User contributions for Frodo

13 February 2014

• 21:3521:35, 13 February 2014 diff hist +672‎ N Adding Static Waters to the Protein Structure ‎ Created page with "If you have ordered waters in your structure, DOCK3.7 can use them, but you have to add hydrogens 'manually' using some visualization program and your intuition. Once this is ..."
• 21:3421:34, 13 February 2014 diff hist +1,669‎ N Protein Target Preparation ‎ Created page with "Protein Target Preparation be-blasti is still the preferred method of downloading PDB files and splitting them into rec.pdb and xtal-lig.pdb files. Run it with be_blasti.csh ..."
• 21:3121:31, 13 February 2014 diff hist +181‎ N Mol2db2 ‎ Created page with "mol2db2 is a program that takes multi-conformation mol2 files and compiles them into the db2 format for docking. {{Template:CC-BY-SA-30}} {{Template:Coleman}} [[Category:DOCK..."
• 21:3021:30, 13 February 2014 diff hist +2‎ DOCK 3.7 ‎No edit summary
• 21:3021:30, 13 February 2014 diff hist +35‎ DOCK 3.7 ‎No edit summary
• 21:2921:29, 13 February 2014 diff hist 0‎ Ligand preparation ‎No edit summary
• 21:2821:28, 13 February 2014 diff hist +1,096‎ N Ligand preparation ‎ Created page with "Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SM..."
• 21:2721:27, 13 February 2014 diff hist +6,248‎ N Mol2db2 format ‎ Created page with "<pre> Mol2db2 Format 2 File Format T type information (implicitly assumed) M molecule (4 lines req'd, after that they are optional, 24 lines max) A atoms B bond X xyz R rigid..."
• 21:2321:23, 13 February 2014 diff hist +4‎ DOCK 3.7 ‎No edit summary
• 21:2221:22, 13 February 2014 diff hist +47‎ Analyzing DOCK 3.7 Results ‎No edit summary current
• 21:2121:21, 13 February 2014 diff hist +4,710‎ N INDOCK 3.7 ‎ Created page with "<pre> DOCK 3.7 parameter ##################################################### # NOTE: split_database_index is reserved to specify a list of files ligand_atom_file ..."
• 21:1921:19, 13 February 2014 diff hist −2‎ DOCK 3.7 ‎No edit summary
• 21:1821:18, 13 February 2014 diff hist +1‎ DOCK 3.7 ‎No edit summary
• 21:1821:18, 13 February 2014 diff hist −25‎ DOCK 3.7 ‎No edit summary
• 21:1721:17, 13 February 2014 diff hist +306‎ DOCK 3.7 ‎No edit summary
• 21:1721:17, 13 February 2014 diff hist +175‎ N Template:Coleman ‎ Created page with "This page is adapted from "DOCK3.7 Documentation" by Ryan G. Coleman. Based on a work at [https://sites.google.com/site/dock37wiki/ https://sites.google.com/site/dock37wiki/]."
• 21:1621:16, 13 February 2014 diff hist −281‎ Template:CC-BY-SA-30 ‎No edit summary
• 21:1021:10, 13 February 2014 diff hist +561‎ N Template:CC-BY-SA-30 ‎ Created page with "[Image:http://i.creativecommons.org/l/by-sa/3.0/88x31.png] This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License. To view a copy of thi..."
• 21:0021:00, 13 February 2014 diff hist +3,440‎ N Analyzing DOCK 3.7 Results ‎ Created page with "Analyzing DOCK 3.7 results The dock37tools in $d37 contain various analysis programs. Once your jobs are done, you can run: $d37/extract_all.py If you ran a prospective run,..."

12 February 2014

• 20:0420:04, 12 February 2014 diff hist +69‎ N Hypervisor ‎ Created page with "ssh into the hypervisor (apes, rocky, pulp) sudo virsh list --all"

30 January 2014

• 17:1717:17, 30 January 2014 diff hist +166‎ N Disk full ‎ Created page with "if the disk is full, here is how you find out who the major culprits are (example here is /raid1) sudo /usr/sbin/repquota /raid1 | sort -nk3 [{Category:Internal]]"

29 January 2014

• 20:4520:45, 29 January 2014 diff hist +862‎ N Get ZINC under program control ‎ Created page with "More things to not forget <pre> teague:~$ wget -q --post-file smiles-to-lookup.smi "http://zinc.uoft.bkslab.org:8080/inchi -O- ZINC01586379 ZINC00000053 ZINC15202372 teague:..."
• 20:4320:43, 29 January 2014 diff hist +825‎ N Ring SQL query ‎ Created page with "From his bestseller, 101 things to not forget <pre> This just came out of some debugging. Thought you may be interested. It will return the number of occurrences of a particu..."
• 20:4020:40, 29 January 2014 diff hist +1,700‎ N Cassidy clustering ‎ Created page with "These are notes to myself from Teague/Cassidy for the new cluster. [[Category::Internal]] I've written some code to generate Daylight-like fingerprints (Base-64) from the ..."

