- phenixbb - phenix-online.org

Can I limit the model's B factor range during refinement
by junfeng liu 18 Jun '09

18 Jun '09

Dear all, Several models have been refined using Phenix recently. It works well . But the model's B factors in some region are very high, higher than 150 or more. Of course, the wilson B is high too, about 60-70. I remembered that the B factor can be limited in the refinement using Refmac. Can I do the similar thing in Phenix ? Thanks in advance! Best wishes, leo

3 2

Molecular replacement
by Colin Levy 17 Jun '09

17 Jun '09

Within Phenix, is it possible to specify and lock the centre of rotation for a molecular replacement search. I have a single intrinsic anomalous scatterer within my protein which I can locate easily, therefore I would like to manually specify this point as the centre of rotation and then carry out a rotation search only about this single fixed point. Thanks for any suggestions, Colin

2 1

Re: [phenixbb] Adding H atoms onto ligand
by Young-Jin Cho 17 Jun '09

17 Jun '09

Thanks a lot Nigel, I could generate new .cif file. Then I need to combine this ligand information while I am adding H atoms to model.pdb (protein+ligand). when I simply type "phenix.ready_set model.pdb" it will wrongly generate strange.pdb file. My question is how I can add this new geometry information (.cif file) while adding H atoms into modle.pdb file to make protein and ligand has H atoms in correct way. Thanks again in advace. YoungJin ----- Original Message ----- From: "Nigel W Moriarty" <NWMoriarty(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Tuesday, June 16, 2009 12:18:50 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Adding H atoms onto ligand YoungJin If you opened the CIF in REEL you can right-click on the P-N bond and change the order to single. You can then use the menu Action -> Build -> Add Atom to add a hydrogen to the nitrogen by clicking on the nitrogen. Nigel On 6/16/09 9:03 AM, Young-Jin Cho wrote: Thanks Nigel, I opened ANP and truncated the terminal PO3 and ran phenix.ready_set. When I opened through phenix.reel, N atom has double bond to PB, thus has only one H atom, which I thought it should be single bond thus has two H atoms like any N6 of adenine. So if you can tell me how I can handle to put correct geometry, it will be great. Cheers, YoungJin ----- Original Message ----- From: "Nigel W Moriarty" <NWMoriarty(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Tuesday, June 16, 2009 11:21:18 AM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Adding H atoms onto ligand Young-Jin You need to check that you and the PDB ligand database are talking about the same thing. You can see what the ligand ANP is by phenix.reel --chemical-components=ANP If you have the non-hydrogen atoms of your truncated ligand, phenix.ready_set will add the hydrogens and may even add the correct number of hydrogens to the terminal nitrogen. But what about its name? I would recommend find the three-letter code that corresponds to your ligand. Nigel On 6/15/09 7:01 PM, Young-Jin Cho wrote: Let me excuse to post another similar issue. I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb. As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's. I did Molprobity as in the general case to add H atoms, but it didn't make it. Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below: Processing inputs. This may take a minute or two. Sorry: Ambiguous parameter definition: remove = element H Best matches: refinement.refine.occupancies.remove_selection refinement.geometry_restraints.remove.angles refinement.geometry_restraints.remove.dihedrals refinement.geometry_restraints.remove.chiralities refinement.geometry_restraints.remove.planarities Thanks in advance, YoungJin ps. Tanks Nat! _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

2 1

Adding H atoms onto ligand
by Young-Jin Cho 17 Jun '09

17 Jun '09

Let me excuse to post another similar issue. I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb. As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's. I did Molprobity as in the general case to add H atoms, but it didn't make it. Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below: Processing inputs. This may take a minute or two. Sorry: Ambiguous parameter definition: remove = element H Best matches: refinement.refine.occupancies.remove_selection refinement.geometry_restraints.remove.angles refinement.geometry_restraints.remove.dihedrals refinement.geometry_restraints.remove.chiralities refinement.geometry_restraints.remove.planarities Thanks in advance, YoungJin ps. Tanks Nat!

3 4

specification of column labels in command line promt
by Raja Dey 16 Jun '09

16 Jun '09

Dear Friend, I was trying to analyse one of my data set. I am getting the following error. Multiple equally suitable arrays of observed xray data found. Possible choices: Cam-pk-hr_scala1.mtz:IMEAN_pk,SIGIMEAN_pk Cam-pk-hr_scala1.mtz:I_pk(+),SIGI_pk(+),I_pk(-),SIGI_pk(-),merged Please use scaling.input.xray_data.obs_labels to specify an unambiguous substring of the target label. Sorry: Multiple equally suitable arrays of observed xray data found. I have the following column labels in my .mtz file * Column Labels : H K L FreeR_flag F_pk SIGF_pk F_pk(+) SIGF_pk(+) F_pk(-) SIGF_pk(-) DANO_pk SIGDANO_pk IMEAN_pk SIGIMEAN_pk I_pk(+) SIGI_pk(+) I_pk(-) SIGI_pk(-) How I can specify column labels in a command line promt? Say, I want to use IMEAN_pk & SIGIMEAN_pk Thanks... Raja

