Pymol show unit cell
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Project Management. Services Business VoIP. Resources Blog Articles Deals. Menu Help Create Join Login. This project can now be found here. Attachments: supercell. Re: [PyMOL] feature request: supercell construction. Oh no! Some styles failed to load. Sign Up No, Thank you. Thanks for helping keep SourceForge clean. X You seem to have CSS turned off. Briefly describe the problem required :. Upload screenshot of ad required :. Hi Nick, I recently was playing with aka learning the crystallographic symmetry information in PDB files and now took your feature request as an exercise.
See attached file, hope it does what you had in mind. It would be great if pymol had support for constructing and displaying a supercell: For data files that support crystallographic information, e. It would be great if one could easily display multiple copies of the unit cell, along the lines of supercell 1,1,2 where pymol would then copy the unit cell along the c-axis and display 2 unit cells.
As a related request it would be great if pymol could construct a unit cell in case the crystallographic information in the input file does not exist. This could come in handy for instance when reading from xyz.Symexp is used to reconstruct neighboring asymmetric units from the crystallographic experiment that produced the given structure. Symexp creates all symmetry related objects for the specified object that occurs within a cutoff about an atom selection.
The new objects are labeled using the prefix provided along with their crystallographic symmetry operation and translation. We now have four objects corresponding to two biologic units the functional protein in a cell.
As you can see, we can begin to understand the crystal environment of our asymmetric unit. Increasing distance will reveal more of the crystal lattice, but will place in increasing demand on your computer's rendering ability.Introduction to WinCoot
PyMOL is known to exit dramatically crash if you provide a scene that is too large or complex. This is a result of the low-level malloc function failing. See Category:Performance for workarounds.
Jump to: navigationsearch. Expand the ''object'' around its ''selection'' by cutoff Angstroms and prefix the new objects withs ''prefix''.
Category : Commands. Navigation menu Personal tools Log in. Namespaces Page Discussion. Views Read View source View history. Navigation Main page Recent changes Random page Help. This page was last edited on 20 Aprilat Ralf Grosse-Kunstleve has provided his SgLite module to enable PyMOL to deduce symmetry relationships from standard space group and unit cell information.
However, it would be only a minor development task to add a means of assigning unit-cell and symmetry to any molecule object directly from the API.
When you use the "load" command to read in a PDB file with symmetry information, matrix information should be output. Verify that this information is produced before attempting to display symmetry related molecules. The "symexp" command is used to display symmetry related molecules in the crystal lattice about an atom selection.
This commands creates a set of new objects with a common prefix. Each object in the series corresponds to one symmetry-related object, which can be treated independently. See "help symexp" or the reference section for usage information.
In order to visualize only symmetry-related atoms within a given distance, you need to break the process down into two steps. First, you use the symexp command to create complete symmetry-related objects. Then you use "hide" commands to restrict what is visible to only those areas which you are interested. NOTE: The symexp command can potentially create large numbers of objects. PyMOL can read large maps of this format and then display arbitrary "bricks" of density within these maps about atom selections.
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It only takes a minute to sign up. I downloaded a PDB file of a dimer, but it only contains the monomer, and it says that the dimer can be obtained from C2 symmetry.
The PDB file contains the asymmetric unit found in a particular crystallographic study. The biological assembly is the quaternary structure known or predicted to be found in living systems. For other proteins, the PDB file may contain the transformation matrix used to create the biological assembly from the asymmetric unit. If you look at the file in a text editorthis information is found under remark You can see that the first matrix is identity ie keeps the original asymmetric unit.
The second matrix transforms the assymmetric unit to create the full hexamer. This matrix is both author and PISA predicted. You can actually go to the PISA website and have it predict the biological assembly of a particular PDB file, and it will spit out the coordinates of the hexamer and other predicted assemblies which you can then load into PyMOL.
Via the symexp command, PyMOL can use this information to recreate neighboring asymmetric units. By limiting the cut-off distance and this requires trial-and-errorthe biological assembly can be recreated. This script, for example, will generate the hexamer:.
If you are looking for information on Coronaviruses, we have prepared this FAQ with information on what is on topic on this site and links to some reputable external resources. Sign up to join this community. The best answers are voted up and rise to the top. Home Questions Tags Users Unanswered. Generate full dimer from monomer with C2 symmetry? Ask Question.SuperSym is a PyMOL plugin providing a large number of tools for visualization of space groups; unit cells; and symmetry axes, operators, and partners.
