User talk:Frodo

alpha;

/usr/sbin/foreman-rake reports:expire

SELECT n_live_tup, n_dead_tup,schemaname,relname from pg_stat_user_tables order by schemaname,relname desc;

if chemdraw makes you want to commit a felony

/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -kill -r -domain local -domain system -domain user ; killall Dock

== during maintenance ==

To pause, run the following query on the slave server:

select pg_xlog_replay_pause();

To resume, run

select pg_xlog_replay_resume();

add new disk

cd /opt/bks/src/cluster/puppet/modules/bks-nfs_mounts/files/dbraw/zinc
 vi manifests/init.pp
puppet module build .
puppet module install -f pkg/bks-nfs_mounts-0.0.31.tar.gz

setenv ZINC_CONFIG_ENV productionSlave2 106

begin; update subname set name='lsd',terms=to_tsvector('english','lsd'),query=plainto_tsquery('lsd') where subname_id=8950;

when restarting zinc on 1-106 and 0-38

setenv ZINC_CONFIG_ENV productionSlave2

on 106 and not on 38 that gets you separate psql servers ugh

edit manifests/init.pp

on alpha
/opt/bks/src/cluster/puppet/modules/bks-nfs_mounts
bump version in modulefile
puppet module build .
puppet module install -f  pkg/bks-nfs_mounts-0.0.24.tar.gz

begin; update substance set tranche_prefix=zinc_mol_tranche(smiles) where sub_id in (select sub_id from substance where tranche_prefix= limit 100); 

renew cert

/opt/eff/certbot-auto renew
/etc/letsencrypt
/opt/eff/certbot-auto run --domains tool-selector.ucsf.bkslab.org,files.docking.org,psicquic.docking.org,zinc15dev.docking.org,jji.compbio.ucsf.edu,johnirwin.compbio.ucsf.edu,reactor.docking.org,excipients.ucsf.bkslab.org,irwinlab.compbio.ucsf.edu,zinc15.docking.org,teague.ucsf.bkslab.org,sea16.ucsf.bkslab.org,zinc15bks.docking.org,jji.docking.org,duc.ucsf.bkslab.org,transporters.ucsf.bkslab.org,duc.docking.org,excipients.compbio.ucsf.edu,sea15.docking.org

basically

/opt/eff/certbot-auto run --domains comma,delimited,list,of,virtual,hosts,to,install,certs,for,no,cnames,allowed

idioms

psql -U root  zinc15 -c "select ('\"vacuum verbose analyze chembl22.' || tablename || ';\"') from pg_catalog.pg_tables where schemaname='chembl22';" | tail -n +3 | xargs -L1 psql -U root  zinc15 -c

push version

• step 1. git pull
• step 2. source python you want to use (e.g. internal for bks)
• step 3. bump version/date in zinc/__init__.py
• step4. python setup.py sdist (builds tar.gz of source code in dist)

(become www via root)

• step 5. install tarball : pip install dist/ZINC15-0.2016xxxx.1.tar.gz
• step 6. restart application server (on tau or wherever running)

powercycle

summarizing:
echo 1 > /proc/sys/kernel/sysrq
echo s > /proc/sysrq-trigger   #sync
echo u > /proc/sysrq-trigger # remount-ro 
echo b > /proc/sysrq-trigger # buttonpress

backups: (use .st source)

aws s3 sync adler s3://docking-archive/backups/adler

conversion

cxcalc -v -S -i smiles -t charge formalcharge --pH 7.4 z6 | molconvert smiles -T name:charge

SEA16

http://sea16.ucsf.bkslab.org/custom/search/target_vs_target?library=chembl_10uM&target_id=SC6A3_HUMAN+5&query_id=SC6A4_HUMAN+5&rank_cutoff=50

Supplier codes and ZINC IDs for list of zinc ids where sold by specific vendors:

curl 'http://zinc15.docking.org/catitems.txt' -F "catalog-has-short_name-in=enamine sial" -F zinc_id-in=@zincids -F sort=no -F count=all

ZINC IDs and all catalogs selling them where at least one catalog is in a specific list of vendors:

curl 'http://zinc15.docking.org/substances.txt:zinc_id+catalogs' -F "catalogs-any-short_name-in=enamine sial" -F zinc_id-in=@zincids  -F sort=no -F count=all

