![]() ![]() It's the most powerful skin but usually requires some testing to get it to work just the way you like.You can create several album projects in jAlbum to make albums with different skins for different clients etc. Yes, please try other skins like Galleria or Chameleon, I personally like Turtle. You can also choose to exclude folders and add your logo. This way navigation links will appear in the album header. Here's a hint that might help since you're using folders and wanted to add about/contact pages:Go to Settings -> Turtle -> Site - Click: Show top navigation. Please check that you entered the data the same way as for example your Mexico album where I can't see your name in the titles. I'm not sure how you've entered the data, if you're using Lightroom, jAlbum will read in the EXIF / XMP data. I found your name in the image titles in this album: Yes, we are working on proper documentation, I know it comes in handy. And how do I get rid of the redundant photo of the grate, down at the bottom? Here's the URL: I'd also like to add a link back to the home page, and add some text to each folder link on the home page, something more that just "Mexico". it must be simple but I can't seem to figure out how to work with text. I'd like to add a statement page and a contact page. I've gone to the jAlbum Forum for help but many users are in Europe and the time difference is a bit of a nuisance, not their fault! Plus, I've been using for years and feel more at ease here with the interface, helpful community, etc. I've started a website but it is by no means complete. I'm using the Turtle skin because it seemed most widely used, but I'm not wedded to it, am open to other skins if need be. In fact I chose jAlbum based partly on what I've seen here from other website builders. (DOI: 10.4231/D35M62761).I've been searching this forum for some tips, and was glad to see there are some jAlbum users out there. Benjamin Rafferty Zachary Carl Flohr Ashlie Martini (2014), “Protein Contact Maps,”. “MDTraj: A modern open library for the analysis of molecular dynamics trajectories.” Biophysical journal 109.8 (2015): 1528-1532. The script could also generate matrix data of contact map, what can we do to that? P References ![]() Print_figure(matrix, filename= "cm-map.png")įinally, I generate a Gif picture for 11 frames of protein trajectory. Matrix = calc_matrix_cm(trj = traj, frame = i) Val = calc_residue_dist(residues = (traj.xyz, traj.xyz))ĭis = calc_residue_dist((scmass, scmass))ĭis = calc_residue_side_dist(frame, row, col) Selection = lect("(resid %d) and sidechain" % i) Return approximate center of mass of each side chain.ĬOM od Glycine is approximated by the coordinate of its CA atom. Return np.sqrt(np.vdot(diff_vector, diff_vector))ĭef calc_side_center_mass(topology, frame): Return the C-alpha distance between two residues. I modified source code obtained from: 1ĭef calc_residue_dist(residues = (0, 0)): The sidechian coordinates of first residue:īelow are functions for contact map calculation. Print( 'The sidechian coordinates of first residue:\n')Īll residues: Selection = lect( "(resid %d) and sidechain" % 0) # Select the sidechain of first residue in structure Print( 'MD imformation: %s\n' % topology) Hape Similarity and Electroshape Similarity Calculation 1 It is pretty convient to use MDtraj select residues and atoms. ![]() Print( 'Time steps: %d ps' % (traj.time - traj.time)) # pico second Print( 'Frames: %d Atoms: %d Dimentions: %d\n' % ) I use gromacs format here because Gromacs is an advaced and open software of molecular dynamics, although MDtraj supports plenty of trajectory formats. :P 1įrom _agg import FigureCanvasAgg as FigureCanvas I will add the internet address after I update this blog next time. I used a protein folding trajectory from internet. Here I found a package named MDtraj, And a package from Benjamin Rafferty (doi:10.4231/D35M62761)! Thanks to them, I can simply achieve my idea. I love python because I could always find usefull packages from internet. I had a project several month ago, and I wanted to use a script to generate contact maps for a molecular dynamic trajectory, so that I use python to write a script to do it. There are several tools or program for calculate and display contact map on internet, here is an collection of them. Some scientists have already applied deep learning on this project and developed programs for structure prediction, such as RaptorX of TTIC. Contact maps can not only be used as illustrations of protein, but also as tools to predict homology protein structure, especially for low homolog in evolution. More detail about contact map can be found here. Protein contact map is a very helpfull tool to represent 3D protein structure in a 2D matrix format. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |