atom.select is unable to select atoms from prmtop file

[Former user]

I am crating a prmtop file with tleap from AmberTools14 (TestCreatePrmtop.leap). I can read the prmtop file with prmtop and it seems that it is correctly read:

testprmtop <- read.prmtop("testpep.prmtop") testprmtop

Call: read.prmtop(file = "testpep.prmtop")

Class: amber, prmtop

System information: Total number of atoms: 74 Solute residues: 5 Solute molecules: 1

Sequence: AAKGK

But I cannot select atoms from it (I am following the same procedure as in the help of as.pdb.)

crds <- atom.select(testprmtop,"calpha") Error in as.pdb.default(xyz = crd$xyz, elety = prmtop$ATOM_NAME, resno = resno, : 'xyz' must be a numeric vector/matrix

crds <- atom.select.prmtop(testprmtop,"calpha") Error in as.pdb.default(xyz = crd$xyz, elety = prmtop$ATOM_NAME, resno = resno, : 'xyz' must be a numeric vector/matrix

packageDescription("bio3d") Package: bio3d Title: Biological Structure Analysis Version: 2.2-2 Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide VignetteBuilder: knitr Imports: parallel, grid Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (>= 0.9.1) Depends: R (>= 3.1.0) LazyData: yes Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information. Maintainer: Barry Grant [e-mail] License: GPL (>= 2) URL: http://thegrantlab.org/bio3d/, http://bitbucket.org/Grantlab/bio3d Packaged: 2015-03-03 00:24:17 UTC; xinqyao NeedsCompilation: no Repository: CRAN Date/Publication: 2015-03-03 07:34:13 Built: R 3.2.0; ; 2015-05-04 15:36:53 UTC; unix

[Lars Skjærven]

This bug should be fixed in one of the later bug fixes which has not reached CRAN yet. You can install the latest version with bugfixes with these commands:

install.packages("devtools")
library(devtools)
install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/", ref="releases")

[Edwin Aponte]

Solved, many thanks.

[Juan Eiros]

Hi,

I wrote some days ago having the same problem, and just now have been trying to install this package with no luck. I am pretty new to R, can you please suggest why I am not able to install the devtools package? This is the error I get when I've tried to do it (I've run the same commands as root, receiving the same error messages)

> install.packages("devtools")
Installing package into ‘/home/je714/R/x86_64-redhat-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
also installing the dependencies ‘xml2’, ‘rversions’, ‘git2r’

trying URL 'http://cran.rstudio.com/src/contrib/xml2_0.1.1.tar.gz'
Content type 'application/x-gzip' length 73772 bytes (72 Kb)
opened URL
==================================================
downloaded 72 Kb

trying URL 'http://cran.rstudio.com/src/contrib/rversions_1.0.1.tar.gz'
Content type 'application/x-gzip' length 4624 bytes
opened URL
==================================================
downloaded 4624 bytes

trying URL 'http://cran.rstudio.com/src/contrib/git2r_0.10.1.tar.gz'
Content type 'application/x-gzip' length 1014817 bytes (991 Kb)
opened URL
==================================================
downloaded 991 Kb

trying URL 'http://cran.rstudio.com/src/contrib/devtools_1.8.0.tar.gz'
Content type 'application/x-gzip' length 141487 bytes (138 Kb)
opened URL
==================================================
downloaded 138 Kb

* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Could not find libxml2. Please install libxml2-devel (rpm) or libxml2-dev (deb).
ERROR: configuration failed for package ‘xml2’
* removing ‘/home/je714/R/x86_64-redhat-linux-gnu-library/3.1/xml2’
Warning in install.packages :
  installation of package ‘xml2’ had non-zero exit status
* installing *source* package ‘git2r’ ...
** package ‘git2r’ successfully unpacked and MD5 sums checked
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for library containing inflate... -lz
checking for library containing SSL_library_init... no
configure: error: in `/tmp/RtmppfBAwI/R.INSTALL1d0e49bd1c98/git2r':
configure: error: OpenSSL library required
See `config.log' for more details
ERROR: configuration failed for package ‘git2r’
* removing ‘/home/je714/R/x86_64-redhat-linux-gnu-library/3.1/git2r’
Warning in install.packages :
  installation of package ‘git2r’ had non-zero exit status
ERROR: dependency ‘xml2’ is not available for package ‘rversions’
* removing ‘/home/je714/R/x86_64-redhat-linux-gnu-library/3.1/rversions’
Warning in install.packages :
  installation of package ‘rversions’ had non-zero exit status
ERROR: dependencies ‘rversions’, ‘git2r’ are not available for package ‘devtools’
* removing ‘/home/je714/R/x86_64-redhat-linux-gnu-library/3.1/devtools’
Warning in install.packages :
  installation of package ‘devtools’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/Rtmp2Ru1SN/downloaded_packages’

I've tried installing the libxml2 packages that seem to be missing, but I cannot find them with Rstudio.

Sorry if I'm missing something really obvious.

[Lars Skjærven]

Hi Juan, You're on a red hat system right? Can you use yum for installing the missing libraries? i.e.

yum install openssl-devel.x86_64 libxml2-devel  

Make sure you have the file /usr/lib64/libxml2.so (or something like that) after the installation. Hope it helps. Lars

[Juan Eiros]

Hi Lars,

I forgot to say that in the message, my bad.

Thanks for your suggestions, they worked perfectly.

Best Juan