Shuguang Yuan, H. C. Stephen Chan, Sławomir Filipek, Horst Vogel,
... use and very versatile. The two tools are PyMOL and Inkscape, and in our hand, using the ... and-simple-way-to-visualize-structural-biology-data). PyMOL (http://www.pymol.org) is a user-friendly tool (Schrodinger, 2015Schrodinger L.L.C. The PyMOL Molecular Graphics System, Version 1.8. Shrodinger LLC, ... clicking the mouse or selecting from the menu. PyMOL is a Python-based tool, and many Python ... sophisticated way. Moreover, the high quality rendering in PyMOL is supported by parallel processing with multiple CPUs, ...
Tópico(s): Genetics, Bioinformatics, and Biomedical Research
2016 - Elsevier BV | Structure
PyMOL is often used to generate images of biomolecular structures. Hundreds of parameters in PyMOL provide precise control over the appearance of structures. ... shortcuts"-that extend and ease the use of PyMOL. A user runs a shortcut by entering its name at the PyMOL prompt. We clustered the shortcuts by functionality into ... the command history window. This documentation includes the PyMOL commands that the user can reuse by copying ... script file. The shortcuts should save the average PyMOL user many hours per year searching for code ...
Tópico(s): Glycosylation and Glycoproteins Research
2019 - Wiley | Protein Science
Blaine H. M. Mooers, Marina Brown,
Abstract PyMOL commands are used to exert exquisite control over the appearance of a molecular model. This control has made PyMOL popular for making images of protein structures for ... of the commands due to infrequent use of PyMOL . This poor recall hinders the writing of new ... Vim, and Emacs). We developed a library of PyMOL code templates or snippets called pymolsnips to ease the writing of PyMOL code in scripts. We made pymolsnips available on ... We expect that the library will help many PyMOL users to be more productive when writing PyMOL ...
Tópico(s): Enzyme Structure and Function
2020 - Wiley | Protein Science
Laura Grell, Christopher Parkin, L. A. Slatest, P. Craig,
PyMOL is a molecular modeling program that can be used in a wide range of studies within ... the laboratory and in the classroom. However, the PyMOL user interface is difficult to use, and the PyMOL User's Manual readily admits that "development has ... set out to develop a new interface for PyMOL that helps eliminate the need for command line ... Other features of the interface include a Chime/PyMOL command converter, nine preset molecular views, four molecular ... Viz could help to further the use of PyMOL, which we believe to be one of the ...
Tópico(s): History and advancements in chemistry
2006 - Wiley | Biochemistry and Molecular Biology Education
Alessio Del Conte, Alexander Miguel Monzón, Damiano Clementel, Giorgia F Camagni, Giovanni Minervini, Silvio C. E. Tosatto, Damiano Piovesan,
Abstract RING-PyMOL is a plugin for PyMOL providing a set of analysis tools for structural ensembles and molecular dynamic simulations. RING-PyMOL combines residue interaction networks, as provided by the ... of non-covalent interactions with the power of PyMOL to manipulate and visualize protein structures. The plugin ... of models and long trajectories in seconds. RING-PyMOL generates a number of interactive plots and output ... Availability and implementation https://github.com/BioComputingUP/ring-pymol
Tópico(s): Microbial Metabolic Engineering and Bioproduction
2023 - Oxford University Press | Bioinformatics
Evan H. Baugh, Sergey Lyskov, Brian D. Weitzner, Jeffrey J. Gray,
... visualizing biomolecules; one of the most popular tools, PyMOL (Schrödinger), is a powerful, highly extensible, user friendly, and attractive package. Integrating Rosetta and PyMOL directly has many technical and logistical obstacles inhibiting ... and energy information via UDP sockets. Rosetta and PyMOL run as separate processes, thereby avoiding many technical ... sent over a UDP network socket to a PyMOL instance running a UDP socket listener. PyMOL then interprets and displays the molecule. This implementation ...
