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• PyMOL mailing list
  ...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

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• Identify
  '''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
  order names-list, sort, location # puts 1frg at the top of the list
  679 bytes (98 words) - 02:16, 28 March 2014
• Set state order
  ''New in PyMOL 1.7.4'' == PyMOL API ==
  521 bytes (71 words) - 22:50, 21 April 2015
• Get object list
  '''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
• Set raw alignment
  ''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
• Ls
  ...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
• PyMOL mailing list
  ...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
• List Secondary Structures
  import pymol pymol.stored_ss = []
  249 bytes (35 words) - 02:16, 28 March 2014
• Set Color
  ...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
• Id Atom
  ===PYMOL API=== list = cmd.id_atom(string selection)
  284 bytes (45 words) - 03:06, 28 March 2014
• Get Color Indices
  ...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
• List Colors
  # 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
• TransformSelectionByCameraView
  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
• Iterate State
  ...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
  '''get_names_of_type''' returns a list of object and/or selection names. ===PYMOL API===
  640 bytes (94 words) - 18:49, 14 October 2019
• Intra fit
  ===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
• Disable
  ...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
• Volume color
  * 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
• FindObjectsNearby
  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
  '''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

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