- phenixbb - phenix-online.org

obtaining f'/f'' from solved structures and comparison to a fluorescence scan
by Francis E Reyes 20 Apr '11

20 Apr '11

Hi phenixer's I'm in need of reliable f'/f'' for my heavy atom (that isn't Sasaki tables which I believe is for free, unbound atoms). I've used group_anomalous in phenix.refine before so I'm sure a phenix utility is capable of extracting it. I wanted to if it's possible to extract it from several solved structures (I have the DANO/SIGDANO, F(+)/F(-), or if needed the original I(+)/I(-)) I'm curious to see if there's wide variation and whether it'd be as reliable (or even better) than actually taking a fluorescence scan (and of course use the values for my current phasing challenge as a starting point). F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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AutoSol
by Nora Cronin 18 Apr '11

18 Apr '11

Is have 2 difference anomalous datasets with two different heavy atoms. I can input 2 SAD datasets in AutoSol using the Wavelength and Group = keywords. How do I input 2 different crystal_info keywords since this keyword does not accept the Group= option? cheers Nora Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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unusual maps and Rfree for 1.75 structure
by Yuri 17 Apr '11

17 Apr '11

>>you did not mention the resolution... From your email I guess it is 1.9A, is it correct? It is 1.75A. But like I said the maps right now do not look like those of 1.75 resolution. my 1.9 maps looked way better... The P1 strategy is valid. I will also try processing without the screw axis P 4 2 2, or maybe even P 4 21 2. It looks like the other systematic absences are ok (they are pretty weak reflections). -- Yuri Pompeu

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unusual maps and Rfree for 1.75 structure
by Yuri 17 Apr '11

17 Apr '11

I am solving a structure of an enzyme that I have solved many times before, the only difference is a single mutation in the active site. The crystal grew in basically exact conditions (macroscopically speaking they look different) as the other mutants I had. I scaled the data P 43 21 2 Rsym 0.068. Like all the other data sets I had before. This time however, the initial model has Rfree of about 0.27 and the maps look more like those of a 2.5 - 2.8 structure. My experinence with this enzyme is that I should be looking at around 0.22 or lower Rfree, and pretty clear maps as I saw for my 1.9 structure. Xtriage does not detect any pathologies. I rececked my scaling log file, and it lists the systematic absences for the data. I see some that are not that "weak" for instance : h k l I/sigma 0 0 1 6.0 0 0 2 5.8 0 0 13 7.8 So I am inclined to reprocess my data in P 4 2 2. Are these "symptoms" of a possible wrong space group assignment? Is there something else obvious I am overlooking? Thank you -- Yuri Pompeu

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Re: [phenixbb] Autobuild error -- merging results of nearly-finished OMIT and autobuild runs
by Thomas C. Terwilliger 15 Apr '11

