search for: bio3d

Is it just me, or is the bio3d package no longer available? Is there another way to do a reasonable nucleic acid sequence alignment in R? Thanks, Jonathan [[alternative HTML version deleted]]

Hello, I have a problem, when I run read.fasta.pdb I get this error: pdb/seq: 1 name: dcluster.1 Error: subscript out of bounds My FASTA file is the sequence of the bovine insuline. Thanks in advance, Rg -- View this message in context: http://n4.nabble.com/problem-with-bio3d-package-tp1012116p1012116.html Sent from the R help mailing list archive at Nabble.com.

Hi everyone,  I am using bio3d package for some sequence analysis because of its nice integrated MUSCLE execution. However, I have been encountering some errors while I was running seqaln function, which calls for installed MUSCLE program. In my case, I stored the MUSCLE program on the desktop with pathway of "./Desktop/mus...

Hi, I'm new with R and I was wondering if there was a way to open a folder containing multiple text files and go through each file. These files contain protein sequences, however, I wanted to see if there was a way of going through each file without using bio3d, just R Thanks a bunch :). ps if you could explain variables/ functions that would be great!!! -- View this message in context: http://r.789695.n4.nabble.com/Analyzing-multiple-text-files-tp4634315.html Sent from the R help mailing list archive at Nabble.com.

...dir=/usr/local/netcdf/include -with-netcdf_libdir=/usr/local/netcdf/lib" ncdf_1.6.tar.gz The installation was successful. But when i try to use ncdf inside R, i get the following error. Kindly help me how to resolve the problem. > trjfile<-system.file('test.netcdf',package='bio3d') > trj<-read.ncdf(trjfile) Loading required package: ncdf Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/lib/R/library/ncdf/libs/ncdf.so': /usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after reloc: Permission denied E...

I am trying to write a program that uses R and takes a pdb file, and converts it to a pqr file. This task is simple generally, using the website, http://pdb2pqr-1.wustl.edu/pdb2pqr/. How do you use R to input a pdb file (that is on hand) into the upload pdb file input, and run the website and give the return file to be a pqr file. Thanks for your help. -- View this message in context:

.... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et G?nomique Int?grative IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 http://www-bio3d-igbmc.u-strasbg.fr/~wraff wolfgang.raffelsberger at igbmc.u-strasbg.fr

i made jDialog through JGR package(Java gui 4 R), i want to export it with imported external package e.g.bio3d,RCOR , into .exe or if not possible convert code to executable jar file how should i go, give me package name,example codes (if possible) -- View this message in context: http://r.789695.n4.nabble.com/how-to-made-exe-of-any-gui-project-in-R-tp4375938p4375938.html Sent from the R help mailing l...

...u-r r-noncran-lindsey gnu-r r-other-gking-matchit gnu-r r-recommended gnu-r r-cran-colorspace gnu-r r-cran-epibasix gnu-r r-cran-epitools gnu-r r-cran-genetics gnu-r r-cran-haplo.stats gnu-r r-cran-qvalue gnu-r r-cran-randomforest gnu-r r-cran-sp gnu-r r-cran-xtable gnu-r r-other-bio3d gnu-r -- Three out of two people have difficulties with fractions.