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inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
12:34 AM
\o @san
 
santiago
santiago
yo
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
It reads 5:04 a.m. and I'm still not asleep. O.O
 
santiago
santiago
tsk
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
Have you seen the latest meta.SE featured thingy?
I wrote an answer for that, which stands at +17. ᕙ(⇀‸↼‶)ᕗ
 
santiago
santiago
link?
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
12:36 AM
43
Q: How do we encourage edits to obsolete/out of date answers?

bluefeetAs the network ages and we have answers that are 7+ years old, we run into situations where changes in technology, etc. result in a once great answer becoming out-of-date, obsolete, or somewhat problematic. We don’t want to lose or delete these answers, due to legacy applications that still need...

discussion featured edits suggested-edits answers
 
santiago
santiago
+18
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
I love you.
 
santiago
santiago
lol
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
I've recently turned meta.chem into a sitcom.
 
santiago
santiago
sitcom eh?
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
12:40 AM
Look at the last five meta Qs.
Holy crud.
 
santiago
santiago
just had a glance - lol, I see what you mean
I haven't being doing much on the site lately
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
You're feeling like me.
Even though you're weird, we end up being the same.
 
santiago
santiago
nah been busy in RL
being weird is a good thing
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
Which brings me to my next question: How is my new profile pic?
 
santiago
santiago
symmetrical
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
12:46 AM
Its small version looks like a butterfly.
 
santiago
santiago
which chemical is this?
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
It's a window. A fenestrane.
I've added a stat in my profile: An up-to-date description of the profile pic.
 
santiago
santiago
i just got a gold on meta.SE
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
Lunatic?
Hullo @Curt!
 
Curt F.
Curt F.
Hi guys!
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
12:58 AM
How're you doing?
 
santiago
santiago
hi @CurtF.
@inɒzɘmɒЯ.A.M electorate
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
@santiago Yay!
 
santiago
santiago
just waiting for the cache to catch up
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
Cache to wait for the ketchup?
 
santiago
santiago
ha
am looking to answer something on SO, have 4 answers (+2, +2, +1 accept and +0)
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
1:04 AM
That's one hell of a record.
 
santiago
santiago
not really
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
Theoretically.
 
Curt F.
Curt F.
SO is super hard.
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
You mean harsh, or stiff?
 
santiago
santiago
yup, it is all of the above
 
Curt F.
Curt F.
1:06 AM
I mean to get upvotes for your answers is difficult.
If you answer a question older than one day, even an unanswered one, IME you don't often get upvotes.
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
Burn SO!
 
santiago
santiago
@CurtF. true and even less chance of an accept
 
Curt F.
Curt F.
There's often a race to post answers for the easy questions. If you lose the race, no upvotes for you!
My best SO answers have no upvotes and the mediocre ones I submitted quickly do the best.
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
Then I hereby invite you to write answers for meta.SE.
No expertise needed, you just need to know a lot about meta and think meta a lot.
So that either people agree with you, or you make them agree with you, or you put a lot of meta memes there, and then you get tons of rep.
 
santiago
santiago
@inɒzɘmɒЯ.A.M i have written 7 answers there and 2 questions
@CurtF. looking...
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
1:11 AM
Heck, my newest answer in meta.SE is +20 @Curt. I couldn't earn that after almost a year participation in chem.SE.
 
santiago
santiago
@CurtF. I see what you mean - your answers on SO are great!
upvoted 2 of them - will look at more a bit later on (so the serial robot doesn't sting us!)
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
I'll sting if you want.
 
santiago
santiago
lol
you should join SO @inɒzɘmɒЯ.A.M
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
I should. Doesn't mean would.
 
santiago
santiago
@CurtF. we should conscript @inɒzɘmɒЯ.A.M into SO
one of us, one of us...
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
1:17 AM
Bring in an army with ya.
I've decided not to sleep.
 
santiago
santiago
uh oh
 
 
8 hours later…
santiago
santiago
9:45 AM
HAHAHAHHAAHA
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
?
 
santiago
santiago
hi
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
\o
 
santiago
santiago
wrote a question on Earth Sciences
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
shrugs
 
santiago
santiago
9:50 AM
jealous
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
ಠ_ಠ
 
santiago
santiago
lol
just been downvoting on SO
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
FFFFFFUUUUUUNNNNNN
 
santiago
santiago
it is
my job interview went well yesterday
but who cares? right?
anyway, how is your day?
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
Ice cream-y.
 
santiago
santiago
9:59 AM
eh?
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
Eh. Just has five.
-1 for giving away my secrets. ლ(ಠ益ಠლ) — inɒzɘmɒЯ.A.M 1 hour ago
 
santiago
santiago
1
Q: What geological structure(s) is responsible for the recent Queensland earthquakes?

santiagoRecently, south-east Queensland has been rattled by 2 moderate earthquakes - a 5.3 a couple of days ago (News report) and a 5.7 tremor just a few hours ago as of writing this post (News Report). These are significant as they are the strongest earthquakes experienced in Queensland. The location o...

seismology earthquakes intraplate
 
inɒzɘmɒЯ.A.M
inɒzɘmɒЯ.A.M
@santiago @Santiago.
That was an easy one.
 
santiago
santiago
eh?
 
santiago
santiago
10:19 AM
@inɒzɘmɒЯ.A.M @inɒzɘmɒЯ.A.M what? what?
 