2 2

phenix and PAE kernels
by nick＠silvaggi.com 15 Jun '09

15 Jun '09

Dear List, Sorry if this is a naive question, but is there a known bug with phenix (or python?) on PAE kernels? I have looked on phenix-online.org, but did not find anything. This problem is independent of the phenix version (I have tried 1.4-92, 1.4-3, 1.3, and several releases of cci_apps) and occurs with almost all of the programs (most fail in the cci_apps test_apps script). The problem appears to be specific to the PAE kernels, since the same programs run fine in the non-PAE counterparts. I am running Fedora 10 with kernel versions 2.6.27.24-170.2.68/PAE and 2.6.27.21-170.2.56/PAE. Phenix programs fail under both PAE kernels, but are fine under the non-PAE kernels. Thanks in advance for any help you can provide. Best regards, Nick Silvaggi long int too large to convert Traceback (most recent call last): File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/builder.py", line 10, in <module> from elbow.chemistry.any_chemical_format_reader \ File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/chemistry/any_chemical_format_reader.py", line 3, in <module> File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/chemistry/SimpleMoleculeClass.py", line 16, in <module> File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/utilities/monomer_utilities.py", line 2, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 4, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 3, in <module> File "/usr/swr/cci_apps/cci_apps_sources/mmtbx/mmtbx/refinement/print_statistics.py", line 2, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 1, in <module> # packaging File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 518, in <module> File "/usr/swr/cci_apps/cci_apps_sources/boost_adaptbx/boost/python.py", line 68, in __init__ OverflowError: long int too large to convert

4 5

phenix refine
by sbiswas2＠ncsu.edu 12 Jun '09

12 Jun '09

Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J " ... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42 Does anyone know how to resolve this thanks, Shya

5 8

phasine error
by vennila Natesan 12 Jun '09

12 Jun '09

Dear members I am having solved strcutures for some five datasets of the same protein. All the cases autobuild builds ~97% of residues. I want to compare the phasing among those. Can we calculate the phasing error in the units of degrees in autosol? In all the cases, the Bayesian CC is between 45 and 56 and FOM is between 0.42 and 0.47.Is there any option in phenix to know the phasing error in degrees?

3 3

not enough memory error in Resolve/AutobuildWizard
by Tatyana Sysoeva 11 Jun '09

11 Jun '09

Hello! I'm trying to run AutobuildWizard on distant computer cluster. Runs failed. In Autobuild log file there is a message: *TRIED resolve_giant ...NEED A BIGGER VERSION... TRIED resolve ...NEED A BIGGER VERSION... TRIED resolve_giant ...NEED A BIGGER VERSION... TRIED resolve_huge ...NEED A BIGGER VERSION... child process stderr output: command: 'AutoBuild_run_1_/TEMP0/temporary.com' Sorry, not enough memory for RESOLVE ---------------------------------- TRIED resolve_extra_huge ...but not OK ******************************************************************************** Failed to carry out AutoBuild_set_up_build: ******************************************************************************** * Some Autobuild runs were ok, some stopped with that error message. What am I doing wrong? I installed Phenix1.4-3, locally to my home folder, run it from script file in queue. As I found this Linux computer cluster has next parameters - 1 login node: -Sun SunFire v20z 1U Rackmount Box -Dual 2.4 GHz AMD Opteron Processors -8 GB of ECC RAM Could you advise something to start with to find a problem? Sincerely, Tanya

8 11

Water/residue alternative conformations
by Roeland Boer 09 Jun '09

09 Jun '09

Dear all, I'm refining a 1.45 Ang structure in which I have several residues that have alternate conformations. These alternate conformations in some cases coincide with additional density that suggests the presence of a water molecule, appropriately positioned to make hydrogen bonds with near atoms. I have modeled partially occupied waters in these additional densities and linked their occupancies with the alternate conformation that is not clashing with the water in question. My problem is that these partially occupied waters are pushed away by the 'overlapping' alternate conformation of the amino acids. I guess there's an antibump restraint somewhere? How can I tell phenix that these alternate waters are not sterically clashing with the amino acid (since the sum occupancies of the water plus alternate conformation is 1)? The attached image shows one of those disordered residues after refinement. Water 1519 is pushed away from one alt conf (A) of Gln13, whereas the density suggests it should be making a hydrogen bond to OE1 of the altconf B of Gln13. I describe the occupancies of the situation in the attached image as below. refinement { refine { occupancies { constrained_group { selection = chain A and resseq 13 and altloc A selection = (chain A and resseq 13 and altloc B) or (resname HOH and resseq 1519 and altloc A) } } } } Thanks, Roeland Boer.

3 5

Re: [phenixbb] autosol error 1.4-3 when trying to specify deriv.inano=noinano
by Thomas C. Terwilliger 07 Jun '09

07 Jun '09

Hi Francis, Thanks again for the files. They did help me debug the autosol wizard for this case. It turns out that on the command line you cannot say something like, native.data=nat.mtz native.labels="I SIGI" \ deriv.data=deriv.mtz deriv.labels="I+ SIGI+ I- SIGI-" deriv.inano=inano because only the first native.something= gets read, the others are ignored, and similarly only the first deriv.something= gets read. instead all this has to go in a parameters file, and then it all works fine. I have adjusted the wizard to catch this situation and to stop and tell the user that they need to use a parameters file to set more than one parameter in the native, deriv, or wavelength scopes. All the best, Tom T

1 0

coordinates and map shifted after phenix.refine without simulated annealing
by hari jayaram 07 Jun '09