15 Apr '11

Dear Nick, I'm sorry for the error ("[Errno 5] Input/output error") that you are getting with your i7-based PC's with Fedora 14. I have not seen this error before, but we can try to debug it with "debug=true" and also I have a work-around for combining the files that you already have created so you don't need to rerun your whole jobs. Can you possibly run this quick test job to try and get it to fail: phenix.autobuild $PHENIX/phenix_regression/wizards/perfect.mtz \ input_labels="FP SIGFP" \ map_file=$PHENIX/phenix_regression/wizards/perfect.mtz \ input_map_labels="FP PHIC FOM" \ seq_file=$PHENIX/phenix_regression/wizards/seq.dat \ resolution=3.0 \ solvent_fraction=.6 \ model=$PHENIX/phenix_regression/wizards/coords.pdb \ rebuild_in_place=True \ n_cycle_rebuild_min=1 \ n_cycle_rebuild_max=1 \ multiple_models=True \ multiple_models_number=1 \ multiple_models_group_number=2 \ highest_resno=200 \ debug=true This takes about 5 minutes. If it fails, can you send me (terwilliger(a)lanl.gov, not the list) the end out the output where it gives a traceback of where the error occurred? Combining files from a nearly-complete autobuild run with rebuild-in-place=true You can combine models with autobuild, providing all models have exactly the same set of atoms (aside from any solvent) by editing this script (basically you run a dummy autobuild run to create a directory and database entries, then you copy your files there, then you run autobuild and tell it to carry on and do the combine step): -------------------------------------------------------- #!/bin/csh -f #COMBINE_MODELS SCRIPT if (-d PDS || -d AutoBuild_run_1_) then echo "Please run in a directory without PDS or AutoBuild_run_1_" exit 1 endif echo "Setting up combine models with a dummy run. NOTE: multiple_models_group_number must be correct" phenix.autobuild fobs.mtz multiple_models=true seq_file=seq.dat combine_only=true multiple_models_group_number=2 multiple_models_number=1>& dummy_autobuild.log echo "Copying files to AutoBuild_run_1_/MULTIPLE_MODELS" mkdir AutoBuild_run_1_/MULTIPLE_MODELS cp coords1.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_1 cp coords2.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_2 cp map_coeffs_1.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_1 cp map_coeffs_2.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_2 ls AutoBuild_run_1_/MULTIPLE_MODELS/ echo "Running autobuild to combine files in AutoBuild_run_1_/MULTIPLE_MODELS" phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 > autobuild_combine.log # END OF COMBINE_MODELS SCRIPT ------------------------------------------------------- Combining OMIT runs that have been run on separate computers or that come from a nearly-completed omit run: You can do this by copying all the individual mtz files with map coefficients for omit regions to a single directory and running a script like this one: (NOTE: you need to ensure that the OMIT regions are defined the same in the runs where you got your overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc files and this run. You ensure that with the n_xyz command that sets the grid. You can copy this from one of your resolve log files created when you ran your omit (i.e., AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/TEMP0/resolve.log will have a line "nu nv nw: 32 32 32 " and you copy those numbers). ------------------------------------ #!/bin/csh -f # COMBINE OMIT SCRIPT phenix.resolve<<EOD hklin exptl_fobs_phases_freeR_flags.mtz labin FP=FP SIGFP=SIGFP n_xyz 32 32 32 # YOU MUST SET THIS BASED ON THE nu nv nw in a resolve log file. solvent_content 0.85 no_build ha_file NONE combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_2 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_3 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_4 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_5 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_6 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_7 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_8 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_9 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_10 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_11 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_12 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_13 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_14 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_15 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_16 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_17 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_18 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_19 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_20 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_21 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_22 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_23 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_24 omit EOD # END OF COMBINE OMIT SCRIPT All the best, Tom T >> Dear Phenix Developers, >> >> I have been experiencing problems with autobuild whenever I try to rebuild >> an MR model or calculate a composite OMIT map. These tasks always end the >> same way: with "[Errno 5] Input/output error". The failure always happens >> when the run is basically finished and trying to combine the output from >> multiple tasks. My first thought was that my hard drive was full or fixing >> to crash, but these problems happen across several machines and have persisted through multiple official and nightly Phenix releases (currently >> running 1.7-634). The computers that cannot run autobuild successfully are >> both core i7-based PCs running Fedora 14 (though these problems also occurred running earlier Fedora versions). My older xeon-based PC runs autobuild without any trouble, which makes me think this a core i7-related >> problem. I have searched the PhenixBB archive and have not turned up any >> similar problems - have any other users experienced trouble with Phenix and core i7? Is there a work-around I ca >> n use to manually combine the various outputs? The core i7 machines are >> so much faster, I would really like to solve this problem so that I can stop relying on my aging xeon PC for these long calculations. I have included the end of two log files for reference. Also, autosol runs fine >> on the core i7 computers and successfully builds wonderful models from my >> SeMet SAD data. Thank you for Phenix and for any advice you can give. >> >> Best wishes, >> Nick Silvaggi >> >> P.S. I apologize if this message appears twice - I sent it once from an address that was not registered with the BB and decided to re-send from a >> registered address. >> >> Autobuild after MR: >> ----------------------------------------------------------------------------------------------------- Standard build in parallel starting with refine.pdb_1 >> This is the first try at building this model >> Try: 1 building 1 model >> Try: 2 building 1 model >> Try: 3 building 1 model >> Running up to 3 jobs in parallel... with total of 3 jobs >> >> Splitting work into 3 jobs and running with 3 processors using sh background=True in >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0 >> >> Starting job 1...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log Starting job 2...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_2.log Starting job 3...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_3.log Collecting all runs now >> *************ERROR ENDING ******************* >> >> ******************************************************************************** Failed to carry out AutoBuild_build_cycle: >> >> [Errno 5] Input/output error >> ******************************************************************************** >> >> *************ERROR ENDING ******************* >> >> >> Calculating SA composite omit map: >> ----------------------------------------------------------------------------------------------------- Starting job 34...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_34.log Starting job 35...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_35.log Starting job 36...Log will be: >> /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_36.log Collecting all runs now >> *************ERROR ENDING ******************* >> >> ******************************************************************************** Failed to carry out AutoBuild_parallel_omit: >> >> [Errno 5] Input/output error >> ******************************************************************************** >> >> *************ERROR ENDING ******************* >> >> Nicholas R Silvaggi, Ph.D. >> University of Wisconsin, Milwaukee >> Department of Chemistry and Biochemistry >> 3210 North Cramer St >> Milwaukee, WI 53211 >> >> Office: Chemistry 272B >> Phone: 414-229-2647 >> silvaggi(a)uwm.edu >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Autobuild error
by Nicholas R Silvaggi 15 Apr '11

