Hello Kathleen, I'm seeing this behaviour: - if I request to view a single FER1_MAIZE structure (1GAQ / 3B2F / 3W5U / 3W5V), I get the prompt and can superimpose on FER1_SPIOL (1A70) - if I request to view 'all 4 structures' then I don't get the prompt, a new window is opened - this behaves consistently if I repeat the process (whether closing the original viewer window or not)
Is that what you're seeing? If not, let me know what you are doing / seeing differently. The fact that Jalview doesn't offer to superpose multiple structures is a bug which we noticed recently and will address in a future version (http://issues.jalview.org/browse/JAL-1761). Thanks, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> ________________________________ From: [email protected] <[email protected]> on behalf of Kathleen McLeod <[email protected]> Sent: 11 June 2015 20:29 To: [email protected] Subject: [Jalview-discuss] JalView 3D Protein Alignment Hello! I am working on aligning two 3D PDB structures. I have followed the instructions on the Jalview 2.8.2 Manual and Tutorial as follows: Exercise 15: Aligning structures using the ferredoxin sequence alignment. 1. 15.a. Continue with the Jalview project created in exercise 14. Use the Discover PDB IDs function to retrieve PDB IDs associated with the FER1_MAIZE sequence. 2. 15.b. Once discovery has completed, use the View PDB Structure submenu to view the PDB file associated with FER1_MAIZE. Jalview will give you the option of aligning the structure to the one already open. To superimpose the structure associated with FER1_MAIZE with the one associated with FER1_SPIOL, press the Yes button. The Jmol view will update to show both structures, and one will be moved on to the other. If this doesn't happen, use the Align function in the Jmol submenu 15.c. Create a new view on the alignment, and hide all but columns 121 through to 132. 15.d. Use the Jmol submenu to recompute the superposition using just columns 121-132 of the alignment. Note how the molecules shift position when superposed using a short part of the two structures. 15.e. Compare the initial and final RMSDs for superimposing molecules with the small section and with the whole alignment. Which view do you think give the best 3D superposition, and why ? I have been having trouble with repeating 15 b, it worked the first time. I have the FER1_SPIOL 3D structure open in JalView from Exercise 14, and then open the FER1_MAIZE 3D structure. The first time I did this it asked me if I wanted to overlay them, and it worked. Now, when I try to redo the whole procedure, when I open the FER1_MAIZE structure it just opens in a separate 3D window and doesn't prompt me about overlaying the two 3D structures, so I am left with two separate structures in different windows, rather than both structures overlapped and aligned in a single 3D view window. How do I get around this? Thanks, Kathleen McLeod The University of Dundee is a registered Scottish Charity, No: SC015096
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