07 Jun '09

Hi i am using phenix version 1.4 release tag 70 hari@charlie:~$ phenix.refine --version ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.4 Release tag: 70 Platform: intel-linux-2.6-x86_64 linux User: hari ------------------------------------------------------------------------------- I am seeing a strange shifting of my coordinates "out of my experimental phases map" before and after refinement without simulated annelaing I am at the final stages of my refinement. When I refine without simulated annealing the resulting model is shifted relative to my experimental phases map into which I build my model The phenix command line strategy i am using are rigid_body+individual_sites+individual_adp+tls .or the same strategy with simulated_annealing=true The output map coefficients fortunately match my model in both cases . But I am wondering why there is a difference. I am using the mlhl target for refinement to 3.1 A , My R and rfree is 28/31 . Any ideas why my model shifts without simulated annealing . All pdbs have the same CRYST record . I am using coot version 0.61 for my building and map display using fft inside of coot . hari

2 1

Re: [phenixbb] coordinates and map shifted after phenix.refine without simulated annealing
by Thomas C. Terwilliger 06 Jun '09

06 Jun '09

Hi Hari, What is your space group? I am guessing that the shift is along an axis where the origin is not fixed, for example the b axis in P21. This could happen with rigid-body refinement where a molecule can move as a whole so that the center of mass could move along that axis. Perhaps someone else can comment as to whether there is or could be an optional term in phenix.refine to maintain the center of mass at the same coordinate in such cases. All the best, Tom T >> Hi i am using phenix version 1.4 release tag 70 >> >> hari@charlie:~$ phenix.refine --version >> ------------------------------------------------------------------------------- >> PHENIX: Python-based Hierarchical ENvironment for Integrated >> Xtallography >> Version: 1.4 >> Release tag: 70 >> Platform: intel-linux-2.6-x86_64 linux >> User: hari >> ------------------------------------------------------------------------------- >> >> >> I am seeing a strange shifting of my coordinates "out of my experimental >> phases map" before and after refinement without simulated annelaing >> >> I am at the final stages of my refinement. When I refine without simulated >> annealing the resulting model is shifted relative to my experimental >> phases >> map into which I build my model >> The phenix command line strategy i am using are >> rigid_body+individual_sites+individual_adp+tls .or the same strategy with >> simulated_annealing=true >> >> The output map coefficients fortunately match my model in both cases . But >> I >> am wondering why there is a difference. >> I am using the mlhl target for refinement to 3.1 A , My R and rfree is >> 28/31 >> . >> >> Any ideas why my model shifts without simulated annealing . All pdbs have >> the same CRYST record . >> I am using coot version 0.61 for my building and map display using fft >> inside of coot . >> >> >> hari >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

2 2

autosol error 1.4-3 when trying to specify deriv.inano=noinano
by Francis E Reyes 06 Jun '09

06 Jun '09

------------------------------------------------------------ Starting AutoSol with the command: phenix.autosol Reading effective parameters from autosol.eff The key inano is not in var_type_dict...this means the command-line Wizard needs a conversion in the autosol.py script under 'Translating inputs' or else in excluded_inputs(['write_run_directory_to_file', 'carry_on', 'run', 'copy_run', 'delete_runs', 'display_runs', 'display_facts', 'display_summary', 'display_labels', 'coot', 'dry_run', 'stop', 'params_only', 'sites', 'atom_type', 'sites_file', 'seq_file', 'quick', 'data', 'f_prime', 'f_double_prime', 'labels', 'sites', 'atom_type', 'peak', 'infl', 'high', 'low', 'remote', 'native', 'deriv']) Any ideas? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 1

Parallel Version of Phenix?
by Angelo Rossi 03 Jun '09

03 Jun '09

Hello Phenix Users and Developers: I am new to Phenix and am trying to help a colleague move his project using Phenix from a single workstation to a Linux cluster. My background is chemistry and high performance computing, but I am not intimately knowledgeable about the workings of Phenix. Are there parts of Phenix that can run on a Linux cluster in parallel. I understand that a good part of Phenix is written in python, but there are certainly numerically intensive aspects of structure refinement that could be amenable to parallelization. It would really help if you could provide an overview of those components that are now running in parallel. A search on the net did not reveal information about a parallel version of Phenix. Thank you for your attention and any possible help. Kind regards, A. R. Rossi

4 6

Fixing coordinates in phenix.refine_gui
by AMIT 03 Jun '09

03 Jun '09

Hi All Is it possible to fix only the coordinates(xyz's) of residues or individual atoms in phenix.refine_gui while refining it for rest of the atoms? Any suggestions will be helpful. Thanks in advance Amit. -- AMIT DAS, PROTEIN CRYSTALLOGRAPHY SECTION, SOLID STATE PHYSICS DIVISION, BARC, TROMBAY, MUMBAI-400085. INDIA. Alt E-mail:[email protected] <E-mail%3Aamitdas(a)barc.gov.in> PHONE:+91-22-25594688/4063 FAX:+91-22-25505151

3 2

mutate to polyAla in phenix.automr?
by Francis E Reyes 29 May '09

29 May '09

Is there an option or a phenix.* utility to mutate a MR model to poly ALA before the MR is done? Thanks! FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

13 39

Failed to carry out AutoBuild_build_cycle: Word too long.
by Gino Cingolani 28 May '09

28 May '09

Hi Folks, does anybody know what this means? My AutoBuild dies off in the middle with this error message ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /home/gino/XTAL/SYN/V1/DASETs/Se3/SAD/REF/AutoBuild_run_2_/TEMP0/RUN_FILE_1' Word too long. ******************************************************************************** Thanks, Gino *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