15 Apr '11

Dear Phenix Developers, I have been experiencing problems with autobuild whenever I try to rebuild an MR model or calculate a composite OMIT map. These tasks always end the same way: with "[Errno 5] Input/output error". The failure always happens when the run is basically finished and trying to combine the output from multiple tasks. My first thought was that my hard drive was full or fixing to crash, but these problems happen across several machines and have persisted through multiple official and nightly Phenix releases (currently running 1.7-634). The computers that cannot run autobuild successfully are both core i7-based PCs running Fedora 14 (though these problems also occurred running earlier Fedora versions). My older xeon-based PC runs autobuild without any trouble, which makes me think this a core i7-related problem. I have searched the PhenixBB archive and have not turned up any similar problems - have any other users experienced trouble with Phenix and core i7? Is there a work-around I can use to manually combine the various outputs? The core i7 machines are so much faster, I would really like to solve this problem so that I can stop relying on my aging xeon PC for these long calculations. I have included the end of two log files for reference. Also, autosol runs fine on the core i7 computers and successfully builds wonderful models from my SeMet SAD data. Thank you for Phenix and for any advice you can give. Best wishes, Nick Silvaggi P.S. I apologize if this message appears twice - I sent it once from an address that was not registered with the BB and decided to re-send from a registered address. Autobuild after MR: ----------------------------------------------------------------------------------------------------- Standard build in parallel starting with refine.pdb_1 This is the first try at building this model Try: 1 building 1 model Try: 2 building 1 model Try: 3 building 1 model Running up to 3 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running with 3 processors using sh background=True in /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0 Starting job 1...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log Starting job 2...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_2.log Starting job 3...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_3.log Collecting all runs now *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: [Errno 5] Input/output error ******************************************************************************** *************ERROR ENDING ******************* Calculating SA composite omit map: ----------------------------------------------------------------------------------------------------- Starting job 34...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_34.log Starting job 35...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_35.log Starting job 36...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_36.log Collecting all runs now *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_parallel_omit: [Errno 5] Input/output error ******************************************************************************** *************ERROR ENDING ******************* Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211 Office: Chemistry 272B Phone: 414-229-2647 silvaggi(a)uwm.edu

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parallel structure comparison
by Kendall Nettles 14 Apr '11

14 Apr '11

Dear PHENIX developers, In this weeks build, when I launch coot from the structure comparison results, no models or maps are loaded. It works in the last major release. Also, in the major release version the ligands are stripped out. Is this a bug? If not, I would like to request that the ligands be left in the structures. Thanks so much Kendall

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The individual site refinement for Low resolution data (~3.8A)
by Zhang yu 14 Apr '11

14 Apr '11

Dear phenixer, Phenix suggested "Individual site" refinement is only suitable for high or midi resolution data (<3.5A). What is the alternate strategy to refine the atom coordinates of low resolution data? Yu

