July 2011 - phenixbb - phenix-online.org

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 15 Jul '11

15 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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Parsing error
by Yuri 14 Jul '11

14 Jul '11

Nat, Thank you. I am still using dev-814. You probably have fixed it already. ill update when I am done running these jobs. -- Yuri Pompeu

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Parsing error
by Yuri 14 Jul '11

14 Jul '11

Hello everyone, I cannot figure out why I keep getting this error. I dont see anything wrong with my PDB. I realize I realize I have breaks in my chain, as there are regions of unclear density as of now I am building in what I can see... Heres what the log says: ======== ================= Separating polymer chains into rigid bodies ================= (chain 'A' and segid ' ' and resseq 393:6) (chain 'B' and segid 'B ' and resseq 401:401) ================== Extract refinement strategy and selections ================= The error is initial RESSEQ index > final RESSEQ index. I do not understand why it is picking them this way It then halts at an error... Any Ideas?

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restraints_edite.params
by Haytham Wahba 13 Jul '11

13 Jul '11

Dear All How to get rid of restraints_edite.params in the following run of phenix.refine, i mean after using it in previous run.and what is .def files. and bond.slack Haytham Udem Biochemi Canada

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R-merge and MOLREP
by Yuri 13 Jul '11

13 Jul '11

Ed and Nathaniel, Thank you for the input. I agree with Ed. The I/sigma values for this data set are well within accepted ranges... I believe the R-merge values are due to some inherent crystal property. They grew in very strange manner. -- Yuri Pompeu

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R-merge and MOLREP
by Yuri 13 Jul '11

13 Jul '11

Hello everyone, I just collected some data on a new protein. It indexes in P3 and looks like I can scale it all the way to P 63 2 2 . My questions are: 1-I see a reasonable chi-square value 1.69 but r-merge 0.15 (0.49 at 2.75 A). It was 0.20 before I excluded some bad frames. I thought this R value is a bit high... Is it? Mosaicty was around 1.00. 2- My search model has an identity of around 40%. I tried MOLREP. Seems I got a solution LLG=486 PAK=10 TFZ ~30 RFZ ~20. My R-free before any refinement is 0.54. Two questions here, a) I think I only fully understand the meaning of LLG, what about PAK and both Z-values? b)is this R-free acceptable or is it also a little high? Thank you for any input

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