Hi! I'm having a great time playing with Jalview Desktop, but I ran across a couple of things that may or may not be related.
Starting with a large alignment from Pfam (PF00532 full alignment with >5K sequences), which apparently includes many blank columns, I get different results when redundancy-filtering to 90% before and after removing the blank columns. Namely I get only a couple of sequences remaining when I filter before removing the blank columns, but hundreds remaining if I do it after removing the blank columns. Could it be due to running out of memory when I still have all the blank columns, or are blank columns somehow used when calculating % identity? Suspecting memory issues, I got the launchApp jnlp for 1G from your website http://www.jalview.org/jvmmemoryparams.html However, when I use that and then from the Tools menu choose to show memory usage, the max value is no different than before. Shouldn't the max be 1G? Also, when I use launchApp it complains it couldn't open the examples file even though I had earlier specified in my Jalview preferences not to open that file. I'm a little unclear on whether it should be using the same settings (apart from memory allocation) as when I start by double-clicking the jalview.jnlp vs this launchApp file. Thanks, as you know I'm a newbie but I try to figure it out from the documentation whenever possible! Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. as to Mark's issue, I'm not having the problem with secondary structure display… I don't know what it looked like originally, but in what I downloaded today I see green arrows for strands and red oblongs for helices _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
