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.
DOCK Blaster
User Support
1135, 1135, 1141
Table 1 & 2
DUD 40
Astex 305
Scrutinizer
autotart
ligand included in target
cofactor, metals handling
jobwatcher
autolaunch clustering on korn
browse calibration results
Results Browser
basic scores and graphs, even if no xtal-lig
flag.pl to flag bad molecules
pattern support
detail page
show and hide toggles
slice and dice. SMARTS filter
General UI
check bookmarking each page
chimera and pymol on mac, linux
pymol finish off top 500
titles, doc links, alts everywhere
CAPTCHA (long term)
usage stats regularly updated
more professional email update message
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
left over bumpf from the old main page.
ZINC || Commercially available compounds || zinc.docking.org
Ligands for my target
- Category:Covalent
- Hit picking party || DOCK 3.7
- DOCK || Our molecular docking software || Latest are DOCK 3.7 and DOCK 6.6
- DOCK Blaster || A public access service for docking screens || blaster.docking.org
- DUDE and DUD || Benchmarks for docking|| dude.docking.org/generate
- HEI || Substrate discovery and function ID || hei.docking.org metabolites.docking.org
Targets for my ligand(s)
- SEA || Similarity Ensemble Approach || Drug repurposing, target ID
- Tutorials
- Assaying Compound Activity
- Topics
- Categories
- Roles
- Article type
- Attributes
- Software
- Databases
- Free || Free to some || Commercial
change log
- June 15, 2016. moved /etc/cron.hourly/pgcluu-update-stats to /root/pgcluu-update-stats