27 January 2014

• 19:3319:33, 27 January 2014 diff hist +491‎ Github ‎No edit summary
• 19:3019:30, 27 January 2014 diff hist +240‎ Nm User talk:Sedigheh ‎ Welcome! current
• 19:3019:30, 27 January 2014 diff hist +16‎ Nm User:Sedigheh ‎ Creating user page for new user. current
• 19:2919:29, 27 January 2014 diff hist +240‎ Nm User talk:Eric Walters ‎ Welcome! current
• 19:2919:29, 27 January 2014 diff hist +68‎ Nm User:Eric Walters ‎ Creating user page for new user. current

22 January 2014

• 18:1118:11, 22 January 2014 diff hist +1,464‎ N Adding memory to a virtual machine ‎ Created page with "Use "virsh", either locally: root@rocky$ virsh (COMMANDS HERE) or remotely: teague@spinaltap$ virsh --connect qemu:///rocky.cluster.uoft.bkslab.org/system (COMMANDS HERE) W..."

15 January 2014

• 19:4319:43, 15 January 2014 diff hist +797‎ N Zinc exact lookup by http ‎ Created page with "New ZINC lookup features wget -q --post-file smiles-to-lookup.smi "http://zinc.uoft.bkslab.org:8080/inchi -O- ZINC01586379 ZINC00000053 ZINC15202372 wget -q --post-file..."

10 January 2014

• 15:3715:37, 10 January 2014 diff hist −4‎ Category:Internal ‎No edit summary
• 15:3715:37, 10 January 2014 diff hist +106‎ Category:Internal ‎No edit summary
• 15:3315:33, 10 January 2014 diff hist −8‎ Lab Security Policy ‎No edit summary
• 15:3215:32, 10 January 2014 diff hist −7‎ Lab Security Policy ‎No edit summary
• 15:3115:31, 10 January 2014 diff hist +4‎ Lab Security Policy ‎No edit summary
• 15:3115:31, 10 January 2014 diff hist +19‎ Lab Security Policy ‎No edit summary
• 15:2915:29, 10 January 2014 diff hist +442‎ Lab Security Policy ‎No edit summary
• 15:2315:23, 10 January 2014 diff hist −21‎ Lab Security Policy ‎No edit summary
• 15:1915:19, 10 January 2014 diff hist +8‎ Lab Security Policy ‎No edit summary

9 January 2014

• 21:1821:18, 9 January 2014 diff hist −42‎ SSH public key authentication ‎ Redirected page to How to generate ssh keys securely current

9 December 2013

• 21:1221:12, 9 December 2013 diff hist +240‎ Nm User talk:Shuiqing li ‎ Welcome! current
• 21:1221:12, 9 December 2013 diff hist +30‎ Nm User:Shuiqing li ‎ Creating user page for new user. current

12 November 2013

• 19:4219:42, 12 November 2013 diff hist +1,009‎ N Metabolites databases ‎ Created page with "There are two three kinds of metabolite docking databases at docking.org, and from each type, there are multiple actual databases. *NB this work is still in progress* = Gr..."

11 November 2013

• 20:3520:35, 11 November 2013 diff hist +3‎ Cluster 1 ‎No edit summary
• 20:0820:08, 11 November 2013 diff hist +66‎ SVN ‎No edit summary
• 20:0720:07, 11 November 2013 diff hist +121‎ N Github ‎ Created page with "This page describes how to use github, which is our version control system. Category:Internal Category:Sysadmin"

6 November 2013

• 17:3117:31, 6 November 2013 diff hist +29‎ Loading ZINC12 ‎ →‎2. Parse SDF into ISM, harvesting data from SD tags into synonyms table
• 17:3017:30, 6 November 2013 diff hist −29‎ Loading ZINC12 ‎ →‎4. Desalt, filter out neverwants, stereochemical expansion, remove N stereochem, take 4 max
• 17:2917:29, 6 November 2013 diff hist +28‎ Loading ZINC12 ‎ →‎4. Desalt, filter out neverwants, stereochemical expansion, remove N stereochem, take 4 max