Dear Elaine from chimera.tkgui import saveReplyLog saveReplyLog("savefilename") Does not seem work, the resulting file is empty. I think the reason is that when idle is open the output of a command like from chimera import runCommand as rc rc("measure mapValues #0 #3 name vdatatom report all") is directed to the python shell instead to the Reply log. So I am still unclear on how I can save the output to a file within a python script? Thanks Hernando Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, November 19, 2018 2:39 PM To: Hernando J Sosa Cc: chimera-users Subject: Re: [Chimera-users] Values at Atom Oositions Yes, that’s basically the same as in the link sent in my previous reply. Elaine
On Nov 19, 2018, at 11:34 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Thanks Elaine and I guess then I could use something like the code below (found it in an old thread) to save the Reply Log within the script:
from chimera.tkgui import saveReplyLog saveReplyLog("savefilename")
H.
Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, November 19, 2018 2:07 PM To: Hernando J Sosa Cc: chimera-users Subject: Re: [Chimera-users] Values at Atom Oositions
Hi Hernando, Unfortunately there is no command to save attributes directly to file.
One idea is use the “report all” option of “measure mapValues” to send the values to the Reply Log and then save the Reply Log as described at the bottom of this page: <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r bvi.ucsf.edu%2Fchimera%2Fdocs%2FProgrammersGuide%2FbasicPrimer.html&am p;data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cf92bc6244f7f4604ab1 a08d64e56b43c%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C63678253162 6670241&sdata=l5CAni%2BZTL6ldDMek%2BlNioVzu7bE%2BlDjh0TH3UFJ%2FNs% 3D&reserved=0>
The “list atoms” command does a similar thing, lists values of an existing attribute in the Reply Log. <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r bvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Flisten.html%23lis tatoms&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cf92bc6244f 7f4604ab1a08d64e56b43c%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C63 6782531626680250&sdata=JBs4UUR8Z%2Br9fG3kHY8Q7NVelC9fWY%2FrQ%2Buk8 Dm4JBk%3D&reserved=0>
Best, Elaine
On Nov 19, 2018, at 10:49 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Thanks Elaine, and it would be possible to save the resulting attributes to a file within the script without using the GUI? Something like: measure mapValues map-model atom-spec <my_att_name> saveattributes2file <my_att_name> <my_file>
OR measure mapValues map-model atom-spec <outfilename>
Thanks again
Hernando.
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