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phenix.phaser multiple models
by G Y 21 Jul '11

21 Jul '11

Dear all, I want to give several input pdb (searching model) at same time and let phaser run MR separately on each of them. I found I can do this by first "Add ensembles" at Ensemble tab and then "Add search" at Search procedure tab then link the correct ensemble ID. However, there is just one output result for the best solution. Is there anyway to get all solutions in separate .mtz and .pdb files for different searching models? Many thanks! regards, G

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problem in rosetta rebuilding
by intekhab alam 21 Jul '11

21 Jul '11

Hi i tried to run rosetta on a unix machine (ubuntu 9.04) for my data. Upto MR step everything goes fine , but during the rebuilding step after 20 cycles the computer shuts down. i have attached the log file for the autobuilding run of rosetta. i am using phenix 1.7.1-743 version. i will be grateful if some one helps me out -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Phenix TLS refined model feeding into next round of refinement
by Daqi Tu 21 Jul '11

21 Jul '11

Hi, I used to think after one round of Phenix TLS refinement, if I need to do further refinements after correcting couple residues, I need to take out the ANISOU records from the pdb file. The reason is if not, all protein atoms might be applied anisotropic individual B factor refinement in the next round. Yesterday, I made a "mistake" directly feeding the pdb file from the previous TLS refinement into the next one. Seems it is fine. Is that true Phenix automatically recognize what I wanted, that is, TLS only, not anisotropic individual B factor refinement? Thank you. Daqi Tu

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How the sharpening were performed in PHENIX.
by zhangh1＠umbc.edu 20 Jul '11

20 Jul '11

Hi, I was trying to do a B-factor sharpening using phenix GUI CreatMaps utilities. The output for the sharpened maps contains 2FOFCWT and PHI2FOFCWT columes, so I think they are sigmaA weighted 2Fo-Fc maps. But from Brunger's paper, the sharpening coefficients seems directly applied on Fo, and I wonder what happened before we get the 2mFoDFc maps. Or, the sharpening coefficients have been applied to the 2mFoDFc maps? Thanks for any information! Hailiang

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Experimental Data Question
by Yuri 16 Jul '11

16 Jul '11

Nat, That helps clarifying things. Thank you -- Yuri Pompeu

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Experimental Data Question
by Yuri 16 Jul '11

16 Jul '11

It looks like phase_and_build only takes reflections input as F SIGF. I had to use a reflection converter as I had a .sca file with I SIGI data. -- Yuri Pompeu

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Re: [phenixbb] Experimental Data Question
by Yuri 16 Jul '11

16 Jul '11

I am not positive, because I had to convert my reflections.sca (I SIGI) into reflections.mtz (F SIGF) -- Yuri Pompeu

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Experimental Data Question
by Yuri 15 Jul '11

15 Jul '11

Hello All, Heres my situation: I collected data on a new crystal, indexed, scaled (2.75 A), ran molecular replacement (40% homologue) and found a solution. I did some building got a new model, did an initial refinement (using my .sca file, not data.mtz from mol rep). I then ran phase_and_build with density modification. The new maps look a lot better and I am able to see some residues I was not able to place before. I did some more building and I am ready to refine. What should I use as experimental data? phase and_build gave me a .mtz file with amplitudes (no I) and "experimental phase" coeeficients (HLAM. HLBM,...) Cheers -- Yuri Pompeu

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Re: [phenixbb] ADP refinement selection
by Pavel Afonine 15 Jul '11

15 Jul '11

Hi Christian, the problem is that you did not ask phenix.refine to refine the rest of the atoms isotropically (with your command below you only refine anisotropic ADPs of atoms in chain Q, and the B-factors of all the other atoms are not refined): > adp { > individual { > anisotropic = "chain Q" > } I would do it like this: adp { individual { anisotropic = chain Q and element CL isotropic = not (chain Q and element CL) } } Pavel.

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off-topic-Question
by Haytham Wahba 14 Jul '11

14 Jul '11

Dear all i have protein soaked in Dimethyltindibromide in the active site 2 cysteine and 1 aspartic acid by help of anomalous map i can see 2 Sn atoms in each subunit in AU there is difference in both subunits, Sub-A shows acetate near Sn and Sub-B show phosphate ion, even the position of one of the 2 cystein is different from unit to other 1-is it normal to see such difference between 2 subunit? also the distances between Sn and surrounding atoms does not suggest covalent binding 2-the important question is how to confirm if the 2 methyl groups or even one methyl group of dimethlytin are still there or cleaved i mean one can not differentiate between density of water and methygroup. How to define coordinate number of Heavy atom and identity of the attached atoms as you will see in the link below (with water) and (with Methyl) the map are the same and as well r-factors 3-what can i do to confirm presence or cleavage of methyl: collect more data or using other technique like exafs, Mossbauer spectroscopy could help (with water) http://dl.dropbox.com/u/12001878/Subunit-A.png http://dl.dropbox.com/u/12001878/subunit-A-anomalous.png http://dl.dropbox.com/u/12001878/Subunit-B.png http://dl.dropbox.com/u/12001878/subunit-B-anomalous.png (with methyl) http://dl.dropbox.com/u/12001878/DimethylTin-subunit-A-alt-conf.png http://dl.dropbox.com/u/12001878/DimethylTin-subunit-B.png N.B: resolution 1.7 A r factors and molprop are perfect. thank you for your time haytham biochimi canada

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