Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.     

Quantu-design and development of a software package dedicated to k0-standardized NAA

This work shortly describes the main steps involved in the design and development of the software package Quantu, created to conduct k ₀-standardized NAA. The package comprises a database as well as two individual programs. Quantu-MCA is dedicated to (g-ray spectrum analysis and Quantu-INAA is the interface for the database administration, also dealing with k ₀-method calculations.     

Quantum-chemical study of spectral and luminescent properties and photochemistry of polyatomic molecules

The potential of a package of quantum-chemical software programs for exploring physicochemical problems pertaining to polyatomic organic molecules is highlighted. The results of investigation into the spectral, luminescent, and photochemical properties of molecules are discussed. The necessity of development of target-oriented models for studying the problems of physics and chemistry of molecules is emphasized.     

Aids to software development for single-board microcomputers

A general-purpose microcomputer running the CP/M disk operating system is used to develop software for minimum-configuration microcomputers. The implementation of the minimum system software is facilitated by a software development package that runs in the general-purpose computer, a powerful monitor that resides in the minimum system, and an erasable programmable read-only memory programmer based on a single-board computer. With this development system, programs can be entered, edited, and assembled and the resulting object code transferred to the small computer for testing interactively via the terminal of the main computer.     

JESS, A joint expert speciation system-I. Raison d'être

JESS is a new computer package for modelling chemical systems in solution and performing numerical analyses on associated experimental data. It was developed to solve problems requiring specialist knowledge of chemical speciation. It currently comprises over 150 programs, 1200 subroutines and 120,000 lines of Fortran code. The main reasons for the development of JESS, and the principles which underpin it, are described. Subsequent papers detail the major facilities which JESS now provides.     

粉末衍射峰形拟合程序包CPOWDER

开发了一个Ｘ射线和中子粉末衍射峰形拟合程序包ＣＰＯＷＤＥＲ,它是由多个最小二乘峰形拟合程序与蒙特卡罗分峰程序组成的。最小二乘峰形拟合程序可用于约束条件下的峰形拟合分析,蒙特卡罗分峰程序可用于寻找全局最优解,为最小二乘拟合程序提供优质的峰形参数初始值,两者结合使用特别适合于多个严重重叠峰的分离。     

Automated identification and plotting of the function y = f(x)

A series of programs has been edited for automated identification and plotting of the function y=f(x). The QN-AU series contains thousands of models, which consists of various functions and their combinations. After input of data, the package selects automatically the most suitable model within a given range and produces a graphic display. The package can be run on various personal computers such as the IBM-PC or Apple II.     

Software package for quantitative analysis of solid materials by energy-dispersive x-ray fluorescence spectrometry without absolute calibration

A software package for quantifying elements in solids from energy-dispersive x-ray fluorescence data is described. The algorithm is based on the fundamental parameter approach and facilitates the simultaneous determination of several elements at widely varying concentrations. The software comprises three programs. One program, for spectrometer control and data acquisition, resides in a dedicated microcomputer. The two other programs, for spectra deconvulution and data evaluation, reside in a larger central computer. On-line communication between the computers is feasible, and the system facilitates the implementation of new improved programs. The performance of the system was tested on standard reference materials, and satisfactory accuracy was obtained for up to 21 elements.     

The computer processing and interpretation of mass spectral information. V—generation of a table of isotopic spectra of structural fragments

A package of dialogue programs intended for generation of isotopic spectra from specified elemental compositions containing any number of elements is described. Structural fragments (super-elements), once in the table, acquire the status of a separate chemical element. All operations with super-elements are analogous to those with polyisotopic elements of the periodic table. The user can modify the table at his discretion to suit his purpose. The table increases the flexibility of interactive data processing programs and thus the dialogue is made to approach the natural chemist's language. The programs written in FORTRAN IV are intended for a minicomputer with a core memory of about 24 K words.     

PCGAP: Application to analyze gamma-ray pulse-height spectra on a personal computer under Windows NT®

PCGAP is a software code, which was written to provide gamma-ray pulse height spectrum analysis on a personal computer platform. The code was specifically developed for Windows NT for either an Intel^® or DEC Alpha^® based processor. PCGAP includes programs which can be used to control data collection using a Canberra INSPECTOR^® multichannel pulse-height analyzer. With suitable spectrum conversion routines PCGAP can be used to analyze data from almost any multi-channel analyzer. Besides the normal functions associated with a robust spectrum analysis package, PCGAP can be used for radionuclide analysis for actinides via L-X and gamma-ray spectrometry. It can be used to control and analyze data from an INEEL developed pulse injection system for individual spectrum validation. The package includes programs for the manual analysis of spectra using displays which permit the spectroscopist to interactively define the spectral continuum and peak fitting limits, and display the resulting function fitting forms.     

