[Chimera-users] Values at Atom Oositions

[Hernando J Sosa]

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 at einstein.yu.edu


-----Original Message-----
From: Elaine Meng [mailto:meng at 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 at 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 at einstein.yu.edu
> 
> 
> -----Original Message-----
> From: Elaine Meng [mailto:meng at 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 at 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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