ResMap

ResMap is a Python (NumPy/SciPy) application with a Tkinter GUI. It is a software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM).

How Do I Use It?

Please read the documentation within the source files.

What Should I Download?

Sourceforge should automatically present you with the latest binary for your platform.

The binaries have been packaged using PyInstaller and were tested on:

• Windows: 10 but unstable at this stage
• Mac: 10.6+ (Binary prepared on 10.13.5 High Sierra)
• Linux: Fedora 14+ and 26, CentOS 6+, Ubuntu 17.04x64, Mint 18.2x64(cinnamon), OpenSuse TumbleWeed_x64, CentOS 6+.

You may also download the source files (Python) and run them using your own Python setup.

Requirements under python3 are:

• Python (3.5.2+) [Python 2.X is no longer supported and not compatible]
• NumPy (Mint: 1.13.3+, Ubuntu-17.04: 1.13.1+, OpenSuse: 1.13.3+, Fedora-26+: 1.13.3+, MacOsX: 1.14.2+)
• SciPy (Mint: 0.19.1+, Ubuntu-17.04: 0.19.1+, OpenSuse: 0.19.1+, Fedora-26+: 0.19.1+, MacOsX: 1.0.1+)
• Matplotlib (OpenSuse: 2.0.2+, same for other Linux, MacOsX: 2.2.2+)
• tkinter (under pyhton3) (MacOsX: 8.5)

GPU Component:

LINUX:

The GPU component have been pre--compiled and provided as a library file, it is typically called

ResMap_krnl-cuda-V9.0.102-sm30_gpu.so ResMap_krnl-cuda-V9.0.102-sm35_gpu.so ... ResMap_krnl-cuda-V9.0.102-sm60_gpu.so

These files are only compatible on a Linux system.

The details of the compilers used to generate the files just mentioned on the system described in the manual and are as follows:

user@host:>which nvcc /usr/local/cuda-9.0/bin/nvcc

user@host:>gcc --version ; g++ --version ; nvcc --version gcc (Ubuntu 6.3.0-12ubuntu2) 6.3.0 20170406 Copyright (C) 2016 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

g++ (Ubuntu 6.3.0-12ubuntu2) 6.3.0 20170406 Copyright (C) 2016 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2017 NVIDIA Corporation Built on Mon_Jun_26_16:13:28_CDT_2017 Cuda compilation tools, release 9.0, V9.0.102

--- *** known issues ***: under python3.5.2 with lower numpy versions than listed

Traceback (most recent call last): File "ResMap.py", line 565, in <module> noiseDiagnostics = args['--noiseDiag'] File "./ResMap_algorithm.py", line 254, in ResMap_algorithm LPFtest = isPowerSpectrumLPF(dataPowerSpectrum) File "./ResMap_spectrumTools.py", line 444, in isPowerSpectrumLPF if peakInd.any(): AttributeError: 'list' object has no attribute 'any'