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occupancy refinement when alternate conformers clash
by Kendall Nettles 13 Apr '11

13 Apr '11

Hi, I am refining an RNA structure where on set of base pairs has alternate conformers, and the B alternates from the paired bases clash. That is, the structure should be viewed as A alternate in one base paired with B alternate in the other base. The refinement blew both B alts out of the density to prevent their clash. How can I fix this? Thanks for your help, Kendall Nettles

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O-linked glycosylation refinement in Phenix
by Qiang Chen 12 Apr '11

12 Apr '11

Dear all, I'm refining a structure which has both N-linked and O-linked glycosylation. I use Phenix to do the refinement. It works well for the N-linked NAG. I defined the link as the following: apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = "chain A and resname NAG and resid 701" residue_selection_2 = "chain A and resname ASN and resid 518" } But it doesn't work when I defined the fucose-threonine link as the similar way: apply_cif_link { data_link = "FUC-THR" residue_selection_1 = "chain A and resname FUC and resid 801" residue_selection_2 = "chain A and resname THR and resid 596" } The error message is "missing CIF link: data_link_FUC-THR". Does anyone have the cif link file of FUC-THR? Thanks a lot! Qiang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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(Anisotropic ADP vs. isotropic ADP) coupling with occupancy refinement
by Young-Jin Cho 12 Apr '11

12 Apr '11

Dear phenix developer and users, I am just wondering while I was taking a small molecule X-ray course. I used to run refinement with anisotropic ADP when it is high resolution about better than 1.5 or 1.6 A. My question is when you do this with occupancy refinement, does phenix.refine take care the alternative conformations with aniostropic ADP (I guess so) even at low occupancy? Due to lack of electrons (scattering factor), I experienced that small molecule refinement applies Anisotropic ADP for the atoms (about more than 2 e- in occupancy) while applying isotropic ADP for the less occupied atoms (in an alternative conformation). Would it help if we apply this method to our macro molecular system when you have residues that have low occupied alternative residues? Is so, could we have something like script or else either to modify a pdb file or to make this in consideration during refinement? Any information or comments are welcome. Thanks in advance, Young-Jin

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help me to install phenix on ubuntu10.4
by 王瑞 11 Apr '11

11 Apr '11

Excuse me,I'm a freshman ,could anyone tell me how to install phenix on ubuntu10.4? I have download phenix-installer-1.7-650- intel-linux-2.6-x86_64-fc12.tar.gz. when I install it in terminal,there was a error notice:"./install:no such file or directory"!Could anyone help me? Many thanks!

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phenix don't start
by albert 10 Apr '11

10 Apr '11

Dear: I installed Phenix-1.7-650 in my SUSE Linux Enterprise 10 SP3 X64 system from source code. When I source /soft/phenix-1.7/phenix-1.7-650/phenix_env and try to run it by typing phenix in terminal, it is said: Traceback (most recent call last): File "/soft/phenix-1.7/phenix-1.7-650/phenix/wxGUI2/command_line/main.py", line 13, in <module> run(sys.argv[1:]) File "/soft/phenix-1.7/phenix-1.7-650/phenix/wxGUI2/command_line/main.py", line 7, in run from wxGUI2 import App File "/soft/phenix-1.7/phenix-1.7-650/phenix/wxGUI2/App.py", line 11, in <module> import wx ImportError: No module named wx The python in my OS is 2.4 with wxpython installed. I don't know why it cannot start. could you please give me some advices? THX

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secondary structure restraints
by Panne Daniel 08 Apr '11

08 Apr '11

I am having problems with the secondary structure restraints in phenix.refine (1.6.4-486). I wrote a ss restraints file and use this as an input file. In the log file I can see that the file is read but the atom selections used by phenix.refine do not correspond to those set in the restraints file. I have turned off automatic ss detection. Any advice? Thanks, Daniel

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difficulties with the refinement of a Cadmium containing pdb file
by Vellieux Frederic 08 Apr '11

