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Strange distance in HEM.cif ligands in phenix library
by Yarrow Madrona 16 Jun '14

16 Jun '14

Hello, After validating a PDB for deposition I received a message that the HEME ligand C2D-C3D distance was longer than ideal. It was 1.52 angstroms, while it was 1.35 for C2A-C3A, C2B-C3B and C2C-C3C. The ideal bond length is listed as 1.544 vs. 1.337 for the other bonds in $PHENIX/chem_data/mon_lib/h/HEM.cif Is there a reason for this? If not, I am inclined to edit it. -Yarrow

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Occupancy refinement of secondary conformation doesn't add up to 1.00
by Benjamin Stauch 15 Jun '14

15 Jun '14

Hi Phenix, I do a refinement of a glycoprotein that has a NAG-NAG attached to an Asn. The data set is very high resolution and I am positive there is indication of a secondary conformation of the entire attachement. I modeled a second conformation in Coot and run my refinement, with the "adjust occupancy" option checked. After initially setting both occupancies to 0.5, I am puzzled to see one of the NAGs to be refined to 0.45 (conformer A) and 0.75 (conformer B) occupancy .. For the other NAG, and indeed all amino acid residues, things always add up like they should. Additionally to this, I was wondering if there was an easy option to restrain each conformer of the entire Asn-NAG-NAG group to have uniform occupancies -- i.e. the Asn and both NAGs of conformer A to have identical occupancy. Thanks and best Ben

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Prime and switch crashing
by Oliver Clarke 13 Jun '14

13 Jun '14

Hi all, I’m getting an error running phenix.prime_and_switch_map that I can’t figure out. It crashes shortly after F(model) initialization. The last part of the log and traceback is appended below - if anyone can figure out what I’m doing wrong I’d be very grateful! I’m running dev-1702 on a Mac (not sure whether this is a mac specific issue though). This happens with multiple different pdb/mtz combinations, so I don’t think it is something specific to my files. Best, Oliver. Command: phenix.prime_and_switch_map model_rs6_refine_001.pdb model_rs6_refine_001.mtz debug=true Error: ----------F(model) initialization---------- Twinning will be detected automatically. |--(resolution: 3.00 - 71.59 A, n_refl.=26875 (all), 5.48 % free)------------| | | | r_work= 0.2683 r_free= 0.3402 coordinate error (max.-lik. estimate): 0.58 A | | | | x-ray target function (ml) for work reflections: 5.858242 | |-----------------------------------------------------------------------------| End of input processing Traceback (most recent call last): File "/Applications/PHENIX-dev-1702/Contents/phenix-dev-1702/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/prime_and_switch_map.py", line 160, in <module> run(sys.argv[1:]) File "/Applications/PHENIX-dev-1702/Contents/phenix-dev-1702/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/prime_and_switch_map.py", line 68, in run map_coeffs = fmodel.electron_density_map().map_coefficients( TypeError: electron_density_map() takes exactly 2 arguments (1 given)

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GRC and GRS on Diffraction Methods in Structural Biology 7/27/2014 - 8/1/2014
by Anastassis Perrakis 13 Jun '14

13 Jun '14

Dear all, As I did give the full promotional message for why these are just outstanding meetings to attend, I will only invite you to look at the latest programs GRC (http://www.grc.org/programs.aspx?id=11654) GRS (http://www.grc.org/programs.aspx?year=2014&program=grs_diff). and also remind you that the registration is closing in 15 days (June 29). There are still spots available for selected abstracts to be presented towards the end of the meeting, and participant places are filling up soon (especially after a wave of 15 new registrations only yesterday!) We hope to see you all at Bates college and promise you two exciting meetings and a great time! On behalf of the GRC and GRS organizers, Tassos

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pdb file with duplicate atom names (Hydrogens)
by Rex Palmer 12 Jun '14

12 Jun '14

I have taken over a high resolution set of protein data which has H atoms built in. For non-H atoms having 2 or three H atoms these H atoms each carry the same atom number in the pdb file. Phenix will not accept this format. Should I delete all H-atoms and reassign them in the next Phenix refinement run? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com

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Re: [phenixbb] NAG-NAG link definition seems to have no effect
by Benjamin Stauch 12 Jun '14

