[phenixbb] (no subject)
rsneha at umd.edu
Thu Oct 2 07:34:09 PDT 2014
After running autobuild, the Rfactors were 26/39 (autobuild removed the first 30 residues from the Nter!) but the maps look much better.
I ran a quick refinement with default settings and the Rfactors are now 31/39 and can now see the density for my peptide (absent in the model) coming up.
I have a few questions-
1) When is a good time to start building the peptide into the density (should I wait until Rfactors improve significantly)?
2) If so, should I be masking the peptide density somehow so that further refinement doesn't flatten out that density?
3) What is a general good strategy for lowering Rfactors? (Esp if the gap between Rwork and Rfree is high..like 28/40 or so)?
Thanks a lot,
From: Sneha Rangarajan
Sent: Wednesday, October 01, 2014 12:54 PM
To: 'Paul Adams'
Cc: phenixbb at phenix-online.org
I think my problem in MR has been one of the chains. Anyway I tried the ideas you suggested and seems like they worked!
I used ensembler to create a merged pdb of the problematic chain and used phaser giving both chains as multiple ensembles. It gave me a solution with LLG=474 (highest I have got so far) and TFZ=18.8.
I also tried MRage and got a solution with LLG=294.
In both these maps, the density for chain1 ("bad chain") is not as good as the other chain but is nonetheless far better than what I have got before.
I am currently running autobuild on the solution hoping my Rfactors would be reasonable this time.
Thanks a lot for your inputs. They really helped!!
From: Paul Adams [mailto:pdadams at lbl.gov]
Sent: Tuesday, September 30, 2014 7:51 PM
To: Sneha Rangarajan
This likes normal orthorhombic data. In this case I suggest that the most likely issue is the search model (I assume your molecule is fairly small given the unit cell dimensions). I would look at ways to create the best search model using using tools like sculptor and ensembler. You can get Phaser to search for the two domains in the same run but using multiple ensembles. You might also want to try MRage in Phenix, where you can just provide the data file and the sequence and it will try to make the best model and solve the MR problem.
On Sep 30, 2014, at 3:32 PM, Sneha Rangarajan <rsneha at umd.edu> wrote:
> Oh I see. I tried to repeat xtriage with the scala.mtz file and am attaching the log file.
> From: Sneha Rangarajan
> Sent: Tuesday, September 30, 2014 5:58 PM
> To: Paul Adams
> Cc: help at phenix-online.org
> Subject: RE:
> Even i thought so but after i run mosflm and process the data in p21 or p1 and run quicksymm/quickscale it always suggests that the chosen space group is not correct and that it should be p212121.
> I will try looking into Zanuda. Thanks.
> From: Paul Adams [pdadams at lbl.gov]
> Sent: Tuesday, September 30, 2014 5:36 PM
> To: Sneha Rangarajan
> Cc: help at phenix-online.org
> Subject: Re:
> It looks like your R-merge etc in P222 is very high, what leads you to think this is the correct point group? Can you send the xtriage output for the unmerged P2 data?
> On Sep 30, 2014, at 2:29 PM, Sneha Rangarajan <rsneha at umd.edu> wrote:
>> Hi Nat,
>> I am attaching the Xtriage log file from p222.mtz.
>> Would you need anything else (mtz,pdb)?
> Paul Adams
> Deputy Division Director, Physical Biosciences Division, Lawrence
> Berkeley Lab Division Deputy for Biosciences, Advanced Light Source,
> Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering,
> U.C. Berkeley Vice President for Technology, the Joint BioEnergy
> Institute Laboratory Research Manager, ENIGMA Science Focus Area
> Building 64, Room 248
> Building 80, Room 247
> Building 978, Room 4126
> Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
> Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][
> 1-510-495-2506 ]
Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area
Building 64, Room 248
Building 80, Room 247
Building 978, Room 4126
Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul
Lawrence Berkeley Laboratory
1 Cyclotron Road
Berkeley, CA 94720, USA.
Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][ 1-510-495-2506 ]
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