2 1

covalently linked ligand
by Joerg Standfuss 28 May '09

28 May '09

Dear phenix users, I am currently building a model where the ligand is linked via schiff base to a lysine residue. To let phenix know about the link I provide the ligand.cif file and created the link parameter file as described in the manual. The type of link I defined with Jligand as it does not appear in the standard ccp4 library. Unfortunately phenix.refine stops with the error message below when I provide the so created files. It seems phenix has problems to apply the needed ligand modifications ie removing hydrogens and oxygens and stops with the refinement. I have no idea why this doesn't work and am getting a little desperate so any suggestions how to do this properly would be greatly appreciated. Could I use for example elBOW to create the link description? many thanks, Joerg File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/pdb_interpretation.py", line 499, in __init__ mod_mod_id=self.mon_lib_srv.mod_mod_id_dict[apply_data_mod]) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/pdb_interpretation.py", line 771, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/cif_types.py", line 339, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ monomer_library/cif_types.py", line 244, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: H151

2 1

AutoBuild can't align sequence file
by Moritz.Metlitzky＠sbg.ac.at 27 May '09

27 May '09

Hi all, i'm currently trying to solve my structure with phenix and i tried to do it via AutoMR. At first everything works fine, it finds a MR solution, but then i get this error: Chain too short or poor match to sequence: MYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELL NOTE: chain A (residues 1-304) MYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELL did not match the input sequence... ignoring alignment and rebuilding segment without sequence information. *************************************** AutoBuild Input failed Sorry, the PDB file and sequence file could not be aligned (with no gaps and >50.0% identity) Please restart the wizard... You have several possibilities to try .... You can set rebuild_in_place=No You can set input_sequence_file=None You can set min_seq_identity_percent to a lower value You can set highest_resno to a higher value You can specify start_chains_list if your PDB file sequence starts with a residue number greater than the number of residues in the sequence. what can i do now? the pdb file has nearly the same sequence (2 mutations) but he says that he can't align them, i use a .dat file for this is this correct? i also have a fasta line in it >... but it doesn't work without this line either. i tried with different phenix versions and have always the same problem Any suggestions would be appreciated.

2 1

refinement of a ligand with alternate conformations in one region but not the other.
by Pascal Egea 26 May '09

26 May '09

Dear All, I am refinining a protein-NAD complex structure at ~1.9A resolution. I have included a main conformation for my NAD ligand but while I see clearly the position for the nicotinamide- first ribose part, my density bifurcates when it comes to the second ribose-adenine. It seems that I have two (at least) conformations for this part of the ligand molecule. Can I refine these two alternate conformations in Phenix knowing that a part of the ligand will be common (have an occupancy of one) while the two other ones will be separate? Do I need to enter two ligand molecules or do I have to do more elaborate things? Last question is it possible that for the variable regions I may end up with a sum of occupancies that is not 1 while for the fixed region it might end up being one? That's three questions for the wizards. Thanks in advance. Pascal Egea UCSF

3 2

Attaching H onto phosphate group and ATP
by Young-Jin Cho 26 May '09

26 May '09

Hello phenix users, I am wondering if phenix.elbow can attach H onto phosphate group for refinement. The reason for that, based on different pH environment, phosphate group should have different charges with respect to how many protons attached. In addition, how can I know normal distance restraints such as ATP? What I only know from the coot is that it shows P-O bond length is 1.61A and P-O bond (delocalized double bond) is 1.5A. The reason for this is, I heard about phosphate ion, if it is protonated, then the bond length of HO-P is longer than that of non-protonated O-P. I want to try if is true for ATP as well. Is there anyone who knows practically testing this fact by using phenix? Thanks in advance, YoungJin

6 7

turbo frodo
by Zhongli Cui 22 May '09

22 May '09

Dear all, I think turbo frodo is a very good software for modelling. I tried to get a licence key from turbo(a)afmb.cnrs-mrs.fr, but got no reply. I would like to know if this software is still in support. Thank you. ---------------- Cui Zhongli Professor, Ph.D Dept. of Microbiology College of Life Sciences Nanjing Agricultural University 1 Weigang, Nanjing, 210095 Jiangsu Province P.R. China. Mail: czl(a)njau.edu.cn Tel: 86-25-84396753 Mob: (0)13951080529

1 0

Autobuild error (ligands)
by Katya Heldwein 21 May '09

21 May '09

Hi, I'm using autobuild in phenix-1.4-59 to rebuild the structure. Autobuild throws the error: **************************************** AutoBuild Input failed Sorry, the generation of cif files from AutoBuild_run_2_/TEMP0/LIGANDS.pdb did not work. Error message was: 'NoneType' object has no attribute 'id' **************************************** I think this may have to do with carbohydrates that I have in the structure. I provided the .eff and the .cif files for the carbohydrates but something must be going wrong. Could you, please, let me know how to troubleshoot this error? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

2 1

Occupancies
by AMIT 21 May '09

21 May '09

Hello I am new to phenix. I am tring to refine the occupancies using the phenix.refine gui. In the refinement settings- refinement strategy : occupancies , when I define the groups for individual atoms as chain A and resseq 1:200 (for protein atoms) and a ligand group in constrained as chain B and resseq 1:10 and chain C and resseq 1:10, the refinement fails with several errors. The refinement runs fine when I do not touch the "occupancies" panel on the gui. How do I refine in Phenix the occupancies defining as well as partitioning the molecule as individual, groups and coupled groups? Thanks in advance, Amit -- AMIT DAS, PROTEIN CRYSTALLOGRAPHY SECTION, SOLID STATE PHYSICS DIVISION, BARC, TROMBAY, MUMBAI-400085. INDIA. Alt E-mail:[email protected] <E-mail%3Aamitdas(a)barc.gov.in> PHONE:+91-22-25594688/4063 FAX:+91-22-25505151