12 Jun '14

Thanks for your quick reply! However now I get the following error message, "Fatal problems interpreting model file: NUmber of atoms with unkown nonbonded energy type symbols: 3 Please edit the model file to resolve the problems nd/org supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Alternatively, to continue despite this problem use: stop_for_unknown=False" the log file says, Monomer Library directory: "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib" Total number of atoms: 11298 Number of models: 1 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain A and resname NAG and resid 401 residue_selection_2: chain A and resname ASN and resid 74 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain A and resname NAG and resid 401 residue_selection_2: chain A and resname NAG and resid 402 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain B and resname NAG and resid 401 residue_selection_2: chain B and resname ASN and resid 74 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain B and resname NAG and resid 401 residue_selection_2: chain B and resname NAG and resid 402 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 319, 4675 Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} Classifications: {'undetermined': 2, 'peptide': 317} Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, 'NH3': 1} Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} Not linked: pdbres="ALA A 317 " segid="A " pdbres="NAG A 401 " segid="A " Not linked: pdbres="NAG A 401 " segid="A " pdbres="NAG A 402 " segid="A " Conformer: "B" Number of residues, atoms: 319, 4675 Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} Classifications: {'undetermined': 2, 'peptide': 317} Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, 'NH3': 1} Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} Not linked: pdbres="ALA A 317 " segid="A " pdbres="NAG A 401 " segid="A " Not linked: pdbres="NAG A 401 " segid="A " pdbres="NAG A 402 " segid="A " bond proxies already assigned to first conformer: 4309 Chain: "B" [...] Chain: "C" [...] Residues with excluded nonbonded symmetry interactions: 26 residue: [...] Number of atoms with unknown nonbonded energy type symbols: 3 "ATOM 5046 HO4 NAG A 401 .*.A H " "ATOM 6215 HD22 ASN B 74 .*.B H " "ATOM 10057 HO4 NAG B 401 .*.B H " Time building chain proxies: 4.05, per 1000 atoms: 0.36 Deleting these atoms (NAG HO4 and ASN HD22) manually doesn't seem to do the trick - as I explicitly want to refine hydrogens I reckon they are added back on. Also it seems BETA1-4 wants to desperately link NAG O4 to NAG O1 which doesn't exist .. Shuld I manually define my NAG-NAG link instead of using the BETA1-4? Thanks again! B 2014-06-12 10:54 GMT+02:00 Benjamin Stauch <bs448c(a)gmail.com>: > Thanks for your quick reply! However now I get the following error message, > > "Fatal problems interpreting model file: NUmber of atoms with unkown > nonbonded energy type symbols: 3 Please edit the model file to resolve the > problems nd/org supply a CIF file with matching restraint definitions, > along with apply_cif_modification and apply_cif_link parameter definitions > if necessary. Alternatively, to continue despite this problem use: > stop_for_unknown=False" > > the log file says, > > > > Monomer Library directory: > "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib" > Total number of atoms: 11298 > Number of models: 1 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain A and resname NAG and resid 401 > residue_selection_2: chain A and resname ASN and resid 74 > apply_cif_link: > data_link: BETA1-4 > mod_id_1: DEL-HO4 > mod_id_2: DEL-O1 > residue_selection_1: chain A and resname NAG and resid 401 > residue_selection_2: chain A and resname NAG and resid 402 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain B and resname NAG and resid 401 > residue_selection_2: chain B and resname ASN and resid 74 > apply_cif_link: > data_link: BETA1-4 > mod_id_1: DEL-HO4 > mod_id_2: DEL-O1 > residue_selection_1: chain B and resname NAG and resid 401 > residue_selection_2: chain B and resname NAG and resid 402 > Model: "" > Number of chains: 4 > Chain: "A" > Number of atoms: 5075 > Number of conformers: 2 > Conformer: "A" > Number of residues, atoms: 319, 4675 > Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} > Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} > Classifications: {'undetermined': 2, 'peptide': 317} > Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, > 'NH3': 1} > Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} > Not linked: > pdbres="ALA A 317 " segid="A " > pdbres="NAG A 401 " segid="A " > Not linked: > pdbres="NAG A 401 " segid="A " > pdbres="NAG A 402 " segid="A " > Conformer: "B" > Number of residues, atoms: 319, 4675 > Unusual residues: {'NAG%DEL-O1%DEL-HO4': 1, 'NAG%DEL-O1': 1} > Unexpected atoms: {'NAG%DEL-O1%DEL-HO4,HO4': 1} > Classifications: {'undetermined': 2, 'peptide': 317} > Modifications used: {'DEL-HD22': 1, 'DEL-O1': 2, 'DEL-HO4': 1, > 'NH3': 1} > Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} > Not linked: > pdbres="ALA A 317 " segid="A " > pdbres="NAG A 401 " segid="A " > Not linked: > pdbres="NAG A 401 " segid="A " > pdbres="NAG A 402 " segid="A " > bond proxies already assigned to first conformer: 4309 > Chain: "B" > [...] > Chain: "C" > [...] > Residues with excluded nonbonded symmetry interactions: 26 > residue: > [...] > Number of atoms with unknown nonbonded energy type symbols: 3 > "ATOM 5046 HO4 NAG A 401 .*.A H " > "ATOM 6215 HD22 ASN B 74 .*.B H " > "ATOM 10057 HO4 NAG B 401 .*.B H " > Time building chain proxies: 4.05, per 1000 atoms: 0.36 > > > Deleting these atoms (NAG HO4 and ASN HD22) manually doesn't seem to do > the trick - as I explicitly want to refine hydrogens I reckon they are > added back on. Also it seems BETA1-4 wants to desperately link NAG O4 to > NAG O1 which doesn't exist .. Shuld I manually define my NAG-NAG link > instead of using the BETA1-4? > > Thanks again! > > B > > > > 2014-06-12 2:12 GMT+02:00 Nathaniel Echols <nechols(a)lbl.gov>: > > On Wed, Jun 11, 2014 at 5:05 PM, Benjamin Stauch <bs448c(a)gmail.com> wrote: >> >>> I want to refine a model that has two NAGs linked to an Asn - the sugars >>> are already part of my initial coordinate file, but upon refinement the >>> link between the NAGs gets lost. I have defined a cif_link file as follows >>> that I load (using the GUI), >>> >>> apply_cif_link { >>> data_link = "NAG-ASN" >>> residue_selection_1 = "chain A and resname NAG and resid 401" >>> residue_selection_2 = "chain A and resname ASN and resid 74" >>> } >>> apply_cif_link { >>> data_link = "BETA1-4" >>> residue_selection_1 = "chain A and resname NAG and resid 401" >>> residue_selection_2 = "chain A and resname NAG and resid 402" >>> } >>> >> >> Okay, I think this may be part of the problem - you are missing the outer >> "scope" for these parameter blocks, so they are not processed correctly. >> If you change "apply_cif_link" to >> "refinement.pdb_interpretation.apply_cif_link" in both places it may fix >> the problem. >> >> Refinement doesn't crash or produce errors as far as I can see, however >>> when checking the MolProbity output after refinement, it complains of >>> missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant) >>> >> >> Sorry, this is actually my bug (those atoms should not be included in >> covalently linked sugars), and I think I still have an email complaining >> about this in my inbox from late 2012. I need to overhaul that bit of code >> anyway so I will see if Nigel and I can come up with something smarter. >> >> -Nat >> > >

