VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 21 2021 - 16:36:16 CST
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Whoever implemented this thought it would be useful this way. There are
lots of these arbitrary choices that need to be made when writing software
like VMD.
Axel
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vRqGy1ENhSqGWt3A6pU2LNjH9qJsOXgzDbHJV1FHHnvo5la0OomHmW0UnjibnXK2jw$ College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste, Italy On Thu, Jan 21, 2021, 17:15 David Alejandro Rincón Daza < darincond_at_unal.edu.co> wrote: > Thank you to both. > But, is there an argument or paper to vmd have chosen that format? > Molecule:Atom > > > > El mié, 20 ene 2021 a las 10:22, Pawel Kedzierski (< > pawel.kedzierski_at_pwr.edu.pl>) escribió: > >> Dear David, >> >> I guess what you refer to is just the default atom label, which is >> completely arbitral; you can label atoms with any text, either via GUI >> (Graphics->Labels..., Properties tab) or using Tcl commands >> <http://www.ks.uiuc.edu/Research/vmd/current/ug/node133.html> (e.g. "label >> textformat Atoms 0 { MY OWN ATOM LABEL }". The default format is " >> %R%d:%a" which is substituted with residue name, residue id, colon and >> atom name. >> However, the residue and atom names are taken from the molecule input >> file and they follow the source format specification. >> <https://urldefense.com/v3/__http://www.wwpdb.org/documentation/file-format.php__;!!DZ3fjg!uKWiixlPzN0Ob7jdx3TOBz8fsTRUMO-tdQaQ8QRtFak6R90whu3STlqvs5y8ftwB0Q$> >> >> Greetings, >> Pawel >> >> Good day colleagues, >> I have an academical curiosity: >> >> What was the reason behind the semantic structure of naming atoms in VMD? >> >> i.e. THR40:HN >> >> Thank you in advance, >> David >> >> >> > *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son > confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. > Se encuentran dirigidos sólo para el uso del destinatario al cual van > enviados. La reproducción, lectura y/o copia se encuentran prohibidas a > cualquier persona diferente a este y puede ser ilegal. Si usted lo ha > recibido por error, infórmenos y elimínelo de su correo. Los Datos > Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra > Política de Datos Personales que podrá consultar en la página web > https://urldefense.com/v3/__http://www.unal.edu.co__;!!DZ3fjg!vRqGy1ENhSqGWt3A6pU2LNjH9qJsOXgzDbHJV1FHHnvo5la0OomHmW0UnjjUeyvzxQ$ > <https://urldefense.com/v3/__http://www.unal.edu.co/__;!!DZ3fjg!pbrYIholGMoVJhp4GTVz5J_ouLiXbhv1BqOmDg87C2DQB7dTa-Wa9numhNrM0lR67w$> > . Las opiniones, informaciones, conclusiones y cualquier otro tipo de > dato contenido en este correo electrónico, no relacionados con la actividad > de la Universidad Nacional de Colombia, se entenderá como personales y de > ninguna manera son avaladas por la Universidad. >
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