Tópico(s): Genomics and Phylogenetic Studies
2011 - Public Library of Science | PLoS ONE
Hitesh Patel, Björn Grüning, Stefan Günther, Irmgard Merfort,
... same family. PyWATER is an easy-to-use PyMOL plug-in and identifies conserved water molecules in ... can be installed via the user interface of PyMOL. No programming or command-line knowledge is required ... are available at https://github.com/hiteshpatel379/PyWATER . PyMOL is available at http://www.pymol.org/ or http://sourceforge.net/projects/pymol/ . Contact : stefan.guenther@pharmazie.uni-freiburg.de
Tópico(s): Mass Spectrometry Techniques and Applications
2014 - Oxford University Press | Bioinformatics
Shuguang Yuan, H. C. Stephen Chan, Zhenquan Hu,
PyMOL , a cross‐platform molecular graphics tool, has been widely used for three‐dimensional ( 3D ) visualization of ... its utilities and facilitate the drug design in PyMOL . To gain an insightful view of useful drug design tools and their functions in PyMOL , we present an extensive discussion on various molecular modeling modules in PyMOL , covering those for visualization and analysis enhancement, protein– ... 3D structures visualization and computational drug design in PyMOL . WIREs Comput Mol Sci 2017, 7:e1298. doi: ...
Tópico(s): Enzyme Structure and Function
2017 - Wiley | Wiley Interdisciplinary Reviews Computational Molecular Science
Abstract Scripts are used in PyMOL to exert precise control over the appearance of the output and to ease remaking similar images at a later time. We ... A horizontal script makes a complete scene in PyMOL like a traditional vertical script. The commands in ... This simpler workflow accelerates script development. In using PyMOL, the illustration of a molecular scene requires an ... scripts both simplify and enhance the use of PyMOL in research and education.
Tópico(s): RNA and protein synthesis mechanisms
2016 - Wiley | Protein Science
Giacomo Janson, Alessandro Paiardini,
... integrated interface between the popular molecular graphics viewer PyMOL, and some of the most frequently used tools ... to make it compatible with the most recent PyMOL versions, and has been extended with a large ... also be used alone, in order to extend PyMOL with a wide range of capabilities. Sequence similarity ... modeling can be performed in the PyMod 3/PyMOL environment.A cross-platform PyMod 3 installer package ...
Tópico(s): Enzyme Structure and Function
2020 - Oxford University Press | Bioinformatics
Alexandra D. Simmons, T Nguyen, Jack L. Follis, Albert Ribes‐Zamora,
... designed a three hour teaching module using the PyMol software. The activity starts with two pre-laboratory assignments, one to learn how to use PyMol and the other to read about a specific ... grade distribution in students that participated in the PyMol activity relative to a control group. We also ...
Tópico(s): Biomedical and Engineering Education
2014 - Public Library of Science | PLoS ONE
José R. Pinto, Michelle S. Parvatiyar, Michelle Jones, Jingsheng Liang, Michael J. Ackerman, James D. Potter,
... D145E, whereas E134D was the same as WT. PyMol modeling of each cTnC mutant within the cTn ... D145E, whereas E134D was the same as WT. PyMol modeling of each cTnC mutant within the cTn ... All of these results considered together with the PyMol illustrations suggest that structural changes are present in ... and each mutation was 0.2 mg/ml. PyMol is an open source molecular visualization program that ...
Tópico(s): Trypanosoma species research and implications
2009 - Elsevier BV | Journal of Biological Chemistry
Francisco J. Enguita, Lı́gia O. Martins, Adriano O. Henriques, M.A. Carrondo,
... CotA or other multicopper oxidases were made using PyMol (44DeLano W.L. PyMol. DeLano Scientific, San Carlos, CA2002Google Scholar). Domain analysis ... Procedures." All the molecular representations were generated using PyMol (44DeLano W.L. PyMol. DeLano Scientific, San Carlos, CA2002Google Scholar). Left column, ...
Tópico(s): Biotin and Related Studies
2003 - Elsevier BV | Journal of Biological Chemistry
Qian Han, Howard Robinson, Jianyong Li,
... in the CCP4 suite. Figures were generated using Pymol (50DeLano W.L. The PyMOL Molecular Graphics System. Delano Scientific, San Carlos, CA2002Google ... Protein and substrate interaction also was analyzed using Pymol (50DeLano W.L. The PyMOL Molecular Graphics System. Delano Scientific, San Carlos, CA2002Google ...
