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  • ...and share news related to PyMOL. And is also a place to interact with the PyMOL community, a community that spans the whole world. ...igh that your questions has already been asked and answered in the mailing list, hence always is a good idea to check that before asking a question. If you
    798 bytes (131 words) - 01:04, 19 October 2015
  • 144 bytes (25 words) - 04:12, 28 March 2014

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  • '''identify''' returns a list of atom IDs corresponding to the ID code of atoms in the selection. == PYMOL API ==
    429 bytes (61 words) - 01:04, 19 October 2015
  • order names-list, sort, location # puts 1frg at the top of the list
    679 bytes (98 words) - 02:16, 28 March 2014
  • ...The structures are available in PDB and mmCIF format, that can be read by PyMOL. In order to exploit these resources, some plugins have been developped. === Plugin list ===
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • ''New in PyMOL 1.7.4'' == PyMOL API ==
    521 bytes (71 words) - 22:50, 21 April 2015
  • '''cmd.get_object_list''' is an API only command which returns the list of all molecular objects in selection. It will not return selection names o == PyMOL API ==
    1 KB (176 words) - 02:46, 3 April 2017
  • ''New in PyMOL 2.3'' * '''raw''' = list: list of lists (columns) with <code>(model, index)</code> tuples
    691 bytes (94 words) - 03:14, 7 January 2019
  • This is a list of all commands in the Help Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the View Module for PyMol's interface.
    18 members (0 subcategories, 0 files) - 01:30, 28 March 2014
  • This is a list of all commands in the Language Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Display Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Movies Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Settings Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Scripts Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Selections Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Distances Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Editing Module for PyMol's interface.
    16 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Symmetry Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Imaging Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:30, 28 March 2014
  • This is a list of all commands in the Fitting Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Atoms Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Maps Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:30, 28 March 2014
  • This is a list of all commands in the Color Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Stereo Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:30, 28 March 2014
  • This is a list of all commands in the Ray Tracing Module for PyMol's interface.
    0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands in the Input/Output Module for PyMol's interface.
    5 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • ...tool if you have many directories full of files --- you don't have to quit PyMOL, you can just '''cd''' to the directory and '''ls''' to find the contents. # list all files in the current directory
    644 bytes (101 words) - 02:16, 28 March 2014
  • ::Find connected clouds of objects in PyMOL :: Retrieves atom coordinates as Python array (list object).
    37 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • ...and share news related to PyMOL. And is also a place to interact with the PyMOL community, a community that spans the whole world. ...igh that your questions has already been asked and answered in the mailing list, hence always is a good idea to check that before asking a question. If you
    798 bytes (131 words) - 01:04, 19 October 2015
  • import pymol pymol.stored_ss = []
    249 bytes (35 words) - 02:16, 28 March 2014
  • ...een 0 an 255 can be used as well. (If at least one value is larger than 1, pymol will interpret all 3 values as between 0 and 255). If an existing color nam ===PYMOL API===
    1,016 bytes (138 words) - 18:49, 14 October 2019
  • A list of available scripts and plugins available through the Pymol-script-repo git repository.
    80 members (0 subcategories, 0 files) - 01:29, 28 March 2014
  • This is a list of all commands for PyMol's interface and cmd module. ...ation, please read [[:Talk:Main_Page#Organizing_PyMol_Commands| Organizing PyMol Commands]].
    225 members (20 subcategories, 0 files) - 01:29, 28 March 2014
  • ===PYMOL API=== list = cmd.id_atom(string selection)
    284 bytes (45 words) - 03:06, 28 March 2014
  • ...trieve the Pymol color names and corresponding internal color indices. The Pymol names can be used to designate color for objects, see [[Color]]. To retrie ...to convert that to RGB color values if you need to use the colors outside Pymol.
    2 KB (273 words) - 19:27, 29 May 2018
  • # This is how to do it from the PyMOL command line or .pml script: import pymol
    384 bytes (59 words) - 02:16, 28 March 2014
  • This little script was posted to the PyMol list. It will orient the molucule like cmd.orient() does, but does so by the ca https://sourceforge.net/p/pymol/mailman/message/10097639/
    862 bytes (127 words) - 04:40, 14 December 2015
  • ...he current atom. One common usage is to extract the positions as a python list to alter then write back to the molecule using alter_state. * space = dict: namespace dictionary (API only) {default: pymol namespace}
    2 KB (253 words) - 07:02, 3 January 2016
  • '''get_names_of_type''' returns a list of object and/or selection names. ===PYMOL API===
    640 bytes (94 words) - 18:49, 14 October 2019
  • ===PYMOL API=== Warren provided a great example on the PyMOL list. If the NMR ensemble has all the structures loaded as multiple states (whi
    2 KB (222 words) - 04:31, 26 June 2017
  • Why not clean up the [[colorByRMSD]] page and then let folks on the PyMOL list know about it. It could be helpful to someone.
    349 bytes (63 words) - 04:13, 28 March 2014
  • ...tions of an object. It is the equivalent of deselecting the object in the list in the top panel of the [[Internal_gui|Internal GUI]]. ===PYMOL API===
    636 bytes (90 words) - 23:57, 20 May 2014
  • Please place your PyMOL script requests here. A few other people might have the same request and s :: Example text of what the new awesome script is supposed to do in PyMOL. Consider posting some contact information, so once the script is posted y
    2 KB (390 words) - 01:30, 28 March 2014
  • * ramp = str, list or empty: named ramp, space delimited string or list with (x, color, alpha, ...) or (x, r, g, b, alpha, ...) values. If empty, g PyMOL>volume_color vol
    1,020 bytes (123 words) - 03:15, 5 March 2018
  • finds all PyMOL object names within [radius] Angstroms of [target]. fileName, string, if not blank the list called [fileName] is written to disk
    2 KB (325 words) - 02:16, 28 March 2014
  • '''get_raw_alignment''' is an API only function that returns a list of lists of (object,index) tuples containing the raw per-atom alignment rel * ''Reimplemented in PyMOL 2.3, order of returned atom tuples can differ to previous versions''
    2 KB (255 words) - 03:14, 7 January 2019
  • == PyMOL API == * '''coords''' = list: Nx3 float array
    814 bytes (101 words) - 22:50, 21 April 2015
  • ''New in PyMOL 1.7.2. See the [[center_of_mass]] script for older PyMOL versions.'' PyMOL> fetch 1ubq, async=0
    757 bytes (92 words) - 00:06, 17 October 2016
  • Reading the [[PyMol list]] for years, we users noticed a trend: person A would ask a question, perso
    365 bytes (66 words) - 22:31, 28 March 2014
  • * list multiple residues once * '''output''' controls if the list is hidden (default), printed on screen (S) or saved in a file (P)
    3 KB (399 words) - 23:33, 26 May 2014
  • Reading the [[PyMol list]] for years, we users noticed a trend: person A would ask a question, perso ...created by Jason Vertrees for the purpose of founding a knowledgebase for PyMOL users. The site also espouses the open-source mode: to post any code on th
    986 bytes (164 words) - 00:49, 28 March 2014

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