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NAG-NAG link definition seems to have no effect
by Benjamin Stauch 11 Jun '14

11 Jun '14

Hi Phenix, apologies for the beginner question, and I do realise that there are some related threads already but nothing so far has helped me to solve this problem. I want to refine a model that has two NAGs linked to an Asn - the sugars are already part of my initial coordinate file, but upon refinement the link between the NAGs gets lost. I have defined a cif_link file as follows that I load (using the GUI), apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = "chain A and resname NAG and resid 401" residue_selection_2 = "chain A and resname ASN and resid 74" } apply_cif_link { data_link = "BETA1-4" residue_selection_1 = "chain A and resname NAG and resid 401" residue_selection_2 = "chain A and resname NAG and resid 402" } when checking the .geo file phenix.refine outputs, I do not see any restraints between Asn and NAG, nor NAG and NAG. There might be some clues in the refine.log file: Build ligand and use monomer library to name atoms : NAG Using monomer library entry NAG as template which I guess looks good, and then something like this which could be where things are going wrong: Monomer Library directory: "c:\phenix-1.8.4-1496\phenix-1.8.4-1496_sources\chem_data\mon_lib" Total number of atoms: 11298 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 319, 4675 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2, 'peptide': 317} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, None: 2, 'TRANS': 287, 'PCIS': 2} Not linked: pdbres="ALA A 317 " segid="A " pdbres="NAG A 401 " segid="A " Not linked: pdbres="NAG A 401 " segid="A " pdbres="NAG A 402 " segid="A " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Refinement doesn't crash or produce errors as far as I can see, however when checking the MolProbity output after refinement, it complains of missing atoms O1 in NAG 401 and 402. (Not sure if this is relevant) Furthermore there's still a HO4 attached to the O4 of NAG ... while the BETA1-4 should care to delete it .. however the mon_lib reads BETA1-4 . DEL-HO4 pyranose . DEL-O1 pyranose glycosidic_bond_beta1-4 which doesn't seem entirely relevant for my case? Any help would be appreciated Thanks! Ben

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Using .fcf file with Phenix
by Rex Palmer 10 Jun '14

10 Jun '14

Can I run Phenix with a .fcf file and a .pdb file? If not how can I convert .fcf to the correct format? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com

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Run PHENIX commands on GUI verison?
by 李翔 09 Jun '14

09 Jun '14

Hi, I currently can only access to PHENIX with my laptop which has a Windows system (GUI). I want to run some commands for generating restraints for my models such as: iotbx.show_distances MR.1.pdb > contacts.distances, phenix.secondary_structure_restraints model.pdb Is there a way I can run commands in GUI version or can I run the above commands in the GUI version? Thanks for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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B-factors for some sidechains were not refined well
by Zhou, Tongqing (NIH/VRC) [E] 08 Jun '14

08 Jun '14

Dear colleagues, I am refining one structure at 1.94 A with phenix.refine with individual b, TLS, and xyz. The Rwork and Rfree are now at 16.1 and 19.8%. But when inspecting the maps, I noticed that the sidechain tip of some residues showed positive density and the b-factor for those atoms were very high while those for the other atoms of the same residues were normal; The b-factors for newly added ligands were also not refined well showing high b-value and positive density at the same time; the disulfide bonds also show positive density and high B. The occupancy were all set to 1. Please give suggestions. Thanks! Best regards, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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