- phenixbb - phenix-online.org

XYZ refinement vs individual sites refinement
by Yuri 13 Mar '11

13 Mar '11

I am new to phenix and I am trying to probe two residues that are putative H-bond partners, after refinement they seem to be put in orientations that would make it impossible for them to be interacting with a ligand. My SA composite omit map may suggest that one of the Asn could be in a different position. My question: If I manually change its conformation is it wise to keep its position fixed during refinement to see what the new maps would look like? If so where would I do that under the real space or individual sites tab on GUI phenix? I am not sure what these 2 tasks accomplish exactly. Any guidance would be appreciated. Thanks Yuri Pompeu

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Fwd: XYZ refinement vs individual sites refinement
by Yuri 13 Mar '11

13 Mar '11

Thats better! thank you

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most appropriate map for ligand fitting/interaction with FMN
by Yuri 13 Mar '11

13 Mar '11

I am refinig a structure at 2.1 A. I have 2 questions: a) Is the best way to identify a ligand refining the protein and water molecules and at the end looking at the 2mfo-dfc and mfo-dfc maps? Or looking at a SA composit omit map? b) In almost every map i look at during refinement I see density that smears/joins my ligand (cyclopentenone type molecule) and flavin's isoalloxazine ring. Has anyone ever seen that? they seem to be 3.1 A apart? Thanks -- Yuri Pompeu

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Elbow problem
by Jerome Nwachukwu 11 Mar '11

11 Mar '11

Hi all: For some reason, phenix.elbow converts a specific double-bond (C=C) in my ligand to a single bond (C-C) and therefore generates a wrong .cif file. Is there away to avoid or correct this problem? Thank you, -Jerome Jerome C. Nwachukwu, PhD Kendall Nettles' Lab Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

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Binary Installation failure on Ubuntu
by Katherine Sippel 11 Mar '11

11 Mar '11

Hi all, I am trying to install the latest nightly build (dev-694) using the Kernel 2.6 (64-bit; Fedora Core 3) binary. The OS is Ubuntu 10.10 installed as a dual boot through Wubi. I get as far as configuring PHENIX components at which point it heaves out a binary.log file. I can send the whole file to anyone whose interested but it's a bit too large for the bb. The juicy bit is as follows... Could not find platform independent libraries <prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site How can I determine which libraries are missing? Thanks for any help you can provide, Katherine

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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 11 Mar '11

11 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 11 Mar '11

11 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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