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Re: [phenixbb] [ccp4bb] phenix installtion problem
by Alexandre OURJOUMTSEV 26 Jun '15

26 Jun '15

Dear Weifei, I am neither in the Phenix nor in the CCP4 teams so I let me remark that it does not look reasonable, just a few minutes after Tom Terwilliger's mail : "I'll answer you on the Phenix BB as you've asked specific questions about Phenix tools." sending your mail (see below) asking explicitly phenix questions again through the CCP4bb. I do not think that you "disturb", you should not sorry for this, the BB are for this, but we need to follow the rules. I ask everybody to respect both ccp4 and phenix teams, who assures a lot of service and help for our community, and send your requests properly (for your own benefit), through the BB concerned. My another request (luckily not applicable to the Weifei mail) is that people always sign properly their mails and give their name when asking their questions : ccp4, phenix teams and other experts answer you openly and this looks quite weird seeing anonymous requests. Again, this is for your own benefit, for your better integration into the research community. With best regards, Sacha Urzhumtsev ________________________________ De : CCP4 bulletin board <CCP4BB(a)JISCMAIL.AC.UK> de la part de ChenWeiFei <weifei_c(a)OUTLOOK.COM> Envoyé : vendredi 26 juin 2015 15:05 À : CCP4BB(a)JISCMAIL.AC.UK Objet : [ccp4bb] phenix installtion problem Dear all, Sorry to disturb you. I have install Phenix to my computer Centos 7.0. When I want to use it I need to cd /usr/local/phenix-1.9-1692/ and . /usr/local/phenix-1.9-1692/phenix_env.sh then type phenix in the command line every time. I wish to use phenix in every terminate window and just type phenix. Some told me use export PATH to do it but I don't know how to do it. I am new to linux(centos) Thank you so much! Best, Weifei

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anomalous phasing with HySS - phaser - Autobuild
by Almudena Ponce Salvatierra 26 Jun '15

26 Jun '15

Hi all, I have SeMet data for which HySs locates 127 Selenium atoms with a CC of 0.31, which I think is decent. Then I run Phaser to generate the first maps, and it gives a score of 25 and LLG of 190 or so... The next step would be running Autobuild, however, the first models I realize it is building have R work and R free between 50 and 55%. So I guess it is just some random stuff there. If the result from HySS and Phaser looks more or less good, why does AutoBuild show these numbers?? Any idea of what I could do to improve so? Any ideas are welcome. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Optimal Linux configuration for Phenix.refine
by Colin Levy 25 Jun '15

25 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]>

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Fw:Re: Autobuild Density
by Smith Liu 19 Jun '15

19 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

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Autobuild Density
by Appu kumar 19 Jun '15

19 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

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Get R values without refining in phenix.refine
by Murpholino Peligro 18 Jun '15

18 Jun '15

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

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Re: [phenixbb] anomalous difference map calculation
by Alexandra Marques 18 Jun '15

18 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 > > >

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anomalous difference map calculation
by Alexandra Marques 18 Jun '15

18 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

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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 ******************************************************

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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

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