July 2012 - 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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links in phenix summary
by Christian Roth 04 Apr '13

04 Apr '13

Dear all, thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions. I have summarised a few things which one might consider if nonstandard links are necessary. Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script: elbow.ligand_linking model.pdb Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary. Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement. For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using iotbx.show_distances your.pdb > all_distances Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix! Christian

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Memory and CPU usage
by Jon Agirre 05 Mar '13

05 Mar '13

Dear community, I'm planning on buying a new macbook for my first abroad postdoc venture, and I'm currently trying decide what amount of RAM & CPU to choose. My question is a little bit intricate: is there any rule of thumb to estimate the needed RAM versus the number of input atoms for any particular refinement type? I'm planning on tackling some big (18,000 residues/asu) refinements but I don't have any estimation as to how many GBs of RAM they might require. The maximum amount of RAM I can install is 16GB, but it is a non-standard configuration that might void Apple's warranty. About the CPU: how scalable are typical phenix processes? Would it be sensible to invest in a quad-core machine with HT? In this particular case, and since HT would present 8 logical cores, would I get any speed up from launching phenix tasks configured for 8 processors instead of 4? Thanks in advance! Jon

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July 2012 Computational Crystallography Newsletter
by Nigel Moriarty 31 Jul '12

31 Jul '12

Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles ----------- cctbx tools for transparent job execution on clusters On the analysis of residual density distributions on an absolute scale Short communications -------------------------------- DETAC: tools to detect alternative conformations by unrestrained refinement ERRASER, a powerful new system for correcting RNA models Fitting tips - Rotamer correction with backrub -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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what installer would work with a cluster with Darwin 9.8.0 if any?
by Tatyana Sysoeva 27 Jul '12

27 Jul '12

Hi all, I am starting to use a new computer cluster and just found out by uname that it runs Darwin OS? It is totally new to me and I am wondering if Phenix would run on it? should I use just some Mac installer? I would really appreciate any advices! Thank you! Sincerely, Tanya

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Re: [phenixbb] what installer would work with a cluster with Darwin 9.8.0 if any?
by Tatyana Sysoeva 27 Jul '12

27 Jul '12

Thank you Miguel and Ben! I did found the newest release at the cluster after I learned how to use "find" properly! In particular, thank you for pointing out the script to source! Best regards, Tanya

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refinement problem
by Afshan Begum 27 Jul '12

27 Jul '12

Dear Experts I am refining my structures in windows mode and every time i got this crash message i do not know how to solve this issue? If any one encountered this problem kindly suggest me how to solve it. While when i refine with refmac the file proceeds smoothly but i want to refinement in phenix due to utilize some parameters. its end like this: Exporting results ============================== Writing refined structure to PDB file: C:\Documents and Settings\pc user\Desktop\Refine_2\jbu_refine_2.pdb n_use = 7514 n_use_u_both = 7514 n_use_u_iso = 0 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 331 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 7514 After that its not produce the map file and gave errore crash mesage. <module> Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Your suggestion highly obliged I would be very thankful to you AFSHAN

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need help
by Afshan Begum 25 Jul '12

25 Jul '12

Dear Experts I am refining my structures in windows mode and every time i got this crash message i do not know how to solve this issue? If any one encountered this problem kindly suggest me how to solve it. While when i refine with refmac the file proceeds smoothly but i want to final refinement in phenix due to utilize some parameters.its end like this: Exporting results ============================== Writing refined structure to PDB file: C:\Documents and Settings\pc user\Desktop\Refine_2\jbu_refine_2.pdb n_use = 7514 n_use_u_both = 7514 n_use_u_iso = 0 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 331 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 7514 After that its not produce the map file and gave errore crash mesage file attached. Your suggestion highly obliged I would be very thankful to you Best Regards AFSHAN

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problem on phenix refine 2
by herohonan 21 Jul '12

21 Jul '12

Hi all: I do not know if someone mentioned this problem here before. Recently I ran the AutoBuild to build the structure model, and it outputs a best model(R/Rfree 0.20/0.24). After that, I tried the program Phenix Refine using the .pdb and .mtz generated by AutoBuild. The R value increased to 0.23/0.30 by the end of this refine. I wonder why this happened? Or if I have done something wrong? (After AutoBuild, I modified the structure and added the substrate moleculars into the structure by hand. I thought the increase of the R value was resulted from the inapposite position of the substrates. But the R value still increased when I ran the Phenix Refine just by inputting the output of the AutoBuild without any manual modification.) -- Tong Huo Ph.D candidate College of Life Sciences Nankai University Tianjin, China

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problem on phenix refine
by 霍彤 20 Jul '12

20 Jul '12

Hi all: I do not know if someone mentioned this problem here before. Recently I ran the AutoBuild to build the structure model, and it outputs a best model(R/Rfree 0.20/0.24). After that, I tried the program Phenix Refine using the .pdb and .mtz generated by AutoBuild. The R value increased to 0.23/0.30 by the end of this refine. I wonder why this happened? Or if I have done something wrong? --

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