accessible

My manual “Exploring Protein and Nucleic Acid Structure with Jmol” can be downloaded at www.csulb.edu/~cohlberg/Jmolmanual.html. It contains self-guided exercises that enable the user to learn how to download structures from the PDB and display