Comment by marcin on How do I decompress a DSN6 file into a readable format?
You can't view DSN6 file as a model, because it's not a model, it's volumetric data (electron density). For details of the format see web.archive.org/web/20170721175122/http://… Converting it to text...
View ArticleComment by marcin on How to select only RNA with Hetero atoms from pdb file...
maybe this question could be moved to bioinformatics.SE.
View ArticleComment by marcin on How to compare two txt files and then apply changes in...
@MrFuppes it's PDB format. But I agree that it'd be easier to use a dedicated parser: from BioPython, BioPandas, cctbx or gemmi (disclaimer: the last one is written by me).
View ArticleComment by marcin on Converting segments of large .cif files to smaller .pdb...
@IllimarRekand yes, I know that when I answer after a few months the original poster already moved on. But I thought I'd post it for other people who may have this problem in the future.
View ArticleComment by marcin on Why is Travis CI showing failing build icon althought...
similar question: stackoverflow.com/questions/33011816/…
View ArticleComment by marcin on Replace values in a column while preserving the format
The pdb format is a fixed-width format. In your example you replace B-factor, which is in columns 61-66 (column = position in the line).
View ArticleComment by marcin on How to add a Chain, Residues and atoms in pdb file?
shouldn't you have brackets after topology.Topology?
View ArticleComment by marcin on Clang undefined behavior sanitizer in shared library...
a workaround for the error (based on stackoverflow.com/a/50621267/104453) is to to preload the shared library with the symbol: LD_PRELOAD=$(clang -print-file-name=libclang_rt.ubsan_standalone-x86_64.so)
View ArticleComment by marcin on Locale-invariant string processing with strtod strtof...
another option is stb_sprintf from stb libraries
View ArticleComment by marcin on Keeping format of a pdb file with conditionals
This is clearly the PDB format. Columns here have fixed width but don't need to be separated with whitespace.
View ArticleComment by marcin on confused about the annotation on pdb website
The PDB can rename chains after deposition. auth here stands for author. B [auth C] likely means that originally it was named (by author) C and then renamed by the PDB to C. Note: this is not a...
View ArticleComment by marcin on Merging covariance from two sets to create new covariance
The link redirects to authentication page.
View ArticleComment by marcin on How can I parse alternative atom information in a PDB file?
You can either use a library for parsing PDB files (biopython, BioJava, cctbx, gemmi, …) or read the format specification.
View ArticleAnswer by marcin for How to retrieve the GCC version used to compile a given...
Yet another two ways (maybe a bit simpler) that I've just read about here: https://unix.stackexchange.com/questions/719/can-we-get-compiler-information-from-an-elf-binary$ readelf -p .comment...
View ArticleAnswer by marcin for vector and const
in addition to other answers, it's worth reading C++ FQA Lite where this (and many others C++ features) are discussed from a critical POV:http://yosefk.com/c++fqa/const.html#fqa-18.1
View ArticleAnswer by marcin for Multi-peak fitting in Java with a gaussian and...
You may look at libfityk, a part of fityk (source code at GitHub). Disclaimer: I'm the author. Fityk is a program for (multi) peak fitting and more generally curve fitting and xy data analysis....
View Articleminimal Fortran file that compiles with any compiler
CMake developers recommend adding a dummy Fortran file to tell CMake that static libraries need to be linked with Fortran libraries (for example when linking C program with LAPACK).My first thought was...
View ArticleAnswer by marcin for CMake: find wxWidgets built with MinGW/MSYS?
From FindwxWidgets.cmake:if(WIN32 AND NOT CYGWIN AND NOT MSYS) set(wxWidgets_FIND_STYLE "win32")else() if(UNIX OR MSYS) set(wxWidgets_FIND_STYLE "unix") endif()endif()So Unix-style tree is assumed for...
View ArticleAnswer by marcin for Call external program from autoconf-generated makefile
I don't know protoc, but I run other programs from Makefile.In my case programs generate platform-dependent data and don't work when cross-compiling. You probably don't need these checks.in...
View Article