Tópico(s): Bipolar Disorder and Treatment
2007 - Elsevier BV | Journal of Biological Chemistry
S. Hare, Wolfgang Fischer, Robert P. Williams, Laurent Terradot, Richard Bayliss, Rainer Haas, Gabriel Waksman,
... GRASP; Nicholls et al, 1991), were produced using Pymol (DeLano, 2002). Download figure Download PowerPoint The second ... B, respectively. All the panels were produced using Pymol (DeLano, 2002). Download figure Download PowerPoint Each HP1451C2 ... of HP0525. All the panels were produced using Pymol (DeLano, 2002). Download figure Download PowerPoint HP1451C2 has ... are disordered. All the panels were produced using Pymol (DeLano, 2002). Download figure Download PowerPoint In all ...
Tópico(s): Microbial Metabolites in Food Biotechnology
2007 - Springer Nature | The EMBO Journal
Jelena Zaitseva, Jingping Lu, Kelli L. Olechoski, Audrey L. Lamb,
... Appl. Crystallogr. 1991; 24: 946-950Crossref Google Scholar), PyMOL (30DeLano W.L. The PyMol Molecular Graphics System. DeLano Scientific, San Carlos, CA2002Google ... contoured at 1σ. This figure was generated with PyMOL (30DeLano W.L. The PyMol Molecular Graphics System. DeLano Scientific, San Carlos, CA2002Google ...
Tópico(s): Protein Structure and Dynamics
2006 - Elsevier BV | Journal of Biological Chemistry
Emanuele Bramucci, Alessandro Paiardini, Francesco Bossa, Stefano Pascarella,
... interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ... homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity ... with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, ...
Tópico(s): Genomics and Phylogenetic Studies
2012 - BioMed Central | BMC Bioinformatics
Robin A.J. Smith, Richard C. Hartley, Helena M. Cochemé, Michael P. Murphy,
... Professor John E. Walker and were generated using PyMOL (DeLano, www.pymol.org) by Dr Martin King. Complex I is ... Professor John E. Walker and were generated using PyMOL (DeLano, www.pymol.org) by Dr Martin King. Complex I is ...
Tópico(s): Adipose Tissue and Metabolism
2012 - Elsevier BV | Trends in Pharmacological Sciences
... PyKnot, a plugin that works seamlessly within the PyMOL molecular viewer and gives quick results including the ... which to learn topology and macromolecular visualization. Availability: PyMOL is available at http://www.pymol.org. The PyKnot module and tutorial videos are ...
Tópico(s): Protein Structure and Dynamics
2012 - Oxford University Press | Bioinformatics
Florence Vincent, G.J. Davies, J.A. Brannigan,
... is rainbow-colored. Both pictures were drawn using PyMOL (32DeLano W.L. PyMOL. DeLano Scientific, San Carlos, CA2002Google Scholar).View Large ... in divergent ("wall-eyed") stereo was drawn using PyMOL (32DeLano W.L. PyMOL. DeLano Scientific, San Carlos, CA2002Google Scholar) and shows ...
Tópico(s): Biochemical and Molecular Research
2005 - Elsevier BV | Journal of Biological Chemistry
M. St-Jean, Julien Lafrance‐Vanasse, B. Liotard, J. Sygusch,
... the present paper were prepared using the program PyMOL (22DeLano W.L. The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, ... Structure Comparisons—Superpositions were performed with the program PyMOL (22DeLano W.L. The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, ...
Tópico(s): Diet, Metabolism, and Disease
2005 - Elsevier BV | Journal of Biological Chemistry
... Google Scholar). Molecular graphics images were generated using PyMOL (26DeLano W.L. The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA2002Google ... Google Scholar). Molecular graphics images were generated using PyMOL (26DeLano W.L. The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA2002Google ...
