tag:blogger.com,1999:blog-5744790168115177005.comments2013-04-18T17:16:17.423+02:00Proteins and Wave FunctionsJan Jensenhttps://plus.google.com/113593600676820394169noreply@blogger.comBlogger201125tag:blogger.com,1999:blog-5744790168115177005.post-2432793841676940752013-04-18T17:16:17.423+02:002013-04-18T17:16:17.423+02:00Is it available on arXiv?Is it available on arXiv?Anders Steen Christensenhttps://www.blogger.com/profile/18123073028209991396noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-61868233130754689942013-04-18T17:06:07.923+02:002013-04-18T17:06:07.923+02:00"I expected a more competent answer from Revi..."I expected a more competent answer from Reviewer #1."<br /><br />Requiring a vibration analysis from an adiabatic mapping? I guess I'm not able to submit my other PLoS ONE paper, then.Anders Steen Christensenhttps://www.blogger.com/profile/18123073028209991396noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-80989193773321077422013-04-18T13:55:26.530+02:002013-04-18T13:55:26.530+02:00Yes, one would hope.Yes, one would hope.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-21663626928059325572013-04-18T13:49:37.337+02:002013-04-18T13:49:37.337+02:00It will be interesting to see whether they stick t...It will be interesting to see whether they stick to their review criteria. I guess it's not unexpected that reviewers assume that the review criteria are similar to other journals, but one would hope that an editor would appreciate the difference.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-78403826994527896712013-04-18T12:21:09.235+02:002013-04-18T12:21:09.235+02:00Well, it's better than "this is exactly t...Well, it's better than "this is exactly the kind of incompetent answer I would expect from the group of Prof. Jensen" :) <br /><br />I sign all my reviews, and I would advice anyone who don't to write their reviews as if they did. Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-25614952873214033112013-04-18T12:14:29.867+02:002013-04-18T12:14:29.867+02:00I think the comment "I expected a more compet...I think the comment "I expected a more competent answer from the group of Prof. Jensen instead of no answer at all." was uncalled for. that's not professional at all. sadly.Casper Steinmannhttps://www.blogger.com/profile/10508646868117037632noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-17055287143646939762013-04-17T10:53:40.596+02:002013-04-17T10:53:40.596+02:00Well, my latest experiences with PLoS ONE have bee...Well, my latest experiences with PLoS ONE have been OK in terms of efficiency: http://proteinsandwavefunctions.blogspot.dk/search/label/plos%20one<br /><br />But I had a bad experience with an Elsevier journal: http://proteinsandwavefunctions.blogspot.com/2013/02/journal-of-molecular-catalysis-b-get.htmlJan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-39790745858072486852013-04-16T18:45:19.180+02:002013-04-16T18:45:19.180+02:00I too have had a similar experience with PLOS one,...I too have had a similar experience with PLOS one, as well as a series of emails which didn't actually make sense and were contradictory. Very frustrating.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-20028715568704950072013-03-20T13:51:03.998+01:002013-03-20T13:51:03.998+01:00Glad of being of help!Glad of being of help!lucahttps://www.blogger.com/profile/14520546290899102320noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-9974770700806693832013-03-15T08:16:13.643+01:002013-03-15T08:16:13.643+01:00This comment has been removed by the author.lucahttps://www.blogger.com/profile/14520546290899102320noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-33670859329378419382013-03-15T02:05:28.928+01:002013-03-15T02:05:28.928+01:00Hi guys. It would have been easier to read the dra...Hi guys. It would have been easier to read the draft if it would have been indexed. Check this post:<br /><br />http://proteinsandwavefunctions.blogspot.dk/2011/05/importance-of-being-indexed.html<br /><br />I put together a few comments, but it was too cumbersome to post them one by one. You can see them here:<br /><br />https://www.dropbox.com/s/vng1txb03pt71od/Interface_of_the_polarizable_continuum_model_of_solvation_with_semi_empirical_methods_in_the_GAMESS_program.pdf<br /><br />Cheers!