February 2013 - 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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install on ubuntu 12.04?
by Alastair Fyfe 19 Mar '13

19 Mar '13

Hi, I've installed previous phenix builds on ubuntu without problem, but with both 1.8.1-1168 and dev-1269 installers on 12.04, the command "./install --prefix=/home/afyfe" ends with "Error configuring: see /home/afyfe/phenix-installer-dev-1269/build-binary/intel-linux-2.6/svr/log/binary.log for details" and the tail of the binary.log file suggests: -- Creating files in build directory: "/home/afyfe/phenix-dev-1269/build/intel-linux-2.6" dispatcher_include_template.sh dispatcher_head.sh Please re-configure from scratch your cctbx_build:cd cctbx_build; /your/path/to/python ../cctbx_project/libtbx/configure.py [options] [modules] --- I don't see a cctbx_build directory under either the installer or destination directories. Any clues/suggestions? many thanks, Alastair

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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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Unusually low B factors with phenix 1.8, but not with phenix 1.7 (data set has ice rings)
by Oliv Eidam 04 Mar '13

04 Mar '13

Hi, I would like to continue the B-factor discussion started by Demetres D. Leonidas on Nov 2, 2012 on CCP4BB: http://www.mail-archive.com/[email protected]/msg29012.html I make the same observations like Demetres and Mingzhu Wang: unusually low B-factors when refining with Phenix 1.8-1069 and 1.8.1-1168, but not with Phenix 1.7.1-743. In numbers: the average B-factor is 10 A2 but it should be 20 A2 (based on Wilson B and similar structures). A few atoms (~20) have Bf = 0.00. The following is important: I refined dozens of similar structures without that problem and I observe this phenomenon only for a single data set. That specific data set is different because 1) I excluded regions with ice rings in XDS and 2) I limited the resolution to 2.28 Angstroem, although the crystal diffracted to ~1.8 Angstroem. While the preparation of the data set might be questionable in itself, I would prefer that this would not be the topic of this thread. My questions are: What can I do to refine my structure with Phenix 1.8.X using this truncated data set? What causes the difference in average B-factor values between Phenix 1.7 and 1.8 for this data set? Your advice is much appreciated. Oliv On 11/04/12 19:21, mingzhu wang wrote: > Pavel, > > 1.8.1-1168 also has this problem. > > I found this problem existed with some dataset, but not all dataset. > > 1.8.1 give better map, so I built model with 1.8.1 map and go back to > 1.7.3 before I deposit the structure to PDB. > > When I compared the B factor from 1.8.x and 1.7.3, I found > B(1.7.3)=B(1.8.x)+Boverall(1.8.x). Perhaps this is the problem. > > > > 2012/11/3, Pavel Afonine<pafonine(a)gmail.com>: >> Joao, >> >> I am using the latest version of phenix 1.8.1-1168 >> >> >> 1.8.1-1168 should not have that "problem". >> >> If you suspect there is still a problem, you can send me the data and model >> files off list, explain what exactly the problem is, and I will have a look >> right away. >> >> FYI: there is Phenix mailing list for Phenix-specific questions, where I >> can also explain in great details the behavior with the B-factors you >> observe. >> >> All the best, >> Pavel >> -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email:[email protected]

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mr_rosetta fails after autobuild stage
by Huw Jenkins 01 Mar '13

01 Mar '13

Hi, I've been having some problems with mr_rosetta. All the regression tests run fine but when I run it on some real data it gets as far as the autobuilding stage and then fails with an error message. All I can find in the log files GROUP_OF_AUTOBUILD_1/RUN_FILE_1.log GROUP_OF_AUTOBUILD_1/RUN_FILE_2.log is ******************* ERROR ENDING *************** Failed to carry out autobuild ******************* ERROR ENDING *************** The autobuild jobs themselves seem to finish fine i.e the end of the log files in GROUP_OF_AUTOBUILD_1/RUN_1/AutoBuild_run_1_ and GROUP_OF_AUTOBUILD_1/RUN_2/AutoBuild_run_1_ has the tables of Rfactors per cycle and the list of citations with no indiction of any error. Is there anywhere else I should be looking for a more detailed error message? Thanks, Huw

