Dear Chimera Developers, Perhaps I have missed it, but I would find a menu for selected aliases very useful. Having returned to Chimera from PyMol recently, it would be great to have an option for the alias command that allowed the particular alias to be listed in a separate window and ran the alias by clicking on the alias name listed there. Best regards, Tim ------------------------- ETH Zurich Prof. Timothy J. Richmond Institute of Molecular Biology and Biophysics HPK F 18 Schafmattstr. 20 8093 Zürich SWITZERLAND richmond@mol.biol.ethz.ch http://www.mol.biol.ethz.ch/groups/richmond +41 44 633 24 70 phone +41 44 633 11 50 fax
Dear Tim, I see where you are coming from, but aliases are not necessarily commands. I use them all the time, but mainly to refer to some set of residues, e.g. alias refats #1:57.a,230.a,301.a alias matchats #0:10.a,218.a,287.a alias residues #0:8.a,10.a,164.a,218.a,287.a alias showchain :.a [...] match matchats refats ~modeldisp #1 ~disp ribbon showchain ribrepr smooth disp residues repr stick residues (taken from real command files I used a couple of days ago) One purpose of aliases is to make a hard-to-type thing into an easy-to- type thing, so perhaps it would help to make shorter aliases. If it is a matter of remembering what they are, the command "alias" without any arguments will show all the aliases and their definitions in the Reply Log. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote:
Dear Chimera Developers,
Perhaps I have missed it, but I would find a menu for selected aliases very useful. Having returned to Chimera from PyMol recently, it would be great to have an option for the alias command that allowed the particular alias to be listed in a separate window and ran the alias by clicking on the alias name listed there.
Best regards,
Tim
On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote:
Dear Chimera Developers,
Perhaps I have missed it, but I would find a menu for selected aliases very useful. Having returned to Chimera from PyMol recently, it would be great to have an option for the alias command that allowed the particular alias to be listed in a separate window and ran the alias by clicking on the alias name listed there.
Best regards,
Tim
Hi Tim, As Elaine pointed out in her reply, aliases are frequently used as shorthands for long atom specs rather than as replacements for complete commands. However, the form of the alias command that uses '^' (so that matching only occurs at the start of the line) typically is used to define full command aliases. So my thinking is this: aliases defined with the '^' character would be placed in an 'Aliases' top-level menu (created on the fly as needed). Such aliases would automatically be remembered across Chimera invocations (and populate an Aliases menu). The menu could be torn-off (except on Aqua) to make a stand-alone window. Those aliases could be deleted as normal with the ~alias command (which would remove them from the menu and no longer remember then in subsequent Chimeras). Would this be good enough? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Elaine Meng -
Eric Pettersen -
Richmond Timothy J.