PH13
PH13
ಠ_ಠ
o/
 
santiago
santiago
hi
 
PH13
PH13
everything is fine?
 
santiago
santiago
just realised that I've not answered anything in over a week, nor asked a question in over 2 weeks - I start writing an answer (or question) but then stop myself
@PH13 easiest to assume so
There was one question a couple of days ago, I had researched and written the answer, and pressed 'discard' after some thought
 
PH13
PH13
@santiago why that?
 
santiago
santiago
10:33 AM
self concious probably
 
PH13
PH13
that's a hard problem ... solve it :)
 
santiago
santiago
meh, I'll get my confidence back for here eventually - but are doing the background stuff in the meantime
 
PH13
PH13
bakcground stuff is also important
 
santiago
santiago
though I am not editing much at all either
heck, I am not even 'greeting' as much as before
but are always lurking around the review queues and commenting on occasion
@PH13, you and @Martin-マーチン were right in pulling me up on my contributions (especially lately)
 
santiago
santiago
11:13 AM
hi @diffracteD
 
santiago
santiago
11:24 AM
I think I'll just quietly contribute in the background...
 
 
1 hour later…
PH13
PH13
12:46 PM
@santiago I think you should answer the questions that you want to answer
 
 
3 hours later…
Wildcat
Wildcat
3:41 PM
Hi!
 
Wildcat
Wildcat
3:54 PM
='.'=
=(^.^)=
:D
 
PH13
PH13
@Wildcat of course I meant $\ce{AB^{n+}}$ ... dumb me ^^
 
Wildcat
Wildcat
@PH13, sure, I knew that.
But still thought it is a good idea to clarify.
 
PH13
PH13
sure, of course!
 
Wildcat
Wildcat
Still trying to find some info on HHe2+...
:D
 
PH13
PH13
I would like to see read about it
you do not coincidentally work from time to time with openbabel ?
 
Wildcat
Wildcat
4:08 PM
@PH13, worked with it few years ago. Wrote my own crappy molecular viewer in C++ using OpenBabel. :D
 
PH13
PH13
cewl
I try to use obconformer with confab but have to change somehow the force field that is used ... do you know how to do that?
the current command is from "documentary"
obabel bostrom.sdf -O confs.sdf --confab -nconfs 100000
and it uses mmff94 ... but I want uff
 
Wildcat
Wildcat
--ff <name> - select a forcefield (default = MMFF94)
Works?
 
PH13
PH13
D:\Theoretische Chemie\confab>obabel borons1.sdf -O confs.sdf --confab -nconfs 100000 --ff uff
**Starting Confab 1.1.0
**To support, cite Journal of Cheminformatics, 2011, 3, 8.
..Input format = sdf
..Output format = sdf
..RMSD cutoff = 0.5
..Energy cutoff = 50
..Conformer cutoff = 1000000
..Write input conformation? False
..Verbose? False

==============================
*** Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Cannot initialize database 'types.txt' which may cause further errors.
it's the boron that makes the problems
 
Wildcat
Wildcat
Hmm... Strange...
 
PH13
PH13
at least the force field related ones ^^
 
Wildcat
Wildcat
4:14 PM
maybe capitalise the UFF word?
-ff UFF
--ff UFF
I mean
 
PH13
PH13
nope
nothing changes
how long will you stay online? I have to go for shopping now ... will take some 30 mins, or so
 
Wildcat
Wildcat
I'll be here. :D
Confab is now part of Open Babel, and is no longer available from this website.
Maybe confab is outdated.
And you better go with Open Babel itself.
 
PH13
PH13
hmmm
I treid using confab, because this paper states, that confab together with rdkit is one of the best free choices to search conformers
but I'm unsatisfied with rdkit, because It generates so many similar/identical structures because it's a random approach ... and I don't know how to delete the duplicates
 
Wildcat
Wildcat
Yes, but it is said that confab now is part of Open Babel.
 