08 Apr '11

Hi all, I have some difficulties refining (what happens is an error status, i.e. no refinement taking place) of a coordinate file that contains Cadmium ions. The person here who has already refined a structure containing Cd ions using Phenix is not here at the moment (otherwise I would have asked him). In case you wonder: the CD is shifted 1 position to the left as is required for metal ions in a PDB. Phenix choked. So I ran ReadySet on the input pdb file and gave the output file to Phenix for the next attempt. Still failed, and the error message I get is: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 2 Please edit the PDB file to resolve the problem and/or supply a Cif file with matching restraints definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix_ready_set and phenix.elbow are available for creating restraints definitions (CIF files). Running phenix.elbow (phenix.elbow input_file.pdb --do-all) does not seem to do anything - no output file seems to be generated. Hence I am quite at loss here. Ready Set (from the gui) generated a file called name_of_the_coordinate_file.metal.edits , which is used by phenix for the next attempt but which does not seem to solve the problem. Thanks for any advice, Fred.

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Re: [phenixbb] How to define link in phenix (rna3p) ?
by Ralf W. Grosse-Kunstleve 07 Apr '11

07 Apr '11

> Hi. I came across with the following post when I was dealing with a > similar issue (adding a modified nucleotide to RNA). I could create > .cif using elbow/reel as well, but I was wondering where to define > the link type between residues in phenix. You can use the apply_cif_link parameters. > For RNA, I typically see "rna3p', but with my newly created residue > linked to normal oligo, the link is formed, but recognized as Link ID > 'p'. Also, the newly created molecule is recognized as 'peptide', > although I defined _chem_comp.group in .cif file as RNA. The _chem_comp.group value is ignored by phenix.refine. The classifications are obtained via analysis of the atom names and the bonding in the monomer definitions. >------------------------------------------ >Chain: "Q1" > Number of atoms: 74 > Number of conformers: 1 > Conformer: "" > Number of residues, atoms: 3, 74 > Classifications: {'RNA': 2, 'peptide': 1} > Modifications used: {'5*END': 1, 'rna3p': 2} > Link IDs: {'p': 1, 'rna3p': 1} >------------------------------------------ It is strange that it thinks there is a peptide but still applies two rna/dna links. Could you send me (not the list) the part from the pdb file with the Q1 chain? Ralf

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CUA Ligand issue
by Bradley Hintze 07 Apr '11

07 Apr '11

Hello, I am trying to refine PDB 1YEW using the default phenix settings. $phenix.refine 1yew.pdb 1yew.mtz yields: ''' Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 6 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. ''' $ phenix.ready_set 1YEW_H.pdb yields: ''' Sorry: Atoms in the input are supposed to be bound CU1(CUA) - CU2(CUA) = 2.58 Fix the input file and retry ''' I assume this means that the Cu atoms in CUA are at an inappropriate distance. Is there an easy way to find out what the appropriate distance is? Can I fix this in coot? Thanks, Bradley

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How to define link in phenix (rna3p) ?
by Maehigashi, Tatsuya 07 Apr '11

07 Apr '11

Hi. I came across with the following post when I was dealing with a similar issue (adding a modified nucleotide to RNA). I could create .cif using elbow/reel as well, but I was wondering where to define the link type between residues in phenix. For RNA, I typically see "rna3p', but with my newly created residue linked to normal oligo, the link is formed, but recognized as Link ID 'p'. Also, the newly created molecule is recognized as 'peptide', although I defined _chem_comp.group in .cif file as RNA. ------------------------------------------ Chain: "Q1" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Classifications: {'RNA': 2, 'peptide': 1} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'p': 1, 'rna3p': 1} ------------------------------------------ Any input will be appreciated. Sincerely, "T" On Wed, Nov 17, 2010 at 7:43 AM, Gerwald Jogl <Gerwald_Jogl at brown.edu<http://phenix-online.org/mailman/listinfo/phenixbb>> wrote: > Hi All, > > I am refining several modified nucleotides in ribosomal RNA > (N2-methyl-guanosine and similar). While the restraints generation with > phenix.reel work quite well, I am unable to get the phosphate oxygen > restraints applied properly. Phenix.refine recognizes the links but for some > reason the phosphate groups come out quite distorted... > > For example, angles after refinement: > O3 (1) - P (2, modified) - OP2 (2) = 80 deg and > O3 (1) - P (2, modified) - OP1 (2) = 127 deg > > > Here is part of the phenix.refine log on reading the coordinates: > > Chain: "A" > Number of atoms: 32526 > Number of conformers: 1 > Conformer: "" > Number of residues, atoms: 1513, 32526 > Unusual residues: {'MA6%rna3p': 2, '5MC%rna3p': 3, '5MC%rna2p': 1, > '7M > G%rna3p': 1, '2MG%rna3p': 1, 'UR3%rna2p': 1, 'M2G%rna3p': 1, '4OC%rna3p': 1} > Classifications: {'undetermined': 11, 'RNA': 1502} > Modifications used: {'5*END': 1, 'rna3p': 1318, 'rna2p': 195} > Link IDs: {'rna3p': 1318, 'rna2p': 194} > Chain breaks: 1 > > I am at a loss about how to fix this as all links and restraints seem to be > in place. > > Many thanks for advice, > Gerwald ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Re: [phenixbb] B-factors vs resolution
by miket＠chem.ucla.edu 07 Apr '11