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real_space_correlation
by Jianghai Zhu 28 Feb '13

28 Feb '13

Hi All, I was trying to use "phenix.real_space_correlation *.pdb resolve_composite_map.mtz" to get some real space cc for my ligand against the SA composite omit map. But I am not sure that the map used here was the SA composite omit map. Will phenix use the omit map I provided or will it just simply calculate a sigmaA weighted 2Fo-Fc map based on the pdb? Thanks. --Jianghai

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mr_rosetta: two proteins, one chain placed, build second chain
by Tobias Beck 28 Feb '13

28 Feb '13

Dear phenixbb, I would like to use mr_rosetta to build a second protein chain. For the first protein, I have a search model with known structure. The search model can be placed with Phaser (TFZ 10). For the second protein, the structure of a homologue has been determined. The second protein accounts for about 2/3 of the residues in the ASU. I would like to fix the first protein chain and build the second protein chain with mr_rosetta. I have obtained fragment files for both proteins from robetta. What input parameters are required to tell mr_rosetta to build the second chain only? I have tried the fixed_ensemble_ID_list = ensemble1 option. Here is an excerpt of my parameter file with the input files: run a) search_models = "path/chainA.pdb" (from Phaser) search_models = "path/chainB.pdb" (homologue structure) fixed_ensembles { fixed_ensembleID_list = ensemble1 fixed_euler_list = 0.0 0.0 0.0 fixed_frac_list = 0.0 0.0 0.0 fixed_frac_list_is_fractional = True } alignment_files = "path/chainA.dat" alignment_files = "path/chainB.dat" with chainA.dat having twice the same sequence and chainB.dat with the target and template alignment. I have set fragment files with chain_list for both chains. I get this error when running phenix.mr_rosetta (running from command line with .eff file) "Sorry, the file /path/GROUP_OF_PLACE_MODEL_1/RUN_2/chainB_al_0.pdb representing group 0 has no atoms? This could indicate a problem with sequence alignment in rebuilding. It could be that there are near-duplicate sequences in your sequence file ...if this is the case then you may need to artificially rename your duplicated chains and renumber residues to make a single chain containing a duplication" This error also occurs run b) Without any alignment files run c) Without any alignment files and with just chainA.pdb as search model. An alignment of the sequences from chainA and chainB gives low identity (no duplicate regions), so I suspect the problem is located somewhere else? I have seen a post by Tom Terwilliger, explaining how to deal with two identical chains with different conformations where no alignment files are required. However, I would like to use the information from the homologue structure, that is why I specified the alignment file. By inputting chainB.pdb as search model, mr_rosetta also tries to use this model as a search model for molecular replacement, but I think this is not necessary (and gives a warning that the space group of the search model and the data file do not match). I just want to provide the structural information from structure chainB.pdb to mr_rosetta for building. ----- So in summary this is what I would like to do: chain A: keep fixed - use chainA.pdb as fixed model chain B: build - use information from homologue structure (chainB.pdb) and fragment files to build chain What is the best strategy to do this? What input parameters are required so that I do not get the error described above? ----- Thanks a lot in advance, Tobias.

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phaser output and packing
by Ursula Schulze-Gahmen 26 Feb '13

26 Feb '13

Could somebody explain to me how phaser decides if there is a solution. When I look at the log file there are a few solutions in the translation function that have fewer than the allowed clashes, but they are still not recognized as potential solutions. Why is that. Is there another parameter that I should be looking at? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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WCPCW 21
by Williams, John Charles 22 Feb '13

22 Feb '13

All, We will be finalizing the program for the workshop on Monday, Feb 25th. The Monterey Plaza and Spa has confirmed that we can accommodate a few more people. So, if you are interested in attending and would like to be considered for an oral presentation or would like to present a poster, please register and submit an abstract no later than Monday, 12 noon (PST). The meeting will be March 17th-20th with Wayne Hendrickson as the Keystone speaker! Best, John wcpcw.org --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) ---------------------------------------------------------------------

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