Hi everyone, Time to join the party, a bit late perhaps but christmas got in the way! First of all, great challenge Paul! It was really fun to try to push my time and I finally got around to implement some scripting which I put off as well.
*If you are not interested in the details skip to the end so see the times. * My first attempt without prior information (except the extension sequence and the fact there are three ligands) ~10 min. I have little to no experience with modelling X-ray data though so it took a long time to get subsequent runs to regularly meet the validation metrics. Below is a short outline of my experience so far. Strategy and approach: I am using coot via the ccpem 1.5.0 stable release for comparison. I don't use any more advanced scripts but have several key bindings set for minimising clicks and mouse micro. The general strategy revolves around simply performing the minimal amount of edits and inputs required to meet the requirements as fast as possible. I try not to move the center of rotation or the view manually with the mouse, at some places it's required or faster to do so but I try to avoid it. The general approach of things to fix are as follows. To Do: Fix the rotamers Gln/32, Asp/33 and Phe/89. Add alternative conformations to Asp/25. Delete the stub and add Cys/72 with alternative conformations. Remodel Arg/40 including backbone and rotamers. Add terminal residues QTC. Add OXT oxygents to both chains. Add two SO4 ligands and the 3GP. Add waters with and RMSD of 1.3 with default distances. 1) Preparations: Open the 'Other modelling tools' panel and load and place the "accept refinement" popup far away from the main gui, it gets in the way. Set the map in the refmac gui. And turn on all restraints in the R/RC menu, set the weight to 200. 2) Manual edits: Run the script and immediately hit space to center on A/1. Navigate down the chain to Asp/25 and add an altconf in the most common rotamer. Further translate until Gln/32-Asp/33, refine and place the side chains manually as they dont match the rotamers very well (correct map weight is key here). Accept and continue to Arg/40, refine and flip the carbonyl. With the right flick the rotamers will fix themselves. Got to Cys/72, delete it and add a new residue as well as the alternative conformation. Go to Phe/89 and go for the third rotamer. Translate to the end of the chain and add 3 terminals resudies, serially mutate to QTC. Navigate to the end and change the cys rotamer. Add OXT for chain A and then B though the other modelling tools panel (you could script adding OXT to all but felt that was cheating). 3) Heteroatoms: Open the validate panel and find unmodeled blobs. Go to the first blob and place the 3GP (here I orient the density before placing as to get the default ligand orientation correct for the purine). Quickly refine and fit the phosphate manually. Go to the second blob and place SO4. Manually shift the view to center on the second SO4 and place it. Click "Find waters..." and change the threshold to 1.3 (most consistent R/Rfree for me without manual intervention) and then run. 4) Cleanup: Merge all the ligand chains, sphere refine the entire molecule for ~1-2 seconds and run refmac. (Optional: curse refmac and or yourself for mistakes and time lost) The binds and custom settings I use are the following (roughly following most to least important for this challenge): e = accept regularization !/@/# (SHIFT+1 2 or 3 depending on keyboard layout this changes) = real space refine zone 3, 7 or 21 residues. z and x = shift 5 residues along the chain (space * 5) Z and X = shift to the beginning or end of the chain a = add terminal residue r = cycle through rotamers R = sphere refine (specifically for this challenge I set the radius to 200 to get everything) t = place ligand from library q = mutate chain to sequence With this setup and my preliminary route I have tried perhaps a dozen times seriously and gotten varying results. Initially times would hover around 3 minutes and then steadily decrease as I made fewer mistakes. So far my fastest times are; *Time (fastest accepted): 2 min 29 sec (R/Rfree: 0.170/0.1995) * *Time (fastest overall): 1 min 42 sec (R/Rfree: 0.169/0.203)* The times are still very unrefined and I am not really happy with 2.29. The big challenge is definitely pushing the Rfree low enough with the rough edits I make. I lose most runs around the 1.50 mark due to Rfree, I never go for second refinements as it would be too slow and It can definitely be done in one round. I usually lose time when fixing the rotamers for Gln-Asp/32-33, they are super tricky to do fast and precise. Also the orienting of the 3GP can be a bother sometimes. Overall quick clean movements seems to be the way forward. I believe times around 55 seconds are definitely possible for someone fast with good mouse movement and macros. I still hesitate several times and have to think about what to do next. I would be interested to see if any of you routinely fix some significant mistake I miss! Happy new year everyone! Best, Victor On Tue, Dec 29, 2020 at 4:54 PM Paul Emsley <[email protected]> wrote: > For the record, my time, the first time, was 8:10 (I didn't record the > R-factors). > > I wrote a couple of extra key-bindings ("Add OXT" and "Other Solvent > Molecules Dialog" (I'll add them to Curlew)) and, after a few practices, > I trimmed a bit of time off. > > > Paul. > > ######################################################################## > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
