search for: rmsd

Hi R users This is not related to R but general stats terms. I f any one help me to figure out how they differ and when I need to use which one, i will appreciate it. I read several simulation studies and found that RMSE (Root Mean Square Error) and RMSD (Root Mean Square Difference) appered to be used interchangeablely. The formula for calculating for both RMSE and RMSD are, to me, the same. Are they the same or am I misunderstood ? TM

Hi everybody, I'm trying to create a script that picks a txt file with 2 columns of coordinates (depth and variable1) and automatically tries to fit several polynomial with the function nls(). After that, it creates a list of observed, predict, residuals and other, and then it calculates AIC, RMSD, MAD and R^2. At the end of the script I create a series of vectors with MAD for all polynomials, RMSD for all polynomial and so on, and from a matrix a .csv file. This script is completely automatic, but there is a problem if one or more models don't fit, because if one or more data is missing...

Hello!!! I have a question about clustering. I'll present my problem first. I have a simulation of a protein trayectory (a file with a time series of protein 3D-coordinates), from it I can calculate the Root Mean Square desviation (RMSD) beetween any pair of structures in the trayectory, which is a rough idea of 3D similarity beetween them. If for every conformation (trayectory frame) I calculate the RMSD with all other frames in the trayectory, I get a RMSD matrix, which is the data i have now. In some published works a confor...

This is an updated and extended version of the original patch: https://www.redhat.com/archives/libguestfs/2010-August/msg00163.html This adds OCaml and Perl bindings (both tested), support for progress bars in virt-resize, and adds progress notifications to a number of the simpler commands. Still to do is to add progress messages to more commands. There are still a few commands which would be

http://bugzilla.mindrot.org/show_bug.cgi?id=394 ------- Additional Comments From markus at openbsd.org 2002-09-11 22:52 ------- openssh does not have the bug described in http://www.tartarus.org/~owen/putty-docs/AppendixA.html#A.6 what do you see? what ciphers are used? what hmac? what does sshd -ddd say when a client connects? do you have more information? ------- You are receiving

Hi everyone, I have two matrices of 2000x2000 size. They consist of a measurement of RMSD deviations of a protein structure. The basic question i want to answer is the following: are there a significant differences between the two matrices? I aim to use the Mantel test. I don't really know if this is a good idea or if there are better solutions for these mega matrices. Thanks [[...

...m successfully setting up a number of panels (25) in which I have two box and violin plots. I would like to colour - one plot as RED and the other as BLUE (in each panel). I can do that with the box plots, but the violin density areas just take on one colour. My basic call is as follows: bwplot(rmsd ~ file | code, data=spread_data.filtered, panel = function(..., box.ratio){ panel.violin(..., col = c("red", "blue"), cut = 1, varwidth = FALSE, box.ratio = box.ratio) panel.bwplot(..., fill = c("red", "blue"), box.ratio = .1, pch=&quo...

I tried to use R version of package I noticed the original MatLab Pckage is much better documented. I had a look at the R demo code "gtm_demo" and found that variable Y is used in advanced of being created: I wrote my own few lines as follows: inDir <- "C:/Documents and Settings/Monville/Alanine Dipeptide/DBP1/DHA" setwd(inDir) T <-

Hi, Standard correlations (Pearson's, Spearman's, Kendall's Tau) do not accurately reflect how closely the model (GAM) fits the data. I was told that the accuracy of the correlation can be improved using a root mean square deviation (RMSD) calculation on binned data. For example, let 'o' be the real, observed data and 'm' be the model data. I believe I can calculate the root mean squared deviation as: sqrt( mean( o - m ) ^ 2 ) However, this does not bin the data into mean sets. What I would like to do is: oangry...

...t. Have you seen this kind of problem, or is there some other data that we can provide that would help provide a software workaround for this problem? -- Michael Below I have copied several relevant entries from our internal bug tracking system =================Trouble log================== RMSD Update 4/29/04 by Villanueva, Jorge (4/29/2004 4:58:31 PM) >From the traces I am seeing that after the Reset is issue the host (Linux DSA 8.2) does not issue Read commands for a very large portion of data when compared with a passing case. This could be the cause of the corruption. When compa...

Hi, I have a PHILIPS CD-RW/DVD-ROM SCB5265 and I have problems reading of some DVDs. I found two different firmware updates which contains .exe files: TD17 (5/1/2007): http://ftp.us.dell.com/rmsd/PHILIPS-SCB5265-TD17.zip TD19 (12/13/2005): http://ftp.us.dell.com/rmsd/SCB5265_fwTD19.zip If I set up the IDE SCSI emulation, the firmware updater can recognize my CD-RW/DVD-ROM drive. # rmmod ide-cd # modprobe -k ide-scsi The dmesg now contains the following lines: SCSI subsystem initialized...

These two patches are probably not completely independent, but separating them is a lot of work. With *both* patches applied, all the tests and extra-tests pass. That's no guarantee however that there isn't a mistake, so I don't think this patch is a candidate for the 1.16 branch, until it's had a lot more testing in development. Rich.