- phenixbb - phenix-online.org

Optimal Linux configuration for Phenix.refine
by Colin Levy 24 Jun '15

24 Jun '15

Apologies for the slightly off topic question. I am configuring a Linux workstation and would like your thoughts on an optimal setup for running Phenix. A lot of my computing time is spent in refinement and I am keen to put something together that will see a considerable increase in speed from my creaking Mac Pro (2 2.4GHz Quad core Intel Xeon with 24Gb RAM). Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk<mailto:[email protected]>

5 5

Fw:Re: Autobuild Density
by Smith Liu 18 Jun '15

18 Jun '15

Dear All, Is any method to make the density modified map (from AutoBuild) comparable to the 2mFo-DFc map (from phenix.refine)? Smith -------- Forwarding messages -------- From: "Pavel Afonine" <pafonine(a)lbl.gov> Date: 2015-06-19 00:16:45 To: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Autobuild Density Hi Appu, a guess: perhaps you are comparing density modified map (from AutoBuild) with 2mFo-DFc map (from phenix.refine). If that's the case the maps are going to look differently indeed, so it's not too unexpected. Pavel On 6/18/15 08:47, Appu kumar wrote: > Dear All, > I have query about the density map from autobuild. The density map > from the autobuild look exceptionally good at 3.8A resolution. But > when i refined the autobuild pdb against the original mtz file, the > density become worse. Is it i am doing something wrong or i have to > use some parameterization? Structure is solved with the MR. > Appu _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

2 1

Autobuild Density
by Appu kumar 18 Jun '15

18 Jun '15

Dear All, I have query about the density map from autobuild. The density map from the autobuild look exceptionally good at 3.8A resolution. But when i refined the autobuild pdb against the original mtz file, the density become worse. Is it i am doing something wrong or i have to use some parameterization? Structure is solved with the MR. Appu

2 1

Get R values without refining in phenix.refine
by Murpholino Peligro 17 Jun '15

17 Jun '15

How can I get R values without refining anything? Just to check if my newest model is better than the old one?

3 4

Re: [phenixbb] anomalous difference map calculation
by Alexandra Marques 17 Jun '15

17 Jun '15

Thank you very much for your replies. Here is what I did: 1)I rerun xdsconv again with Friedls law=false in order to get the mtz file with the F(+) and F(-) columns (new.mtz). 2) I used my pdb file from the last refinement together with the new.mtz file as input for “Calculate maps” in Phenix and selected the option for anomalous map. Now I obtained the ANOM PHANOM map. I hope this is correct… In the anomalous map the largest density is in the Mo and Fe atoms. There is no density in the S of SO3 or SO4 groups, so, this will not help me to decide whether there are SO3 groups in the structure (because for the SO4 I have no doubt). However, while searching the mailling list I foud this post http://www.phenix-online.org/pipermail/phenixbb/2009-September/013799.html which worried me. Should I have used from the beginning this “new” mtz file with F+/F- in order to obtain anomalous differences map at each refinement step? Do you think that I should go back, transfer the R-free flags to my new mtz file and repeat all the refinements? Best regards, Alexandra 2015-06-17 16:59 GMT+01:00 Pavel Afonine <pafonine(a)lbl.gov>: > Hi Alexandra, > > to get anomalous difference map you do not need to do anything special: > phenix.refine calculates this map by default as long as your input data are > Fobs(+) and Fobs(-) or Iobs(+) and Iobs(-). > > Refining occupancy of Mo may not be a bad idea given it is likely to be > partially occupied. > > Pavel > > > On 6/17/15 06:04, Alexandra Marques wrote: > > Hi, > > > I am in the last refinement steps of a MR model and I want to calculate > an anomalous difference map essentially to confirm the presence of a > sulfite molecule and to locate vanadium (present in soaking solution). I > read that it is necessary to have a mtz file with anomalous data (i.e. > F+,F- or I+,I-). However, my data was collected at “normal” wavelenght > (0.97) and it was processed with XDS considering Friedls law= true and my > mtz file contain the following columns: H K L FP SIGFP. So, can I still > calculate a anomalous difference map based on my data? > > > Since I also have a Mo atom in the active site can I try to refine its > occupancy by using the option “anomalous groups” in the refinement > strategy? > > > Thank you very much, > Alexandra > > > _______________________________________________ > phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > >

3 3

anomalous difference map calculation
by Alexandra Marques 17 Jun '15

17 Jun '15

Hi, I am in the last refinement steps of a MR model and I want to calculate an anomalous difference map essentially to confirm the presence of a sulfite molecule and to locate vanadium (present in soaking solution). I read that it is necessary to have a mtz file with anomalous data (i.e. F+,F- or I+,I-). However, my data was collected at “normal” wavelenght (0.97) and it was processed with XDS considering Friedls law= true and my mtz file contain the following columns: H K L FP SIGFP. So, can I still calculate a anomalous difference map based on my data? Since I also have a Mo atom in the active site can I try to refine its occupancy by using the option “anomalous groups” in the refinement strategy? Thank you very much, Alexandra

4 4

keep torsion restraint on ligand
by CPMAS Chen 17 Jun '15

17 Jun '15

Hi, All Phenix Users, I am fitting 2-bromoethanol to the density map. I want to keep its gauche conformation, so I edited the cif for this ligand to restrain the torsion angle, loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period BRJ Var_01 BR1 CB CB1 OB1 -60.00 0.0 3 But, after refinement, this angle can be close to 90 or even 120. Even worse is that the fitting at such angles are not better than at -60/60 angle. How could I fix/restrain the angle during refinement? Thanks! Charles *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

3 3

Re: [phenixbb] anomalous difference map calculation
by Ashok Nayak 17 Jun '15

17 Jun '15

Hello Alexandra, I believe you have to reprocess the data keeping friedel pairs (f+ and f- ) separate to make use of the little most anomalous signal (if any) at your collected wavelength. The best thing would be to collect a high redundant set of peak data (if not all the three data sets including mad remote and inflection data) If you have access to a tunable source and xtals left. Once you process differently, you can do all sorts of substructure search and later refine anomalous scatterers using wavelength, atom type and f ' and f“ values. Sulphur sad is also a good possibility if you have a decent nmbr of sulphurs in your protein. Hope this suffices your query. Regards Ashok Nayak CSIR CDRI, Lucknow, India Alexandra Marques <at.marques(a)fct.unl.pt> wrote: >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb >Unsubscribe: phenixbb-leave(a)phenix-online.org

1 0

phenix refine of my EM data
by Smith Liu 16 Jun '15

16 Jun '15

Dear All, By phenix.real_space_refine, I have fitted the a PDB file to an EM map, with Ramachandran favored around 90% and acceptable level of Ramachandran outlier (1.5%) and rotamer outlier (1.2%). Besides visual checking indicating the fitting of the main chain and sid chains to the dnsity map is acceptable. I hope the refine results can be improved by phenix reciprocal space refine. By phenix.map_to_structure_factors I convert my mrc file to mtz file, with the above mentioned phenix.real_space_refine refined pdb amd mtz files as the input files for the graphical phenix refine, in which I never select real space refine, and I always check xyz coordinates and Group B-factors (sometimes I check xyz coordinates and individual B-factors ). Fot this kind of phenix reciprocal space refine, I find the molprobity anslysis results have improved a little, but I find both the contouring level of 2FOFCWT map and the FOFCWT map is more than thousands of thousands high (and it seems the contouring level of FOFCWT is much higher), and visual checking indicated both the main chain and side chains hardly fit with the density map. But I really find there were publications which did phenix.real_space_refine first, and then process the reciprocal space refine, which get good results as introduced in the publications. Will you please tell me why my phenix reciprocal refine after phenix.real_space_refine did not work? Best regards. Smith

1 0

on phenix.map_to_structure_factors
by Smith Liu 13 Jun '15

13 Jun '15

Dear All For phenix.map_to_structure_factors, it needs to input the resolution d_min. But for an EM map, usually the resolution is the general resolution of the whole map (or to some extent the average resolution of the whole map). Is d_min for phenix.map_to_structure_factors the general EM map resolution, or the best resolution of the whole EM map, which is only for part of the EM map with the best quality? Smith

2 1