07 Apr '11

Usually one will describe ordered parts of a protein vs disordered parts based on B factors. Is the higher resolution protein more ordered and that may have contributed to its stronger diffraction? -- Are the two crystals with different max resolution isomorphous? B-factors contain contributions from both dynamic and static disorder. Your difference in b-factors and resolution are both likely due to the fact that your higher-resolution data comes from a more ordered crystal, not a less dynamic protein. More ordered crystals diffract better, but if the two crystals were grown in the same conditions and the crystals are isomorphous I doubt that there is any difference in the dynamics of the molecules. If you are interested in which parts of your protein are more dynamically disordered you may want to consider (within a single dataset) which atoms have high b-factors relative to the average b-factor for all the atoms in that dataset. Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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tools to obtain ADP?
by Jason 07 Apr '11

07 Apr '11

Hi, Is there a convenient tool to obtain ADP for each chain or ligand or a selective group? phenix.model_vs_data only gives an averaged ADP for everything and it takes really long. Thanks. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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Question about anisotropic refinement
by Louis Lazar 06 Apr '11

06 Apr '11

I have several structures that I am refining (~1.05A), and I have a question about anisotropic refinement. I have read a couple things about whether or not to refine waters anisotropically, as opposed to hydrogen, which I never refine anisotropoically. I am wondering what the general consensus is on it, and if anyone has anything from the archives (I'm having trouble searching through) or papers that I should read, please don't hesitate to let me see them. Thanks very much in advance Regards, Louis

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Ligand conformations.
by Yuri 06 Apr '11

06 Apr '11

Has anyone ever reported seeing 2 different binding confromations for a ligand that was soaked vs. the same ligand co-crystallized? -- Yuri Pompeu

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How to fix c-beta deviation?
by Jason 06 Apr '11

06 Apr '11

Hi, I have tried to regularize my protein structure in coot and use ramachandran restrain to improve statistics (and then release them). However, I can not make the c-beta deviation be zero. Is there some special way to improve c-beta deviation? Thanks. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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B-factors vs resolution
by Yuri 06 Apr '11

06 Apr '11

I am refining a 1.3 A structure the maps look great and I notice the main chain B factors are all around 7~12. I have refined the same enzyme at resolution 2.2 A and the B factors here were around 25~30. The question that comes to mind is: Usually one will describe ordered parts of a protein vs disordered parts based on B factors. Is the higher resolution protein more ordered and that may have contributed to its stronger diffraction? Or are the B factors values artifacts of refinement? -- Yuri Pompeu

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why are my B factors being "refined"
by Scott Classen 06 Apr '11

06 Apr '11

Hello Phenix community, I'm currently using nightly build 718, but this behavior is exhibited since sometime in the 1.6.xx releases too. I've turned off ADP refinement (only doing rigid_body refinement) and set the b_iso specifically as such: modify_start_model { selection = None adp { atom_selection = None randomize = None set_b_iso = 55 convert_to_isotropic = None convert_to_anisotropic = None shift_b_iso = None scale_adp = None } Yet the output PDB file has all b-factors in the 100s. Whazzup with that? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 sibyls.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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