PyMOL, cctbx and numpy must all be compiled with the same Python distribution! Primary coding and development was done by Stuart Ballard.
All comments, questions, and issues should be directed to him at srballard wisc. Code for unit cell and symmetry axis building is borrowed from scripts created by Robert Campbell and Ralf W. Some of this code has been modified for use in SuperSym. FindSurfaceResidues is utilized for some of SuperSym's graphics generation, with some modifications. To install SuperSym v1. In PyMOL, go to:. A file selector dialog will appear. Select SuperSymPlugin Note: previous errors resulting from incorrect naming of the plugin file have been resolved in v1.
Please post any comments, complaints, bug fix requests, useful tricks, or cool adaptations of SuperSym here. Jump to: navigationsearch. Navigation menu Personal tools Log in. Namespaces Page Discussion. Views Read View source View history. Navigation Main page Recent changes Random page Help. This page was last edited on 24 Januaryat You seem to have CSS turned off. Please don't fill out this field. Please provide the ad click URL, if possible:. Help Create Join Login.
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Services Business VoIP. Resources Blog Articles Deals. Menu Help Create Join Login. This project can now be found here. Oh no! Some styles failed to load. Sign Up No, Thank you.
Thanks for helping keep SourceForge clean. X You seem to have CSS turned off. Briefly describe the problem required :. Upload screenshot of ad required :. Lan, Try color color-name, object-name This action both sets the default object color which is used for the cell as well as coloring all of the atoms.
Then you can recolor the atoms independently. Cheers, Warren -- Warren L. DeLano, Ph. Principal Scientist. South San Francisco, CA Biz: Tech: Fax: Cell: Publish reports on the web. Hello, I would like to display crystal packing of my molecule with unit cell labeled and colored in black.
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I was able to show the unit cell by using the command, show cell, hex.Included below are some PyMOL tools to create the drawing commands to show the symmetry axes for a crystal, to draw a fancier unit cell and an attempt at drawing reciprocal space in 3D.
This site will look much better in a browser that supports web standards. Crystallography and Modelling:. Software Links Rob's Home This site will look much better in a browser that supports web standards. All of these scripts require loading into PyMOL before use. You do this with the run command: run scriptname.
Other scripts are available in my scripts page. Name Description Dependencies Click on thumbnail to see larger image General pymolrc. No regexp returns every setting. Aligns all displayed models to one target using one of the "align", "super" or "cealign" commands. Options include the method to use, the target and mobile selections to be used for the alignment, creation of CGO align objects for each pair of structures align and super onlythe alignment method align, super, cealign and a debugging option that prints more information.
Aligns all models read from a set of files to one target already loaded into PyMOL using the "align" command. Options include the target and mobile selections to be used for the alignment, creation of CGO align objects for each pair of structures, the alignment method align, super, cealign and a debugging option that prints more information. Aligns all models in a list to all other models in the list.
Options include the list of models to use, a selection to use in the alignment defaults to all C-alpha atomsprinting of the full matrix of RMSD values instead of the default upper half-matrix, the alignment method align, super, cealign and a debugging option that prints more information. Aligns all models to all other models read from a set of files.
Color a selection by b-factor or occupancy q. Options include a choice of colour gradients'bgr','rgb','bwr','rwb','bmr','rmb', 'gw','wg','gy','yg','gray', 'reversegray', 'user' modes ramp, equal numbers of atoms in each color or histogram equal spaced color boundariessaturationvalue and nbins the number of colors to use and selection.
User-defined gradients can also be specified by three triplets of rgb values -- see the top of the python script for more details. Color by atomtype. Color by residue type. Extract data produced by other programs and alter the B-factor or occupancy of a molecule within PyMOL. CHAIN is optional. This script has been extensively rewritten and improved by Thomas Holder as noted in the copyright notice. Suguru Asai has provided the update to allow reading the "ID data" formatted data file.
Draw unitcell border with labels and with fancy coloring! Now you can have a unitcell frame without reading in a PDB file. The radius and length are options and default to 0.
Draw an arbitrary cylinder between two atoms. Options are the name for the CGO object, the two atoms, the radius and the colour.