- phenixbb - phenix-online.org

Average maps (*not* NCS averaging)
by Stephen Graham 11 Mar '11

11 Mar '11

Hi there, I'd like to average 2Fo-Fc maps from 2 (approximately) isomorphous data sets (one with ligand, one without) to see whether I get better density for some of the noisier bits of the structure. I don't want to do any kind of solvent flattening, histogram matching, cyclical averaging, etc; I just want to sum the equivalent pixels and divide by 2. Is it possible to do this easily using any of the phenix tools? It seems like all the required plumbing is there with get_cc_mtz_mtz or superpose_maps, but I can't find a phenix utility for averaging two superposed maps. Thanks, Stephen -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

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Re: [phenixbb] [ccp4bb] Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
by Francois Berenger 10 Mar '11

10 Mar '11

Sorry, I forgot to mention about what is the .obj file I need. It is a pure ASCII geometric description of a polyhedra. Cf. http://en.wikipedia.org/wiki/Wavefront_.obj_file It looks rather easy to parse compared to some VRML file, for example. Thanks, F. Francois Berenger wrote: > Hello, > > What are the good software to do this? > > I already know of Pymol and Jmol. > > Both can export the result to a .obj file, which is interesting for > later processing. > > However, Pymol's algorithm is not exactly what Connolly described, > cf. > http://www.mail-archive.com/[email protected]/msg00179.html > > Also, Pymol will save the surface with some translation and rotation > which are not present in the PDB read in, which is a real pain. > > For Jmol, sometimes the surface is not a closed polyhedra, so > it is kind of useless for my purpose. > > I know of MSMS, but I don't think it is that robust (I read some source > code where someone was using MSMS, the source code had many dirty things > in order to try handling the apparently many cases where MSMS was > crashing). > > Is there something freely usable for research, using beta shapes > internally, for example? That should be a robust approach. > > A robust software would be much appreciated (not crashing, whatever > the PDB we give it as input). > Open source and not in Fortran would be heaven. ;) > > Thanks a lot for suggestions, > F.

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Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
by Francois Berenger 10 Mar '11

10 Mar '11

(was posted on CCP4 bb also) Hello, What are the good software to do this? I already know of Pymol and Jmol. Both can export the result to a .obj file, which is interesting for later processing. However, Pymol's algorithm is not exactly what Connolly described, cf. http://www.mail-archive.com/[email protected]/msg00179.html Also, Pymol will save the surface with some translation and rotation which are not present in the PDB read in, which is a real pain. For Jmol, sometimes the surface is not a closed polyhedra, so it is kind of useless for my purpose. I know of MSMS, but I don't think it is that robust (I read some source code where someone was using MSMS, the source code had many dirty things in order to try handling the apparently many cases where MSMS was crashing). Is there something freely usable for research, using beta shapes internally, for example? That should be a robust approach. A robust software would be much appreciated (not crashing, whatever the PDB we give it as input). Open source and not in Fortran would be heaven. ;) Thanks a lot for suggestions, F.

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automr renumbered all residues to 0 for final solution in dev-674
by Francis E Reyes 10 Mar '11

10 Mar '11

Is this fixed in a later version? Thanks! F --------------------------------------------- Francis E. 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

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Sorry, I meant judging by distances it is not experiencing interaction in the form of H-bonds. Which I think is concerning.

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Hi Pavel, What I meant it was just that the 2mFo-2DFc map looks really great and corroborates experimental data as far as the stereochemistry. But I dont understand ehy the carbonyl moiety of the ligand would be where it is now, no "driving force to be here". And when I look at my averaged kick and SA omit map it looks ambiguous. Any help?

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Hello everyone, I have this strucuture I solved by Molecular replacement. It is a single mutant of previously solved enzyme. I started refining it and fit the ligand in a way that gives me the experimental stereochemistry. The final map 2mFo-2DFc looks great. After further examination I noticed, I have a carbonyl that does not seem to be bound to anything !!! I started looking at my average kick and SA composit omit-map prior to modeling in the ligand and now I am really lost. Could anyone help? Thank you

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Important change in phenix.refine output: MTZ file with data and map coefficients
by Pavel Afonine 04 Mar '11

04 Mar '11

Hi Everyone, starting development version dev-686: http://www.phenix-online.org/download/nightly_builds.cgi phenix.refine does not output *map_coeffs.mtz file. Instead, it creates prefix_serial.mtz file (example: lysozime_001.mtz) containing four sections: - section 1: Original input data (Iobs or Fobs, and HL coefficients if provided) and flags (as supplied in input); - section 2: Experimental data used in refinement (labels: F-obs-filtered, SIGF-obs-filtered). This can be different from "Original data" due to Iobs->Fobs conversion (if input data are intensities) and outliers filtering; - section 3: Contains total model structure factors (labels: F-model, PHIF-model) used everywhere in refinement (for the formula, see: http://www.phenix-online.org/documentation/fmodel.htm). In the future, this section might be extended to explicitly list all contributions to Fmodel, such as Fcalc (corresponding to atomic model), Fbulk (bulk solvent contribution), and so on. - section 4: Fourier map coefficients (exactly the same as used to be in *map_coeffs.mtz file). This change is meant to reduce the confusion when people tended to use *map_coeffs.mtz file for refinement and PDB deposition, and facilitates the reproduction of refinement statistics (R-factors, for example). Also, thanks to Jeff Headd, by default phenix.refine now converts input intensities (Iobs) to amplitudes (Fobs) using French & Wilson method (Acta Cryst A34, 517, 1978), so no need to run a specific program (Truncate, for example) to do this. To see the content of a MTZ file use phenix.mtz.dump command: phenix.mtz.dump data.mtz Pavel.

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Geometry problem with sugars refined in phenix
by Tirumala Kumar Chowdary 03 Mar '11

03 Mar '11

Hi, I have refined a structure with NAGs linked to ASNs at 3 places in my structure. I used the right link definitions and the NAG definitions are from Phenix library. Phenix refined all the sugars right and made the right links between the NAGs. However, while submitting, PDB found problem with the geometry of NAGs linked to the ASN at two places. This is the issue -the atoms around C1 atom of the sugar molecule NAG A #810 and NAG A #1670 are on a plane and the C1 atom center is far off to be tetrahedral. Please, verify the chirality of C1 and provide the correct coordinates if necessary.- Any ideas on how to fix the geometry of these sugars will be of great help. Regularization and real space refine in Coot is not working or I don't know how to do it. I am looking for alternative ways to fix this problem. Thank You Tirumal

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Re: [phenixbb] number of cycles
by Maia Cherney 01 Mar '11

01 Mar '11

Hi, I am using now the latest phenix version and I am curious how to understand these lines: Flipped N/Q/H residues before refinement: A 28 HIS A 72 HIS A 141 GLN A 202 GLN A 296 ASN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 388 HIS Maia

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