User talk:Frodo

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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

Targets for my ligand(s)

  • SEA || Similarity Ensemble Approach || Drug repurposing, target ID

Introduction, overview, navigation, help

Everything else


change log

  • June 15, 2016. moved /etc/cron.hourly/pgcluu-update-stats to /root/pgcluu-update-stats