Computer-aided drug design platform using PyMOL

The understanding and optimization of protein-ligand interactions are instrumental to medicinal chemists investigating potential drug candidates. Over the past couple of decades, many powerful standalone tools for computer-aided drug discovery have been developed in academia providing insight into protein-ligand interactions. As programs are developed by various research groups, a consistent user-friendly graphical working environment combining computational techniques such as docking, scoring, molecular dynamics simulations, and free energy calculations is needed. Utilizing PyMOL we have developed such a graphical user interface incorporating individual academic packages designed for protein preparation (AMBER package and Reduce), molecular mechanics applications (AMBER package), and docking and scoring (AutoDock Vina and SLIDE). In addition to amassing several computational tools under one interface, the computational platform also provides a user-friendly combination of different programs. For example, utilizing a molecular dynamics (MD) simulation performed with AMBER as input for ensemble docking with AutoDock Vina. The overarching goal of this work was to provide a computational platform that facilitates medicinal chemists, many who are not experts in computational methodologies, to utilize several common computational techniques germane to drug discovery. Furthermore, our software is open source and is aimed to initiate collaborative efforts among computational researchers to combine other open source computational methods under a single, easily understandable graphical user interface.     

Shared-memory parallelization of the TURBOMOLE programs AOFORCE, ESCF, and EGRAD: how to quickly parallelize legacy code

The programs ESCF, EGRAD, and AOFORCE are parts of the TURBOMOLE program package and compute excited-state properties and ground-state geometric hessians, respectively, for Hartree-Fock and density functional methods. The range of applicability of these programs has been extended by allowing them to use all CPU cores on a given node in parallel. The parallelization strategy is not new and duplicates what is standard today in the calculation of ground-state energies and gradients. The focus is on how this can be achieved without needing extensive modifications of the existing serial code. The key ingredient is to fork off worker processes with separated address spaces as they are needed. Test calculations on a molecule with about 80 atoms and 1000 basis functions show good parallel speedup up to 32 CPU cores.     

Paired-permanent approach for VB theory (Ⅱ)——An ab initio spin-free VB program

Paired-permanent approach for VB theory is extensively developed. Canonical expansion of a paired-permanent is deduced. Furthermore, it is shown that a paired-permanent may be expressed in terms of the products of sub-paired-permanents of any given order and their corresponding minors. An ab initio spin-free valence bond program, called Xiamen, is implemented by using paired-permanent approach. Test calculation shows that Xiamen package is more efficient than some other programs based on the traditional VB algorithm, and it provides a new practical tool for quantum chemistry.     

Paired-permanent approach for VB theory (II)

Paired-permanent approach for VB theory is extensively developed. Canonical expansion of a paired-permanent is deduced. Furthermore, it is shown that a paired-permanent may be expressed in terms of the products of sub-paired-permanents of any given order and their corresponding minors. Anab initio spin-free valence bond program, called Xiamen, is implemented by using paired-permanent approach. Test calculation shows that Xiamen package is more efficient than some other programs based on the traditional VB algorithm, and it provides a new practical tool for quantum chemistry.     

A new algorithm for the determination of protolytic constants from spectrophotometric data in multiwavelength mode: Calculations of acidity constants of 4-(2-pyridylazo)resorcinol (PAR) in mixed nonaqueous-water solvents

A new efficient, simple and versatile algorithm is presented for determination of the protolytic constants from spectrophotmetric data in multiwavelength mode based on the combining of hard and soft modeling. The algorithm was checked by determining the acidity constants of a triprotic acid from theoretical and real absorption-pH data. The real spectral data are obtained from photometric titration of different solutions of 4-(2-pyridylazo)resorcinol (PAR) by a standard base solution under an inert atmosphere. The algorithm starts the minimization process using an user supplied number of components and initial guesses of the unknown parameters and refined in a least squares manner. New algorithm is implemented in the new version of DATAN package (version 3.1). The validity of the obtained results was checked by some well known programs such as DATAN 2.1, SPECFIT/32, SQUAD, a modified version of difference spectra and a A-pH curve method. The comparison of the outputs of the DATAN 3.1 with the other programs reveals that there is a very good agreement between the obtained results and mentioned programs.     

CARSA,a computer-assisted system for synthesis research in industry

Computer applications in chemical industry are outlined and the CARSA system (computer-assisted research in synthesis and application) is described. This modular system consists of the three main parts: WIFODATA (data base; substance and finding documentation), QSAR (programs for quantitative structure/activity relationships) and RDSS (reaction design by synthon substitution; program package for planning of syntheses). The vital RDSS component is discussed in more detail; the underlying philosophy is explained, and examples are given from practical work. Some future steps towards a real molecular-design system are outlined.     

A versatile AMBER-Gaussian QM/MM interface through PUPIL

The PUPIL package (Program for User Package Interfacing and Linking) originally was developed to interface different programs for multiscale calculations in materials sciences (Torras et al., J Comput Aided Mater Des 2006, 13, 201; Torras et al., Comput Phys Commun 2007, 177, 265). Here we present an extension of PUPIL to computational chemistry by interfacing two widely used computational chemistry programs: AMBER (molecular dynamics) and Gaussian (quantum chemistry). The benefit is to allow the application of the advanced MD techniques available in AMBER to a hybrid QM/MM system in which the forces and energy on the QM part can be computed by any of the methods available in Gaussian. To illustrate, we present two example applications: A MD calculation of alanine dipeptide in explicit water, and a use of the steered MD capabilities in AMBER to calculate the free energy of reaction for the dissociation of Angeli's salt.