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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

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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

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Re: [phenixbb] Adding H atoms onto ligand
by Young-Jin Cho 16 Jun '09

16 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

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Adding H atoms onto ligand
by Young-Jin Cho 16 Jun '09

16 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!

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specification of column labels in command line promt
by Raja Dey 15 Jun '09

15 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

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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

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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

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phasine error
by vennila Natesan 11 Jun '09

11 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?

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not enough memory error in Resolve/AutobuildWizard
by Tatyana Sysoeva 10 Jun '09

10 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

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Water/residue alternative conformations
by Roeland Boer 08 Jun '09

08 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.

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