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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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