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Re: [Psisoft-devl] high contact
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From: Dan B. <dm...@mr...> - 2004-08-12 10:00:17
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Cheers Wan! How are you mapping scop domain def to PQS? On Thu, 12 Aug 2004, Wan Kyu Kim wrote: >Hi, > >I would like to add a few PDBugs. > ># next if ($mpdb =~ /^(1cwq|1e0p|1gtw|1cm4)$/) ; ### same model with >different chain identifier > >I am using PQS coordinates for X-ray crystallography structures, >which solves many such problems (i.e. 1g7y is splitted into 3 files >without overlap.) > >cheers > >wan > >>The solution (in my experience) is to just apply manual filtering of such >>structures after applying statistics. When I find these things I delete >>them from my psimap database. >> >>These things are so abhorrent they generally skew any analysis by miles, >>allowing us to recognize the problem immediatly. >> >>This mailing list is the perfect place to keep up to date on 'problem >>structures', as subtle different analysis can show up different problems. >> >> >>For example I have the following code in my psimaper... >> >>my $st = " >> SELECT a.PDB, a.SUNID, a.DOMAIN, a.NEAT_SCCS >> FROM $scopDb.domain a # Domain table >> INNER JOIN $pdbDb.pdb b # PDB table >> ON a.PDB = b.PDB >> WHERE ( >> b.TYPE = 'X-RAY DIFFRACTION' # PDB criteria >># OR b.TYPE = 'SYNCHROTON DIFFRACTION' # >># OR b.TYPE = 'NMR' # >># OR b.TYPE = 'ELECTRON MICROSCOPY' # >># OR b.TYPE = 'NEUTRON DIFFRACTION' # >># OR b.TYPE = 'FIBER DIFFRACTION' # >># OR b.TYPE = 'THEORETICAL MODEL' # >># OR b.TYPE = 'FLUORESCENCE' # >> ) # >># AND b.RESOLUTION < 2 # >> "; >> >>The above helps a lot with subsequent domain assignment. >> >>And... >> >> next if $pdb eq '1gtv'; # Multi-Model PDB entries >> next if $pdb eq '1cm4'; # >> next if $pdb eq '1cwq'; # >> next if $pdb eq '1e0p'; # >> next if $pdb eq '1gu8'; # >> >> next if $pdb eq '4cpa'; # Contains null chain AND >> # named chain! >> # PDB stubournly refuse to fix, >> # so you should complain! >> >> >> next if $pdb eq '1g7y'; # Contain 'significant' >> next if $pdb eq '1ygp'; # crystal overlap between >> next if $pdb eq '1hb9'; # subunits - PDB will fix. >> next if $pdb eq '1hb5'; # >> >> >>I see that they don't fully overlap with yours which is interesting. We >>should make a community webpage to name and same these pdb structures. >> >>I call it PDBug, lets set up a Bugzilla! >> >> >> >>I am doing a simple analysis of interface density, where I compare the >>number of residues on each side of a domain-domain interface (a simple >>plot shows an interesting trend). This analysis showed up this problem >>structure... >> >>1ona >> >>Which is a problem both in the PDB and with my domain parser... Anyway it >>has an unnatural 'domain interface' mediated by a mis-labeled ligand. >> >> >>Is Wan a psimapper? I bet he knows of some PDB problems. >> >> >>All the above problems should be fixed by using MSD. I am planning to >>write an O-rily book (mini) called 'MSD', basically because I like the >>idea of adding a virus into the O-rily taxonomy (using a picture of a >>virus from the 3D structure in MSD). >> >>We should start using MSD with PSIMAP ASAP. We can write the book after >>that. MSD will ... >> >> Fix multimodel PDB / NMR structures. >> Fix problems mapping PDB to SwissProt. >> Automatically provide sequence / sturcture alignments. >> Provide clean ;) SCOP/CATH/PFAM/DALI (e-family) assignments to structues. >> Provide clean ligand assignments to stuctures. >> Give us 'biomolecule' data >> Filter crystal contacts >> Do away with the need for parsers in PSIMAP. >> Allow easy integration of domain-domain, domain-ligand and ligand-ligand >>information >> >> etc., etc. >> >> >> >>P.S. I did an analysis of residue connectivity statistics for a second >>year report. >> >> >>You can find this at... >> >>http://interaction.mrc-dunn.cam.ac.uk/Scientists/Dan_Bolser/MyDoc/New%20Folder/ >> >>(I may change the folder name without warning.) >> >> >>Just let me know if you want to turn this into a paper with some extra >>work (actually it looks quite comprehensive). I can work closly with >>anyone on this topic, as I still remeber the literature and the problems >>in detail. >> >>I am half planning to revive this report into a thesis chapter anyway, so >>any help I can get would be great ;) >> >> >>All the best, >>Dan. >> >> >> >>On Wed, 11 Aug 2004, Andreas Henschel wrote: >> >> >> >>>Hi psimap folks, >>> >>>I found some pdb entries that look like superimposed structures, a >>>structural alignment of very similar (they are not NMR!) >>>that cause trouble to psimap. One of them is 1cm4. I found out about >>>them when I counted contacts per residue and some where as high as 50, >>>thus falsifying my hotspot statistics. >>> >>>Also, these guys have suspiciuosly high contact residues: >>>| 1ae6 | >>>| 1bwm | >>>| 1cm4 | >>>| 1cr9 | >>>| 1cu4 | >>>| 1eo8 | >>>| 1ob1 | >>>| 1qfu | >>>For the moment, I will ignore them. >>>Any idea? >>>Cheers, >>>Andreas >>> >>> >>> >>>------------------------------------------------------- >>>SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media >>>100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 >>>Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift. >>>http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 >>>_______________________________________________ >>>Psisoft-devl mailing list >>>Psi...@li... >>>https://lists.sourceforge.net/lists/listinfo/psisoft-devl >>> >>> >>> >> >> >> > > > |