<br />lucahttps://www.blogger.com/profile/14520546290899102320noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-10066827674612411622013-03-09T22:16:38.662+01:002013-03-09T22:16:38.662+01:00It seems to have all the features from JMol. Right...It seems to have all the features from JMol. Right click and choose 'file'.Jimmy Charnley Kromannhttps://www.blogger.com/profile/01362349033236738393noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-790991336068337902013-03-09T15:11:29.062+01:002013-03-09T15:11:29.062+01:00... but that doesn't matter. Post updated... but that doesn't matter. Post updatedJan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-28041091402257575982013-03-09T14:47:39.408+01:002013-03-09T14:47:39.408+01:00Let's try that equation again: $$r=\sqrt{ 1-\f...Let's try that equation again: $$r=\sqrt{ 1-\frac{RMSD_{fit}^2}{\sigma^2_x}}$$ Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-26404271261992705892013-03-09T13:45:55.137+01:002013-03-09T13:45:55.137+01:00Can JSMol write to disk?Can JSMol write to disk?mzhhttps://www.blogger.com/profile/01717022761119254985noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-34744003648072141472013-03-09T09:55:39.794+01:002013-03-09T09:55:39.794+01:00Yes, I should have written $r$ instead of $R^2$. ...Yes, I should have written $r$ instead of $R^2$. This led me to look more carefully at everything and I discovered I made a mistake when computing the RMSD and MUE. <br /><br />I had a look at $r^2$. For linear models this is also the coefficient of determination (http://en.wikipedia.org/wiki/Coefficient_of_determination), which is a measure of how much the total variation in $y$ is described by the linear fit. Long story short: $$r={sqrt{1-\frac{\sigma_y^2/n}{RMSD_{fit}^2}}$$So not exactly easy to interpret in terms of RMSD and no direct relation to the RMSD of the data before the fit.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-66597020518496946772013-03-08T13:30:46.372+01:002013-03-08T13:30:46.372+01:00I do recall having read somewhere that in linear r...I do recall having read somewhere that in linear regressions R-squared can be interpreted as the fraction of the total variance that is "explained" by the regression model. In your data, R-squared is 0.47 and R=0.69 (as computed from your original data. I believe you mistakenly wrote R2 instead of R). That means that the the regression explains 47% of the variance, i.e. 69 % of the original RMSD (which is the square root of the variance). <br /><br />Pedro Shttp://biochemicalmatters.blogspot.comnoreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-75793286232233523392013-03-07T11:15:10.784+01:002013-03-07T11:15:10.784+01:00The correlation coefficient also has a geometric i...The correlation coefficient also has a geometric interpretation:<br />http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient#Geometric_interpretation<br /><br />Another curiosity regarding R is the Anscombe's quartet:<br />http://en.wikipedia.org/wiki/Anscombe%27s_quartetAnders Steen Christensenhttps://www.blogger.com/profile/18123073028209991396noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-80032741217082460552013-02-28T14:28:15.414+01:002013-02-28T14:28:15.414+01:00I could tell you, but ...I could tell you, but ...Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-77391762643105603742013-02-28T14:24:20.536+01:002013-02-28T14:24:20.536+01:00An English major? You've been involving the mi...An English major? You've been involving the military?Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-78019329114066581742013-02-28T12:54:02.824+01:002013-02-28T12:54:02.824+01:00As you can see, I need professional help!As you can see, I need professional help!Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-76636583356000947392013-02-28T12:50:06.525+01:002013-02-28T12:50:06.525+01:00'a but out of date' should be 'a bit o...'a but out of date' should be 'a bit out of date', otherwise one starts to get strange ideas about the contents of this blog.<br />For checking for basic grammar and mispelling errors, why not copying the entire text in a word processor file, and let that program work for you? For example, 'a graphic designers' would have been caught, even if 'I really surprised' would have been accepted.lucahttps://www.blogger.com/profile/14520546290899102320noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-16048465337175567132013-02-28T10:44:18.398+01:002013-02-28T10:44:18.398+01:00A related story, in danish, can be found here: htt...A related story, in danish, can be found here: http://christian.panton.org/post/44065883181/hvordan-skal-vi-tjene-penge-nar-alt-pa-internettet-erCasper Steinmannhttps://www.blogger.com/profile/10508646868117037632noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-45407624957945792132013-02-23T11:57:57.054+01:002013-02-23T11:57:57.054+01:00ups! thanks, Jimmyups! thanks, JimmyJan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-5744790168115177005.post-15058916919839402902013-02-23T11:41:20.673+01:002013-02-23T11:41:20.673+01:00http://proteinsandwavefunctions.blogspot.dk/2013/0...http://proteinsandwavefunctions.blogspot.dk/2013/01/project-status-pm6-and-pcm-in-gamess.htmlJimmy Charnley Kromannhttps://www.blogger.com/profile/01362349033236738393noreply@blogger.com