20180209, 20180213, 20180219, 20180220 pandda rerun prep

• @nick: what set was in spacegroup A and what in sg B? and the datasets you found hits? 
• @jose: split in know sets and rerun pandda there.
1. changed the database and analysis folders: moved nick's original processing to a subfolder inside analysis; renamed the original .pkl file.
2. visit /dls/labxchem/data/2017/lb16978-1/processing/
1. only lb16978-2 selected in the beamline folder
2. 475 crystal folders in analysis/initial_model lifted with xce 
3. compound files: 
1. 455 x 3 compound .cif, .pdb and .png files found
4. using the datasets autoselected as C2: 
1. 108 datasets selected for dimple
1. 107 dimple.pdbs returned
2. x2095 is the starting C2 model 
3. jose left refine-c2-ground-jose.pdb in the reference folder (this is pretty much like smTGR-c2.pdb apart from the waters).
2.  started a pandda "pre-run for ground state" with those 107 datasets
5.  and now, the ones autoselected a/dls/labxchem/data/2017/lb16978-1/processing/references P2 or P21
1. 171 marked for dimple with the P21_orig model
1.  x2064 is the starting from p21_orig
2.  dimple reran with p21_alt model
1.  x2047 is the starting model for p21-alt
6. I moved the ground state effort files so they don't clutter the folders. /dls/labxchem/data/2017/lb16978-1/processing/reference moved to /dls/labxchem/data/2017/lb16978-1/processing/reference/ground-state-model-effort
7. CONCLUSION:
1. from the assessment of the average maps created in the ground state model process, I don't think it's worth modelling a ground state different than what nick had already modelled originally. Yes, it would tweak the waters, but it's just more effort than necessary. Keep the 3 original models to redo pandda: SmTGR-c2.pdb, smTGR-p21-alt.pdb and smTGR-p21-original.pdb. They're the only ones in the reference folder now.
• @all: 16-02 to review pandda rerun with current softwareand others.

20171122 catch up and call with nick and brazil

20171122 - Ray, Barbora and Jose  and nick, floriano, carolina and sabrina.

• May 18 likely target for general call
• Focussed effort through Innovate UK and Ark (Arc?) Light
• Carolina did report with compounds 3+4 considering several flavours of cys oxidation states in active site

• TGR assays: baseline ok-ish with new short and long preps  (one potential inconsistency in short prep's result)
• TGR xtals: PCTs done but not assessed.
• Jose/Barbora to look into Bogar's original trays (199/200/201 - one barcode was 441305059056)
• Barbora's new PCT titration series - 441305075155

20171110 Weekly catch up - new prep

20171110 - Barbora, Ray and Jose'

 See notes below.

20171030 weekly catch up

20171030

• Barbora set JCSG plate and got some 15 hit:
• To cluster them and understand if there are any trends in conditions that show crystalline precipitate (salt conditions vs PEG conditions vs alcohol conditions etc).
• Not to optimise with this protein batch.
• Next protein batch (20 x 20ul aliquotss @ ~13mg/ml) to be ready on Friday 03-11, then to do PCT test for 2,4,8,10,13 mg/ml and use that as reference for what crystallisation condition to use Barbora points out (wisely) that concentrating more could result in full protein crashout given concentrator requires 200ul starting material. 
• Jose's note to self: how does the PCT translate to John William's suggestion to get crashout    vs OD scheme.

20171020 Catch up notes

jose, jo, barbora

1- greiner  3 drops
2- temperature?
3- which screen?

• Dec 2015: Valtteri produced protein: found B2 hit from PCT:
• PCT user guide: https://hamptonresearch.com/documents/product/hr008506_2-140_142_user_guide.pdf
• (From https://hamptonresearch.com/product_detail.aspx?cid=1&sid=29&pid=10 )
•  Dec 2016: Anil + Valtteri screened and found hits in JCSG D6 and Morpheus C(1?). Both similar to the PCT hit.

ACTION PLAN for monday 23-10

• 6 aliquots left frozen (use the leftover ones in fridge to test the protocol before burning the fresh aliquots)
• room temperature
• do PCT like Jo advised on greiner 3 well plates
• dispense 0.5ul each PCT solution in each subwell
• dispense 0.5ul protein at 13mg/ml, 10 mg/ml, 8mg/ml in each PCT solution
• wait some 10 minutes
• check in microscope
• 2x JCSG trays at room temp first
• (Lauro used 4degC only after other things failed)