3 3

Autobuild error
by Katya Heldwein 21 May '09

21 May '09

Hi, I am trying to run Autobuild to generate a very good rebuilt model using phenix.autobuild data=data.mtz model=coords.pdb multiple_models=True \ include_input_model=True \ multiple_models_number=1 n_cycle_rebuild_max=5 with some modifications. When I run it, I get the following error: ******************************************************************************** Failed to carry out AutoBuild_multiple_models: [Errno 2] No such file or directory: 'AutoBuild_run_1_/TEMP0/temporary.com' ******************************************************************************** How can I troubleshoot this problem? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

2 1

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Cyndi Salbego 20 May '09

20 May '09

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Equipped with MD2 microdiffractometer. Variable energy between 6-18keV, ADSC Q315 Detector, MADCapable. Sample Robot. Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV), ADSC Q315 Detector. Contact csalbego(a)anl.gov for further details.

1 0

creating map file only
by Raja Dey 16 May '09

16 May '09

Dear Friends, I was trying to create map file only as follows: phenix.refine 1205A-p21212.mtz may15_1_001.pdb map.params strategy=none output.prefix=may15_2 , map.params is as follows refinement { electron_density_maps { map { mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT likelihood_weighted = True obs_factor = 2 calc_factor = 1 } map { mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT likelihood_weighted = True obs_factor = 1 calc_factor = 1 } map { mtz_label_amplitudes = 3FO2FCWT mtz_label_phases = PH3FO2FCWT likelihood_weighted = False obs_factor = 3 calc_factor = 2 } grid_resolution_factor = 1/4. region = *selection cell atom_selection = name CA or name N or name C apply_sigma_scaling = False apply_volume_scaling = True } } But, still I am getting only the map_coeffs.mtz file in the output. I am expecting 3 map files in the output. Could you please tell what's wrong I am doing. I want to create only the map file without any refinement. Looking forward to hearing from you... Regards... Raja

1 0

Beamtime proposal deadline for ALS GU time
by Peter Zwart 15 May '09

15 May '09

May 15, 2009 is the deadline for the July-August Rapid Access Proposal cycle. Please note that the ALS will be shut down in September, 2009. The deadline for applications of beamtime on the BCSB beamlines in the ALS is today! Other notable features include: * A high-accuracy microdiffractometer on BL 8.2.1 allows for centering and viewing of very small crystals; * Robot automounters on BL8.2.1 and 8.2.2 are now fully commissioned. * A new large format (315mm active surface area) CCD detector on BL 8.2.1 facilitates data collection on large unit cell crystals. * Beamlines 5.0.1 and 5.0.3 now generate 1.5x1011 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. * Beamline 5.0.2 (a tunable beamline) generates a peak flux of 8x1011 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. All beamlines of the BCSB (5.0.1, 5.0.2, 5.0.3, 8.2.1 and 8.2.2) can all be operated remotely. Please contact Peter Zwart (sector 5 beamlines) or Corie Ralston (sector 8 beamlines) for more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html Scroll down to "Structural Biology and SAXS." We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize If you'd like to apply for October-November-December beamtime at the Advanced Light Source, please submit a General User proposal by August 15, 2009. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. Cheers, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

1 0

March 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 15 May '09

15 May '09

Dear Users, The deadline for July/August 2009 Collaborative Crystallography proposals will be May 15, 2009. ============= Thumbnail Description: Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Scroll down to "Structural Biology and SAXS" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only ?) * In question 9, please describe a specific research project with a clear end point. In order to request CC time for July/August 2009allocation period, proposals must be submitted by *May 15, 2009*. Please note that the ALS will be shut down in September, 2009. The deadline for CC proposals for the time period October/November/December 2009 will be August 15, 2009. Regards, Banumathi Sankaran

1 0

--unused_ok, .def, documentation,...
by Bryan W. Lepore 14 May '09

14 May '09

[ phenix v1.4 rel. tag 3 cctbx tag: 2008_12_07_1353 ] using an old .def w/ "latest devel. rel" phenix (but not nightly) i used --unused_ok b/c it looks like that's what its for. i am expecting an "updated" .def to write after the job - yes?... if so, it reads slightly differently than the documentation.. hard to give an example... things look ok in general, but ought i to have a new .def? -bryan p.s: does phenix write version/release info in the .def (i can't find it)?

