[Dock-fans] Need some help with my dataset

Julio Dominguez acheron24 at hotmail.com
Mon Aug 14 07:05:25 PDT 2017


I haven´t tried out what you are describing but actions in UCSF Chimera can be saved to a log file and scripted. That is, you can create python scripts that will execute commands in chimera repeating step to, let´s say, open a file, calculate some properties, close the file and move on to a next one.

Check this instructions out:


Very Basic Chimera Programming Primer - UC San Francisco<https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
Looping Through Data Files and Running Chimera Commands on Them ...and not much else Scenario This primer covers the scenario where you have a set of data files in a ...

I hope this helps you.


From: dock-fans-bounces at docking.org <dock-fans-bounces at docking.org> on behalf of José Ribamar dos Santos Ferreira Júnior <zeribajr at usp.br>
Sent: Thursday, August 10, 2017 8:17:57 PM
To: dock-fans at docking.org
Subject: [Dock-fans] Need some help with my dataset


I have a colleague with whom I work, she did some docking simulations with several molecules and showed me the results in Chimera (https://www.cgl.ucsf.edu/chimera/). She later asked me to transport to an excel plan the data from about 400.000 molecules docked. I´m doing this by hand and sent an email to Chimera developers that told me there is no way to transport this information directly to an excel file. Could someone, please, help me with this problem? Does DOCK has a way to put molecules information directly into a worksheet. The information I need is molecule name; Grid Score;  Int_energy; number of hydrogen bonds, and residues interacting with the receptor. Thank you in advance.


José Ribamar dos Santos Ferreira Júnior
Universidade de São Paulo
Escola de Artes, Ciências e Humanidades
Laboratório de Biotecnologia
Av. Arlindo Béttio, 1000 - Ermelino Matarazzo
Bloco A3, piso térreo, Ala 2
São Paulo - SP
CEP 03828-000
Fone: 11-3091-8873
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