ZINC IDs where catalog in a specific list of vendors:

curl 'http://zinc15.docking.org/substances.txt:zinc_id' -F "catalogs-any-short_name-in=enamine sial" -F zinc_id-in=@zincids  -F sort=no -F count=all

Note: -F sort=no makes the query not sort by ZINC ID, should be slightly faster but safe to turn off

Note: -F count=all returns all results from the query, can also be any integer to take only that many (can be combined with -F page=N to get a later slice)

Compounds recognized by transporters that look like aspirin

http://zinc15.docking.org/majorclasses/transporter/substances/?highlight=aspirin&ecfp4_fp-tanimoto-40=CC%28%3DO%29Oc1ccccc1C%28%3DO%29O

Compounds that have names in ZINC

http://zinc15.docking.org/substances/?substance-hasany=name_entries

Names of all rings of all SERT ligands, in a file

http://zinc15.docking.org/genes/SLC6A4/substances.txt:zinc_id+rings&count=all

as above, with smiles:

htp://zinc15.docking.org/genes/SLC6A4/substances.json:zinc_id+rings

ZINC

• broken - http://zinc12.docking.org/substance/3850657
• C04798508 and C13952160 are the same. many more.
• metal detection in dock blaster. correct treatment of hi library
• 17005395 has charge -1 and 6565555 has charge -1

Blaster

From Oliv: Here are some comments on Dockblaster, which I received as feedback from non-experienced users. It seems that the results page is hard to interpret:

- it is not clear to most people what the 4 schemes (coarse/finer/polarized/Amber) mean and what they should use for docking
- the bug that rank and rmsds do not appear in most cases is confusing. Rank and rmsds should also be labeled.
- Instead of "Browse subset 12" one could write "Click here for a list of the best 100 molecules"
- The results (what people want!) are well hidden at the bottom of the page. Maybe one could give the people only the rec.crg file, eel1/mol2 files? At a more prominent place of the page?

SARAH: hi john- just noticed that indole in the l99a binders set looked funny, so i checked the mol2 files out and ref1 is incorrect; the double bond is in the wrong place. ref2 is the correct form of the molecule. the zinc id is C14516984.

I've had a few goes now with Dockblaster on a couple of targets but am having problems with some Calcium-dependant phospholipases in which the catalytic Ca++ is not being included in rec.pdb . First up I used a couple of structures from our group (e.g. I kqu 1j1a,) but in both cases the calcium doesn't get included. I then tried to prep the protein myself and submit those to Dockblaster but the same problem recurred. Thinking it might just be our structures just this morning I used some other workers PLA2 structure (1DB5 Dockblaster ID #38751) and it also doesn't include the Ca. By comparison a test run with thermolysin (5TLN Dockblaster run # #38752) included it's

blaster

dhi, 3frj, /raid3/people/mysinger/pxc/dude/species/dhi1/P28845/blasti/3frj/dock NAP cofactor decapitated

hivpr, 1upj, /raid3/people/mysinger/pxc/dude/species/hivpr/Q72874/blasti/1upj/dock asymmetric only half the biological, two ASP are 2.5A apart and both protonated

mtor, /raid3/people/mysinger/pxc/dude/species/mtor/P42345/blasti/*/dock All ligands failed to build, so 0/5 were build automatically

-- metacyc update http://bioinformatics.ai.sri.com/ptools/flatfile-samples/compounds.dat

-- pubchem update (quarterly) -- cdd update (quarterly)

https://s3.amazonaws.com/cdd-public/cdd-public-structures-20110219230015.sdf.gz

For future downloads, you can visit https://s3.amazonaws.com/cdd-public/ and figure out the current filename from the XML that is displayed.

Miscellaneous

Brenda is at /raid5/backonce/joha/DB3/5_BRENDA2SDF/ORG_BRENDA_MOL_FILES_PREP/brenda_031306.ism
mysql is at mysql -u joha -p*secret* -h (brenda-machine-name-ask-jji) brenda
wombat is at ~jerome/sets/wombat/wombat_20062/wombat.20062.sdf.gz