January 2015 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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Refinement with new mtz.file
by Aleksandar Bijelic 14 Jul '15

14 Jul '15

Dear CCP4 user and experts, I refined (with PHENIX) a 3.0 A dataset obtaining Rfree of about 0.24 (with good geometry according to Ramachandran, Beta Outliers, etc.) .... Everything seems to be ok (especially in relation to the resolution) .... because the mtz.file I used was quite old and I cannot find my xscale.hkl file, I processed the data set again (this time with optimizng and polishing) and received a "better" file according to almost everything (resolution limit, I/sigma, CC(1/2), Rmeas), thus I used this new mtz.file and put it in my last refinement step (the refinement which led to the above mentioned Rfree = 0.24). Suprisingly, the refinement starts at Rwork = 0.18 and Rfree = 0.19 but ending up with 0.20 and 0.22, respectively. So I wanted to know if this is usual? I was expecting my data to become slightlly better but what is irritating me is the starting R-values of the refinement and that it get worse during refinement. Maybe I did something wrong? Is it reasonable to replace the mtz.file with a new one in the last refinement step or should I start the refinement from the scratch? In the sake of completeness, I deleted the header of the used pdb.file because of the R-flag error which occurs, since Phenix reconizes that the pdb.file was already used with other Rflags. Sorry, but I am still a beginner in this field, so I would be very grateful if somebody could explain me this situation and my mistake and if I need to start refinement from the beginning. Thank you in advance! Best Regards. Aleksandar -- ------------------------------------------- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 A-1090 Wien Tel: +43 1 4277 52536 e-Mail: aleksandar.bijelic(a)univie.ac.at --------------------------------------------

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idealizing structure
by PC 27 Apr '15

27 Apr '15

Is there a way to "idealize" a structure in Phenix? I mean, ideal omega, all residues within allowed regions of Ramachandran maps, no clashes..etc. I know it won't fit the map well but I would like to see what it looks like. Thank you. ____________________________________________________________ FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop! Check it out at http://www.inbox.com/marineaquarium

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Question related to Phenix refinement
by Smith Lee 15 Feb '15

15 Feb '15

Dear All. In the Phenix refine "run status" window, with the progression of the refinement, it occurs 3' bss, 3' rsrl, 3' xyz, 3' adp (for 3rd round of refinement). I guess xyz means the strategy is for x, y, z coordinates? Then what do bss, rsrl and adp mean? I am looking forward to getting your reply. Smith

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Question related to Phenix refinement
by Smith Lee 02 Feb '15

02 Feb '15

Dear All, Which strategy or parameter input can be used to reduce the rotamer outliers? Which strategy or parameter input can be used to reduce the bond outliers? For all the Phenix refine strategies, can you sequence it from rough refinement to fine refinement in order? I am looking forward to getting your reply. Smith

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Rwork and Rfree
by Dialing Pretty 31 Jan '15

31 Jan '15

Dear All, After a Phenix refinement (for crystal 2.5A), my Rwork is about 0.19, and my Rfree is about 0.26. Is the gap between Rwork and Rfree too karge? If too large, why it is too large and how to avoid it? I am looking forward to getting your reply. Dialing

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Re: [phenixbb] making coarse maps
by Terwilliger, Thomas Charles 30 Jan '15

30 Jan '15

Hi Scott, You can use the reflection file converter in the GUI to write out map coefficients with any resolution cutoff that you like. That may be the easiest. Alternatively you can take your refined model and use phenix.maps to calculate a map at any resolution that you like without further refinement. You might also consider just adjusting the sharpening on your map which will have something of the same effect as cutting the resolution. All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Scott Horowitz [horowsah(a)umich.edu] Sent: Friday, January 30, 2015 6:09 AM To: PHENIX user mailing list Subject: [phenixbb] making course maps Hi all, Although I realize this sounds counterproductive, I'd really like to be able to make a map with grid spacing that is around 3 A, even though I have a ~2 A structure, and I don't want to have to cut data before refinement. However, it seems like the max number I can give to the grid resolution factor is 0.5. Is there a way to break this limit without it crashing? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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making course maps
by Scott Horowitz 30 Jan '15

30 Jan '15

Hi all, Although I realize this sounds counterproductive, I'd really like to be able to make a map with grid spacing that is around 3 A, even though I have a ~2 A structure, and I don't want to have to cut data before refinement. However, it seems like the max number I can give to the grid resolution factor is 0.5. Is there a way to break this limit without it crashing? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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calculating map from pdb
by Scott Horowitz 29 Jan '15

29 Jan '15

Hi all, I was wondering how to quickly back-compute an electron density map from a PDB using phenix from the command line. I'm assuming it's not hard, but I can't find documentation that would lead me to it. Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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question about mmtbx.prepare_pdb_deposition
by Gerwald Jogl 28 Jan '15

28 Jan '15

Hi, How does the sequence file for this tool have to be formatted when there are more than one proteins/sequences in the asu? Does the program match this automatically? Thanks, Gerwald

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