分子可視化軟體千千萬, GaussView, VMD, PyMOL, Chimrea等各有各的特點, 也各有各的用戶群. 蘿蔔青菜, 各有所愛, 也沒有必要非爭個一二三四, 你強我弱. 但這些軟體渲染的圖片看多了也不免審美疲勞, 難覺再愛, 所以就有人專門用那些小眾的渲染程序, 特別是那些原本不是為生物和化學分子準備的程序, 如POVRAY, Blender之類. POVRAY吧, 其實用的還多些, 因為很多分子可視化軟體都可以輸出對應的POVRAY文件. 但Blender在分子方面的曝光率就少得多了, 因為這個軟體的複雜度比前面那些高不少, 非3D建模方面的人很難掌握. 就是用, 也只使用最簡單的功能. 更複雜漂亮的, 大多要專門花錢請人給做效果了. Blender複雜雖是複雜, 但要想渲染那些照片級別的圖片, 還真得試試.
最近看了一些Blender的相關資料, 練習了一下, 就把習作放在這裡給大家審醜吧.
小分子環糊精Atomic Blender
Blenderに3D分子モデルをインポートする 〜Atomic Blenderの使い方〜
PyMOL and Blender
Scripting atom color changes as a function of velocity in Blender
如何渲染分子結構？
Molecule visualization with Blender
Visualize a 3D trajectory using Blender
blender_mdtraj_importer
Importing trajectories to create an animation
Three ways to create objects
CREATING A RED SPHERE IN BLENDER WITH PYTHON
Create a UV Sphere / Object in Blender from Python
博士前/博士後Postdoctoral Position Reaction Dynamics & Planetary Sciences, University of Hawaii at Manoa, USAThe Reaction Dynamics Group, Department of Chemistry & W.M. Keck Research Laboratory in Astrochemistry, University of Hawai』i at Manoa, invites applications for one postdoctoral position. The appointment period is initially for one year, but can be renewed annually based on availability of funds and satisfactory progress as defined by first author publications. The salary is competitive and commensurate with experience. Successful applicants should have a strong background in experimental reaction dynamics, UHV technology, and pulsed (tunable) laser systems. Experience in labview programming and/or Autocad/SolidWorks is desirable. The goal of the experiments is to probe the formation of complex organic molecules in Solar System ices and/or the synthesis of water on the moon via interaction of ionizing radiation with low temperature ices and silicates, respectively. Reaction products will be probed via tunable vacuum ultraviolet photoionization generated via four wave mixing schemes.
Solid communication skills in English (written, oral), a publication record in internationally circulated, peer-reviewed journals, and willingness to work in a team are mandatory. Only self-motivated and energetic candidates are encouraged to apply. Please send a letter of interest, three letters of recommendation, CV, and publication list to Prof. Ralf I. Kaiser, Department of Chemistry, University of Hawai』i at Manoa, Honolulu, HI 96822-2275, USA [ralfk@hawaii.edu]. Applicants must demonstrate their capability to prepare manuscripts for publications independently. The review of applications will start January 15, 2018, and continues until the position is filled. A description of our current research group can be found at http://www.chem.hawaii.edu/Bil301/welcome.html. Only complete applications will be reviewed.
PhD position at the FELIX LaboratoryProject description:Vibrational signatures of reactive intermediates in interstellar chemistry
Molecular ions are important drivers of the chemistry in astrophysical environments and are also of fundamental interest in quantum chemistry. However, due to their reactive nature, they are difficult to study with standard spectroscopic methods. In our group we are developing sensitive action spectroscopic techniques to overcome these obstacles, and apply them to astrophysically relevant molecular ions, providing the spectral fingerprints needed to detect new species in space.
The focus of the PhD project is to measure vibrational signatures of a targeted set of reactive hydrocarbon and nitrile cations. You will develop, prepare and perform spectroscopic experiments using a unique combination of a state-of-the-art cryogenic ion trap instrument interfaced to the widely tunable IR free electron lasers of the FELIX Laboratory. The spectroscopic studies will be guided and interpreted by high-level quantum-chemical calculations. You will also be involved in developing and improving the experimental setup to enable kinetic studies on ion-molecule reactions in tandem with spectroscopic probing of the reaction products.
We are looking for a highly motivated candidate holding (or expecting to receive) a Master’s degree or equivalent in (Astro-/) Physics, Chemistry or a related field.
Experience with experimental work, in particular in the fields of gas phase laser spectroscopy and mass spectroscopy under ultra-high vacuum conditions is highly desirable.
The ability to work both independently and within a team is a key asset.
The working language is English.
Willingness to (occasionally) work outside office hours.
Work environment:As a PhD candidate, you will be embedded at the FELIX Laboratory (http://www.ru.nl/felix/) at Radboud University (Nijmegen, The Netherlands) working with Dr. Sandra Brünken in the research line in molecular astrophysics and cold ion spectroscopy. The FELIX Laboratory is an international user facility operating intense, short-pulsed infrared and THz free electron lasers for research of matter, providing a tuning range between 3 and 1500 μm. In user experiments the infrared radiation of the FELIX lasers interacts with molecules and materials, revealing detailed information about 3D structure, functional properties and electronic properties.
Moreover, the FELIX Laboratory is a large research infrastructure and welcomes external users from all over the world to perform research projects with FELIX. As a PhD student, you will also assist external users and participate in collaborative projects at the cryogenic ion trap user station. The FELIX Laboratory is a part of the Faculty of Science at the Radboud University.
The deadline for application is January 14, 2018; the start date of the PhD contract can be as early as March 2018.
Information on the employment conditions, application procedure and required documents can be found here:
http://www.ru.nl/imm/about_imm/vacancies-0/openings-phd-candidates-institute-molecules/
Further details on the PhD project and working environment is available here:
http://www.ru.nl/publish/pages/869701/62_83_17_1_2_phd_vibrational_signatures_of_reactive_intermediates_in_interstellar_chemistry.pdf
For more information, do not hesitate to contact Dr. Sandra Brünken: sandra.bruenken@ru.nl