5 10

Simulated annealing
by Esmael Haddadian 13 May '09

13 May '09

Hi, I have tried to only refine the sidechains in my model using the simulated annealing with commands strategy=individual_sites sites.individual = "sidechain" However after the refinement the backbone was also moved; any suggestions as how to only allow sidechain movements during the refinement? Thanks, Esmael

2 1

Carbohydrate refinement
by Katya Heldwein 13 May '09

13 May '09

Hi, I have several N-linked sugars in my structure. Some are modeled as single NAGs and others, as NAG-NAG chains. How do I specify Asn-NAG and NAG-NAG linkages for phenix refinement? Currently, when I try to refine the model, NAGs move away from Asn and from each other. Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

2 1

a problem with phenix installation
by Tatyana Sysoeva 12 May '09

12 May '09

Hello, I'm new to Phenix as well as I'm not familiar with Linux OSs. I have Windows Vista OS machine (intel, 32 bit) with VM Player on it. on VM Player I run Fedora 7. I downloaded Phenix 1.4 installation package for Intel-Linux-2.6, ran install. It took more then 10 min, stalled on some lines. Then I run usr/local/phenix-1.4-3/phenix-env.sh. No error messages so far. After I'm done with first two steps and try to start phenix - it says that "command not found". Should I change some path variables, how can I test the installation itself? what should I check first? I guess it might be a very basic or silly question, but I would be very grateful if anybody can help me with this and point out what I have to do to start my work with Phenix. Thank you, Tanya

2 2

tls refinement
by sbiswas2＠ncsu.edu 12 May '09

12 May '09

Hi all, I started doing TLS refinement with one of my structures and got the following: Start R-work = 0.3817, R-free = 0.3923 (no bulk solvent and anisotropic scale) Final R-work = 0.3788, R-free = 0.3885 (no bulk solvent and anisotropic scale) Start R-work = 0.2094, R-free = 0.2381 Final R-work = 0.2058, R-free = 0.2358 my question now is why is the R value high without the anisotropic scale? Second question is: can I refine alternate conformations using the command line or is it already there in the default parameters? Thanks, Shya NC State University

2 3

Phaser, Phenix and Em models
by Gino Cingolani 12 May '09

12 May '09

Hi Randy, what about implementing the use of EM-models (e.g. structure factors from EM model) in Phenix to carry out MR and/or MR-SAD? There's a growing number of macromolecular complexes that have been imaged at medium/low res by EM, which could be of great help to phase at low res or located anomalous scatterers in phased maps. And the EM database keeps growing! At this moment, it is certainly possible to use EM models in Phaser, but the Phenix pipeline could add much more to that. For instance, Phenix would allow for better phase extension of low res EM phases to higher res by ncs-averaging or multi-crystal averaging (in Resolve). Or Phenix could help combining low res EM phases with other phase sources such as SeMet sites, poorly occupied heavy atom sites, etc (MR-SAD). Or Phenix could rigid body refine (at low resolution) pseudo-atomic models obtained by filling in EM-models with dummy atoms. This would help defining averaging masks and so on. What do you think? Thanks in advance, Gino *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

4 3

Re: [phenixbb] Phaser, Phenix and Em models
by Gino Cingolani 11 May '09

11 May '09

Hi Randy, thanks for getting back to my email. Yes, I do think it would be very helpful to switch to using density instead of coordinates both for MR and MR-SAD. The interface between cryo-EM and X-ray is growing so fast that in many cases EM densities could be used for initial phasing by Fourier difference, or even ab initio, provided sufficient ncs is available. In our specific case we have at least two macromolecular complexes (1.1-2.2MDa) with >400SeMet, resolutions in the mid 3A with extreme unisomorphism and 10-15A EM densities. SAD/MAD phasing is unrealistic, MIR methods can't work when all crystals are inherently unisomorphic .... MR/MR-SAD could be an alternative. Thanks again! Gino Hi, As it happens, we've been working very hard over the last few months first to make all commands in Phaser available from Python (done) and second to make all options available from the new Phenix GUI (getting close). ("We" in this context mostly means Airlie at our end and Nat at the Berkeley end.) So it should become easy to switch to using density instead of coordinates for your models without switching to the command-line mode of running Phaser. We're also very interested in optimizing the way that we use density from EM, which is something we haven't spent enough time playing with yet. It's not yet possible to use density for a model in the MR-SAD mode--that's been on the wish list and shouldn't be too hard. Do you need that feature right now? I really like your other ideas, so we'll have to talk to Tom about adapting the AutoMR wizard so that it doesn't require a coordinate file. As you say, this will be a real growth area! All the best, Randy On 8 May 2009, at 15:39, Gino Cingolani wrote: > Hi Randy, > > what about implementing the use of EM-models (e.g. structure factors > from EM model) in Phenix to carry out MR and/or MR-SAD? > There's a growing number of macromolecular complexes that have been > imaged > at medium/low res by EM, which could be of great help to > phase at low res or located anomalous scatterers in phased maps. > And the EM database keeps growing! > > At this moment, it is certainly possible to use EM models in Phaser, > but the Phenix pipeline could add much more to that. For instance, > Phenix would allow for better phase extension of low res EM phases > to higher > res by ncs-averaging or multi-crystal averaging (in Resolve). > Or Phenix could help combining low res EM phases with other phase > sources such as SeMet sites, poorly occupied heavy atom sites, etc > (MR-SAD). > Or Phenix could rigid body refine (at low resolution) pseudo-atomic > models > obtained by filling in EM-models with dummy atoms. > This would help defining averaging masks and so on. > What do you think? > > Thanks in advance, > > Gino > > > *********************************************************** > Gino Cingolani, Ph.D. > Assistant Professor > Dept. of Biochemistry and Molecular Biology > SUNY Upstate Medical University > 750 E. Adams Street, Syracuse, NY, 13210 > Tel. (315) 464 8744 > Fax. (315) 464 8750 > Email: cingolag(a)upstate.edu > *********************************************************** > "Nati non foste per viver come bruti, ma per seguir virtute e > conoscenza" > ("You were not born to live like brutes, but to follow virtue and > knowledge") > Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www- structmed.cimr.cam.ac.uk _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