Tópico(s): Bacterial Genetics and Biotechnology
2004 - Elsevier BV | Journal of Biological Chemistry
Heather L. Wilson, K.V. Rajagopalan,
... were used to create Fig. 6 using the PyMOL Molecular Graphics System (W. L. DeLano; available on the World Wide Web at www.pymol.org).Fig. 6Structure of the chicken SO substrate- ... The molybdenum atom is shown in green. The PyMOL Molecular Graphics Program (W. L. DeLano; available on the World Wide Web at www.pymol.org) was used to create this figure after ...
Tópico(s): Ion Transport and Channel Regulation
2004 - Elsevier BV | Journal of Biological Chemistry
Laura Spagnolo, I Törö, Melania D’Orazio, Peter O’Neill, Jens Z. Pedersen, Oliviero Carugo, Giuseppe Rotilio, Andrea Battistoni, Kristina Djinović‐Carugo,
... according to A. The figure was prepared by PyMOL (58DeLano W.L. PyMOL. DeLano Scientific, San Carlos, CA2002Google Scholar). C, phylogenetic ... W448) are shown. The figure was prepared by PyMOL (58DeLano W.L. PyMOL. DeLano Scientific, San Carlos, CA2002Google Scholar). B, superposition ...
Tópico(s): Metal complexes synthesis and properties
2004 - Elsevier BV | Journal of Biological Chemistry
Hajime Sugawara, Masami Kusunoki, Genji Kurisu, Tokiko Fujimoto, Haruhiko Aoyagi, Tomomitsu Hatakeyama,
... Scholar). Fig. 2 was drawn by the program PyMOL (49DeLano W.L. The PyMOL Molecular Graphics Systems. DeLano Scientific, San Carlos, CA2002Google ... dots. Fig. 5 was drawn by the program PyMOL (49DeLano W.L. The PyMOL Molecular Graphics Systems. DeLano Scientific, San Carlos, CA2002Google ...
Tópico(s): Carbohydrate Chemistry and Synthesis
2004 - Elsevier BV | Journal of Biological Chemistry
... easy‐to‐use graphical user interface based on PyMOL. WATsite identifies hydration sites from a molecular dynamics ... the hydration site analysis can be displayed in PyMOL. A key feature of WATsite is that it ... user specified ligand. The WATsite program and its PyMOL plugin are available free of charge from http:// ...
Tópico(s): Enzyme Structure and Function
2014 - Wiley | Journal of Computational Chemistry
Andreas Warnecke, Tatyana Sandalova, Adnane Achour, Robert A. Harris,
... plugin implemented with the commonly used visualization software PyMOL. PyTMs enables users to introduce a set of ... is a useful, user-friendly modelling plugin for PyMOL. Advantages of PyTMs include standardized generation of PTMs, ... PyTMs is freely available as part of the PyMOL script repository project on GitHub and will further ...
Tópico(s): Click Chemistry and Applications
2014 - BioMed Central | BMC Bioinformatics
Tomasz Makarewicz, Rajmund Kaźmierkiewicz,
... describes functionality of the newly created plugin for PyMOL (the popular and easy to use program for ... of those calculations and displays them back in PyMOL. All the components of the stack are open ... gives researchers easy access to the molecular dynamics PYMOL plugin and creates an opportunity to modify its ...
Tópico(s): RNA and protein synthesis mechanisms
2013 - American Chemical Society | Journal of Chemical Information and Modeling
Alejandro Panjkovich, Dmitri I. Svergun,
... To facilitate this task, we present SASpy, a PyMOL plugin that provides an easy-to-use graphical ... github.com/emblsaxs/saspy/. Working installations of both PyMOL (www.pymol.org) and ATSAS (www.embl-hamburg.de/biosaxs/ ...
Tópico(s): Advanced NMR Techniques and Applications
2016 - Oxford University Press | Bioinformatics
Tomasz Makarewicz, Rajmund Kaźmierkiewicz,
... that purpose. Unfortunately they lack GUI. The Dynamics PyMOL plugin allows researcher to perform MD simulations directly from the PyMOL software by GUI-based interface of GROMACS tools. ... paper describes many improvements introduced into the Dynamics PyMOL plugin 2.0 including: an integration with ProDy ...
Tópico(s): Microfluidic and Capillary Electrophoresis Applications
2016 - Springer Science+Business Media | Journal of Molecular Modeling