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phosphate stereochemistry
by Luca Pellegrini 20 Jan '12

20 Jan '12

Hi, I have noticed that Phenix mangles O-P bond lengths and angles in the phosphate groups of my DNA chain (example in pict attached). This only happens to 3 out of 28 phosphates. The refined protein-DNA structure does not present any other unusual stereochemistry issues and refinement runs normally. Could anybody advice on what is going on and how to fix this, please? I am using Phenix-1.7.3-928. Refinement is with default target weights, hydrogens on and does not include simulated annealing. I could make the stereochemistry targets more stringent, but the default values seem strict enough (bond and angle rmsd is 0.005 and 1.225). Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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phenix.refine is auto selecting an old .pdb file for refinement
by Andrews, Forest Hoyt 20 Jan '12

20 Jan '12

I'm having a bit of an issue with phenix.refine. I was receiving the following error "number of groups of duplicate atom labels: 4789 total number of affected atoms: 9578" However when I looked inside my .pdb file there where only 4789 atoms total....No duplicates. I discovered that phenix.refine is auto selecting a .pdb from a previous run. I found this out by not selecting any .pdb file and found phenix.refine refining my data with an older model I use to refine a previous round. How can I stop phenix.refine from auto selecting a .pdb during refinement? __________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Pavel Afonine [pafonine(a)lbl.gov] Sent: Friday, January 20, 2012 12:20 PM To: PHENIX user mailing list Subject: Re: [phenixbb] phosphate stereochemistry Hi Luca, what kind of NCS restraints did you use: torsion or Cartesian? I wonder if torsion NCS would naturally avoid this problem? I hope Jeff comments on this. Pavel On 1/14/12 10:51 AM, Luca Pellegrini wrote: > I think I discovered what was happening to my DNA molecule during > refinement, that caused distortion of the phosphate groups. It was > something along the lines of what Dale suggested, I mention it here so > that it might be useful to others. > > I have two DNA molecules in the ASU and I didn't realised that I had > accidentally swapped OP1 and OP2 in 3 out of 28 phosphates (so that, > if the two DNA molecules were superimposed, OP1 ended on top of OP2). > Because I had NCS restraints on during refinement, I guess phenix was > trying to move OP1 in one DNA molecule towards the NCS-equivalent > position of OP1 in the second molecule, hence the altered geometry. > > I have fixed the atom nomenclature problem and now the geometry of my > DNA is ok. I appreciate that most people tend to avoid such mistakes > ;-) but perhaps it would be good if phenix could flag situations such > as these. > > Luca > > On 6 Jan 2012, at 16:15, Pavel Afonine wrote: > >> Hi Luca, >> >> phenix.refine always generates a *.geo file that lists all the >> geometry restraints (bonds, angles, planarities, chiralities, >> dihedral, non-bonded, ncs(if any)) used in refinement for all atoms. >> For each restraint it list current model value, target (library) >> value, etc. >> >> Can you have a look at *.geo file for O-P bonds in question? May be >> this gives a hint about what's going on? >> >> Pavel >> >> On 1/6/12 4:31 AM, Luca Pellegrini wrote: >>> >>> Hi, >>> >>> I have noticed that Phenix mangles O-P bond lengths and angles in >>> the phosphate groups of my DNA chain (example in pict attached). >>> This only happens to 3 out of 28 phosphates. The refined protein-DNA >>> structure does not present any other unusual stereochemistry issues >>> and refinement runs normally. Could anybody advice on what is going >>> on and how to fix this, please? >>> >>> I am using Phenix-1.7.3-928. Refinement is with default target >>> weights, hydrogens on and does not include simulated annealing. I >>> could make the stereochemistry targets more stringent, but the >>> default values seem strict enough (bond and angle rmsd is 0.005 and >>> 1.225). >>> >>> Thanks, >>> Luca _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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Real_space_refinement at low resolution question
by fulvio saccoccia 20 Jan '12

20 Jan '12

Dear phenix users, I was wondering if it could be correct to exclude the real_space_refinement step working with a 3.3 A resolution map: I noted that in every real_space_refinemet step phenix told me that it was not useful. How can I exclude the routine from the command line? I am using 1.7.3-928 version.