1 0

AutoMr
by Zhongli Cui 11 May '09

11 May '09

Dear all, I am using phenix automr to solve my structure. I have 2 search models with identiy of 44% and 31% respectively aligned by ClustalW. I used thiese two pdbs as search models directly in phenix, it gave a llg of about -60 and Tfz of 7. The refined structure fit the map quite well. But I wonder if the solution is OK for the negative LLG. So what should I do next? How should I prepare the search model? Shall I edit the seach models such as remove some loops or surface side chains? If I the a search model prepared by Chainsaw was used, then what is identity I have to tell phenix? Another question, I built 2 models of the same protein and of the same x-ray diffraction data with phaser in CCP4 and Phenix. In my mind, these models should be the same. But in fact they differ from each other significantly in orientation. Is there something wrong with my calculation? ---------------- Cui Zhongli Ph.D Dept. of Microbiology College of Life Sciences Nanjing Agricultural University 1 Weigang, Nanjing, 210095 Jiangsu Province P.R. China. Mail: czl(a)njau.edu.cn Tel: 86-25-84396753 Mob: (0)13951080529

3 2

If HL coefficients are in the .mtz phenix.refine is ignoring my refinement.target= ml specification?
by Francis E Reyes 09 May '09

09 May '09

Hi all (again) It seems that despite me specifying refinement.main.target=ml in my def file, phenix.refine seems to want to keep refining against HL coefficients. It seems overtly out of the way to remove the HL coefficients definition (both the label and file) from the def file as well. Am I doing something wrong then (i.e. does it keep going back to refining experimental phases for some valid reason?) Over 80% of the ASU is built with R/Rfree in high 20's for 1.7 A data. Cheers FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 1

changes to phenix autosol?
by Francis E Reyes 09 May '09

09 May '09

Hi all It seems that AutoSol now does some initial building when before (at least 1.3-final) it just output a phaser_x.mtz and resolve_x.mtz which would go onto phenix.autobuild after_autosol . What's this new initial building? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 1

Refining atoms on special positions
by Oliver Clarke 08 May '09

08 May '09

Hi, I'm running phenix.refine v1.4-3, and I'm refining a 3.3A structure that has potassium ions present on a crystallographic fourfold axis. I believe (based on previous refinement in REFMAC5.5), that these ions are at full occupancy, so I set the occupancy of each ion to 1. Despite this, there is still a lot (several 7-10sigma peaks in the Fo- Fc) of unexplained positive density, the potassium ions do not converge to their previously refined positions, and their B-factors refine upwards to values several times higher than the surrounding protein. When the same structure is refined in refmac (with ion occupancy set to 0.25), there is little to no unexplained density and the R/Rfree are substantially lower (21.9/25.9 as against 24.5/31) Does anyone have any ideas/suggestions as to what might be going on? Cheers, Oliver

2 1

torsion_angles
by Imre Toeroe 08 May '09

08 May '09

Dear phenixers, I have seen a new strategy option, *torsion_angles* in the def files produced by recent (1.4-5x) phenix.refine. Is it active? How can one use it? Thanks, Imre

2 1

Refining f'/f"?
by Leigh Allen 08 May '09

08 May '09

Hello, I'm new to the world of x-ray crystallography. I just solved my first SAD structure and I'm on to the refinement stage. The difference map generated by phenix.refine has really big positive peaks all around my MET residues. If I switch the atoms to MSE, then I get large negative peaks. Firstly, I'm not sure if I'm supposed to represent these residues as MET or MSE because it's a "native," high resolution (1.85) dataset, but it the protein had MSE residues. When scaling this data, I did not keep F(+) and F(-) separate. The protein's phases were generated using SAD data to 2.7A, which using SHARP led to a remarkably interpretable map that allowed me to build in the protein by hand. My second question is, how should I handle the issue with large + MET/large - MSE peaks? Do I need to rescale my data to treat it as anomalous data or is there something I can do within Phenix to fix my problem. I tried the phenix.refine GUI and set it up to refine f' and f", but it appears that nothing really changed. Thanks! Leigh Allen ******* Ph.D Candidate McCafferty Lab Department of Chemistry Duke University