PH13
PH13
I know
I read that :D
I mean ... I think that I use obconformer from within openbabel
 
Wildcat
Wildcat
4:25 PM
Then I think you have to download OB and give it a shot.
what is the version then?
obabel -V
 
PH13
PH13
Open Babel 2.3.90 -- Jul 1 2015 -- 16:39:46
 
Wildcat
Wildcat
the recent one
 
PH13
PH13
yeah :D
 
Wildcat
Wildcat
well then there is some problem with setting up UFF for your molecule
some not parametrised in UFF atom type
 
PH13
PH13
in avogadro UFF works with it
but I don't know how to save all conformers in one file with avogadro
 
Wildcat
Wildcat
4:31 PM
a have no idea as well
 
PH13
PH13
and for sure I don't save each conformer at it's own
 
Wildcat
Wildcat
I used a python script to do it
 
PH13
PH13
avogadro and obabel are imo heavily underdocumented
now shopping, cu later
 
Wildcat
Wildcat
that is my old script
it is from 2011
so might not work without modifications
basically it reads a geometry from a Gaussian out file
then does conformer search
and creates an input file for each and every conformer
and yeah you need Python bindings for OB
 
getafix
getafix
4:53 PM
Hi. How is everybody?
 
Wildcat
Wildcat
5:05 PM
@getafix, hi!
 
PH13
PH13
@Wildcat I will have a look :D
 
PH13
PH13
5:45 PM
@Wildcat it's a secret file ... mysterious
@Wildcat how to use your script?

python main.py name.log?
 
Wildcat
Wildcat
@PH13, gimme a minute. I"M ANSWERING A QUESTION!
:D
 
PH13
PH13
@Wildcat answer it, captain capslock!
 
Wildcat
Wildcat
6:03 PM
@PH13, input file name is fixed in the source code. :D
input_file_name = "job.out"
 
PH13
PH13
saw it now :D
why do you use weighted rotor?
 
Wildcat
Wildcat
it is just an exmple
 
PH13
PH13
which unit is the threshold?
 
Wildcat
Wildcat
change to systematic
in the unit of energy of conformers which Open Babel uses :D
 
PH13
PH13
ok ... then I have to find out what they use
 
Wildcat
Wildcat
6:04 PM
but for systematic search it should not be used by the way
the problem is with random/weighted search usually
 
PH13
PH13
do I have to set it to 0.0 then?
 
Wildcat
Wildcat
let me read the code
to recall the details
 
PH13
PH13
 
Wildcat
Wildcat
yeah, set it to zero
:D
but there will be dupes then
you see
 
PH13
PH13
and without dupes? :C
 
Wildcat
Wildcat
6:07 PM
there is a parameter called optimization_steps
basically each and every conformer is optimised at the MM level
for this number of steps
 
PH13
PH13
yes
 
Wildcat
Wildcat
even if you do systematic search
the optimisation will run then for each and every conformer
 
PH13
PH13
when I set the steps to 1 or 0? ^^
 
Wildcat
Wildcat
well, that is the question!
1 or 0?
:D
 
PH13
PH13
intuitively I would tend to 0
 
Wildcat
Wildcat
6:09 PM
my guess is 1! :D
 
PH13
PH13
xD
 
Wildcat
Wildcat
WE NEED TO PERFORM AN EXPERIMENT! :D
 
PH13
PH13
as you command, cpt. capslock!
script is made for linux, right?
@Wildcat
 
Wildcat
Wildcat
should work on win as well, in principle :D
 
PH13
PH13
D:\Theoretische Chemie\confab>C:\Python32\python.exe main.py
File "main.py", line 18
print "\nSystematic rotor search started."
^
SyntaxError: invalid syntax
:O
 
Wildcat
Wildcat
6:13 PM
yeah
Python 3 syntax is different :D
it should be print("\nSystematic rotor search started.")
print is now a function
let me work on it myself
i will try to update it for Py 3
and test
 
PH13
PH13
I changed every print now ... let's see
he dies now instantly after start xD
 
Wildcat
Wildcat
yeah, same for me
ImportError: DLL load failed: The specified module could not be found.
:D
 
PH13
PH13
i have both installed ... i'll try the other version
2.7
 
Wildcat
Wildcat
Typical Python.
That's why I hate it.
In fact, OB should die.
With all respect to its devs, it is a mess. :(
 
PH13
PH13
@Wildcat why that?
^^
 
Wildcat
Wildcat
6:26 PM
RDKit is way better.
 
PH13
PH13
ok ... then tell me how to properly create conformers with it xD
 
Wildcat
Wildcat
Ask RDKit peoples!
Maybe, you can ask even here at Chem.SE.
I did conf. analysis just once.
 
PH13
PH13
I thought of asking for an easy way to generate conformers.
 
Wildcat
Wildcat
Many do that stuff regularly, so they must have ready-to-use solutions.
You have to make them share their workflows!
:D
 
PH13
PH13
then I will make it so
 
PH13
PH13
6:44 PM
this would be offensive, right?

The first thing that I have in mind is Avogadro (in Geoff's version I guess everything works fine)
 
 
5 hours later…
PH13
PH13
11:23 PM
@inɒzɘmɒЯ.A.M you should go to bed as I do now o/
@inɒzɘmɒЯ.A.M ಠ_ಠ
 

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