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Real_space_refinement at low resolution question
by fulvio saccoccia 20 Jan '12

20 Jan '12

Dear phenix users, I was wondering if it could be correct to exclude the real_space_refinement step working with a 3.3 A resolution map: I noted that in every real_space_refinemet step phenix told me that it was not useful. How can I exclude the routine from the command line? I am using 1.7.3-928 version. Fulvio Saccoccia, PhD student Dept. of Biochemical Sciences Sapienza University of Rome

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problem converting PDB file to mmcif for deposition
by Salameh, Mohd A., Ph.D. 20 Jan '12

20 Jan '12

Hi Everybody, I encountered a problem recently in converting my PDB file to mmcif using the pdb_extract tool in rcsb. It simply writes out an empty file!! I wonder if any of you have faced such a problem before and know the solution!! I carefully examined the PDB file header and I couldn't really find a reason why this PDB failed to be converted. I only use PHENIX for molecular replacement and refinement. I used the default TLS refinement so I assume the whole structure will be refined as a group. I hope somebody is familiar with this can help me out. Thank you very much, Mohd

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real space correlation
by Jerome Nwachukwu 19 Jan '12

19 Jan '12

Hi: I am trying to run phenix.real_space_correlation from the command line and received the following error message. Is there a specific syntax i should use? Thank you, -Jerome Syntax error: expected "=", found "Date" (file "3_refine_001.pdb", line 1) Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/command_line/real_space_correlation.py", line 9, in <module> command_name = "phenix.real_space_correlation") File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/real_space_correlation.py", line 332, in cmd_run track_unused_definitions = True) File "/usr/local/phenix-1.7.1-743/cctbx_project/libtbx/phil/__init__.py", line 1718, in fetch assert source.name == self.name AttributeError: 'NoneType' object has no attribute 'name'

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noisy sa-omit maps in solvent region.
by Francis E Reyes 19 Jan '12

19 Jan '12

Hi phenixers I'm calculating a composite sa-omit map for my entire molecule at 4 A. While my molecule more or less has density (very good for backbone, not so much for sidechains), the solvent region seems to be particularly noisy. Is this the normal experience for composite sa-omit maps at this resolution? I'm particularly interested in what autobuild does when it 'stitches' the individual maps together, is it a direct stitch of the 2fo-fc's after refinement or is there some kind of real space density modification involved? Or a combination of both? Any suggestions appreciated, F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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adding exchangeable H to a perdeuterated structure with ready set?
by Maxime Cuypers 19 Jan '12

19 Jan '12

hello, how can i add exchangeable H to a perdeuterated structure with readyset? (other than manualy editing the file please) i see readyset does the opposite. thanks in advance Maxime

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an error in the operation of SF-Tool
by Dialing Pretty 19 Jan '12

19 Jan '12

Dear All, By the RCSB SF-Tool I have tried to convert my PDB file and the corresponding mtz file into mmCIF for the purpose of RCSB depositation, by the Automatic (default) mode. I got the following message: "Converting structure factor to mmCIF format.... Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done. Header of the mtz file can be seen from here Click here to see the converted mmCIF file" Obviously there is an error message, although the conversion is succesful. As for I intend to deposit the structure including the mmCIF file into RCSB, I am afraid I have lost some message in the MTZ file and mmCIF file. Will you please tell me how can I add the labels, which have been lost I think, to the mtz file, so that the labels message will also be included into the mmCIF file if it was necessary? Cheers, Dialing

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tool for dispersive difference fourier ?
by Francis E Reyes 17 Jan '12

17 Jan '12

I'd like to make a dispersive difference fourier using phases from a model. Is there a tool to do so? phenix.maps doesn't seem to have the 'map_type' to do this.. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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