4 5

phenix.refine Ile peptide bond breaks
by SIPPEL,KATHERINE H 07 May '09

07 May '09

Hi all, I've got a 2.1 angstrom structure that I am refining. The space group is P212121. The structure is a dimer which I am refining without NCS restraints. Each monomer has 333 residues and one ligand, there are 33 Ile residues in each monomer. The first couple of rounds of refinement I had no problems, but during the third round phenix started breaking the main chain at the peptide bond and the side chain between CA and CB on some of the Ile residues. Specifically there are two breaks in chain A and four breaks in chain B, with two additional residues in chain B breaking only the CA-CB bond. Only one of the breaks is between the same residue in both chains. I'll be boring and run through my refinement process. This is the first time I've used phenix for anything but AutoSol and it is very likely that I have messed something up. Feel free to correct anything else I've done wrong along the way. Round 1, I rigid body refined chain A and B independently, performed simulated annealing, and refined individual coordinates. In COOT I manually refined and removed some bad loops. A few of the Ile were deleted but none of the problem ones Round 2, I refined individual_sites and individual_adp and turned off simulated annealing. In COOT I rebuilt some of the loops and fitted the ligand into the density. I generated a .cif file in eLBOW. Round 3, I refined the same as round 2 except that I included the .cif file. This is when I got the peptide bond breaks for Ile residues. I figured it was a fluke, fixed the breaks in COOT and rebuilt a few more residues in the loops. I ran another round of refinement and the same breaks showed up in the pdb file. I double checked the .geo file to see if Real Space Refine had made the bond distances were too long, but all the input distances were within one or two hundredths of an angstrom from ideal. I considered it was maybe the ADP refinement as I was borderline pushing the number of parameters I was refining given the number of reflections I had. I turned off the individual_adp refinement and reran refine_003. No luck. I tried increasing the weight of the geometry restraints over the observed data. I did this by increasing target_weights.wxc_scale = 1.5. (I suspect that I got this wrong. As I understood the wxc_scale is the ratio of the geometry restraints to the observed data. Feel free to point and laugh as long as you also provide an explanation as to what this parameter really means and how I should have done it,please.) Still no luck. For future information none of the problem isoleucines were located near the ligand or near any of the loops I was rebuilding. I think that's everything. Any help would be appreciated, Thanks, Kat -- SIPPEL,KATHERINE H Ph. D. candidate McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine University of Florida

2 1

difference density maps
by rpai＠berkeley.edu 07 May '09

07 May '09

Hi, I have a question on difference density maps. We are soaking in a substrate into my enzyme and am trying to see if it is in there by looking at difference density maps. We looked at an fobs-(fobs-fcalc) map and see density and 5 sigma at each catalytic active site in roughly the same place, its not great, but it seems like there is something there. so then, I thought I would confirm this by an fobs-fobs map. But I just used the phenix fobs-fobs difference electron density map and I dont see anything there. So I am curious as to an explanation of the difference. Any ideas? Raj

2 1

SA-omit map
by James Fraser 06 May '09

06 May '09

Is there anyway to get phenix.autobuild to NOT delete multiple conformers when doing a SA-omit map? Thanks, jf -- James Fraser jamesfraser(a)berkeley.edu Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

2 1

(no subject)
by Leigh Allen 05 May '09

05 May '09

A Python error was detected. This is almost certainly a bug; please send an email containing this message to phenixbb(a)phenix-online.org so we can fix it. Thanks! AttributeError : 'ResultsNotebook' object has no attribute 'file_base' Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/MainWindow.py", line 257, in launch_coot (file_name, file_prefix) = self.pick_model() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 386, in pick_model file_base = result_page.file_base AttributeError: 'ResultsNotebook' object has no attribute 'file_base'

2 1

Missing plotting libraries
by Leigh Allen 05 May '09

05 May '09

How do I fix this? You appear to be missing one or more libraries required by the plotting module; plots will be disabled for now. The original error is shown below. liblapack.so.3: cannot open shared object file: No such file or directory You appear to be missing one or more libraries required by the plotting module; plots will be disabled for now. The original error is shown below. liblapack.so.3: cannot open shared object file: No such file or directory Plot library disabled: wxGUI2.Plot disabled. Graphing will be turned off. You appear to be missing one or more libraries required by the plotting module; plots will be disabled for now. The original error is shown below. liblapack.so.3: cannot open shared object file: No such file or directory You appear to be missing one or more libraries required by the plotting module; plots will be disabled for now. The original error is shown below. liblapack.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/usr/local/phenix-1.4-55/phenix/phenix/command_line/refine_gui.py", line 16, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.4-55/phenix/phenix/command_line/refine_gui.py", line 9, in run from wxGUI2.Programs import Refine File "/usr/local/phenix-1.4-55/phenix/wxGUI2/Programs/Refine.py", line 13, in <module> from wxGUI2.Programs import RefineNotebook File "/usr/local/phenix-1.4-55/phenix/wxGUI2/Programs/RefineNotebook.py", line 802, in <module> class ResolutionBinStatsPlot (Plot.Loggraph) : AttributeError: 'NoneType' object has no attribute 'Loggraph'

4 6

Switching off symmetry related van der waals in phenix.refine
by Chandrika Deshpande 01 May '09

01 May '09

Hello everyone, I am using Phenix.refine to refine one of my protein structures. My protein crystallised in the spacegroup P6522 with one protein molecule in the asymmetric unit. I have a PEG molecule from the crystallization condition which crosses a two-fold crystallographic symmetry axis. PEG is symmetric hence this does not violate the crystal symmetry. However, this situation causes a problem which I need to solve : How can I refine this structure to include the PEG molecule? Is there a way to remove van der Waals repulsion between one half occupancy PEG and its crystallographic symmetry mate ? Is there a way to switch off symmetry related van der waals terms from the penalty function in phenix.refine ? I have already tried refining by changing the occupancy of PEG to 0.5 but this does not work as after running refinement the PEG molecule is pushed out of the electron density map. Thanks, Chandrika

2 1

Geometry analysis
by Ulrich Baumann 30 Apr '09

30 Apr '09

Hi, I am just wondering whether there is a tool/feature in Phenix that (i) prints out all bonds/angles deviating by some specified number of standard deviations, and (ii) reads a user-defined .cif file for ligands as well so that this ligand appears in (i) as well. Phenix.pdbtools prints a bond histogram and I did not manage to include an external .cif file. Most likely this is easy to do and I haven't found it in the manual yet. Thanks in advance, Ulrich

2 1