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<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas">Dear All,</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> </SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas">I�m refining a 2.1A</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> <FONT FACE="Consolas">with phenix 1.5-2 and get</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> <FONT FACE="Consolas">when I click on automatically add hydrogens to model</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> <FONT FACE="Consolas">following</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas"> error message:</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> <FONT FACE="Consolas">refinement</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas">.</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas">pdb_interpretation.clash_guard.failure: Number of nonbonded interaction distances <</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas"></FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> <FONT FACE="Consolas">0.5:391</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">I suppose that this comes, because coo</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas">t mixes up the hydrogens. </FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">See</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> </SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas">Re: [COOT] hydrogen restraints</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">Paul Emsley</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">Wed, 09 Dec 2009 14:11:34 -0800</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">Sara Zueger wrote:</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> Hi everybody,</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">Hi Sara,</FONT></SPAN></P>
<BR>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> as I did not find a final solution to the hydrogen restraints problem</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> (flying or exploding during real space refinement) in any of the mailing</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> lists, I wanted to pick this topic up again.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> If one adds hydrogens by phenix.ready_set or reduce the labels for these</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> hydrogens on let's say a Cbeta atom will be HB2 and HB3 (according to the</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> pdb v3.2 convention). However, the coot/ccp4 library names them HB1 and HB2,</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> so there are no restraints for HB3 atoms. I see that probably this naming</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> problem can be overcome by using phenix.reduce -OLD, or renaming them</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> manually in the pdb file (but if one deposits the structure to PDB does one</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> have to name them back again?). Is there already some new solution?</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">There is not a solution yet.</FONT></SPAN></P>
<BR>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> And how about hydrogen restraints for the most N-terminal amino acid, where</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> one has H1, H2 and H3? How are these handled? There seem to be no restraints</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas"> for those as well, because they also fly around during real space refinement.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">Same situation.</FONT></SPAN></P>
<BR>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">We need to do some drudge work to convert the hydrogen names in the libraries. AFAICS it is straightforward, but just hasn't been done by anyone in the CCP4/Coot community.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">I wonder what dictionary the Phenix fellow use? If they have updated the dictionary to 3.2 format, perhaps we could use their copy too.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">(However, we deal with this, it should be done by the end of the 0.7.x series.)</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">Paul.</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">What can</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas"> -</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas"> should I do now, to get my structure in the pdb</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas">, because just to remove them is according to</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> <FONT FACE="Consolas">the manual not allowed</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> </SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">See:</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas">To remove hydrogens from a model:</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">% phenix.pdbtools model.pdb remove="element H or element D"</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">or Reduce programs can be used for this:</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">% phenix.reduce model_h.pdb -trim > model_noH.pdb</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">We strongly recommend to not remove hydrogen atoms after refinement since it will make the refinement statistics (R-factors, etc...) unreproducible without repeating exactly the same refinement protocol.</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas">2.</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> <FONT FACE="Consolas">Have you ever seen that coot looses the restraints? I have a heme in the structure which</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas"> I could refine without any problems, but now he gives me</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> <FONT FACE="Consolas">following</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas"> error message:</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> </SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas">No restraints found</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas"> Non-existent or minmal description of restrained residues.</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"> <FONT FACE="Consolas">Are you sure that you read a non-minimal mmCIF dictionary for this monomer? Are you sure the PDB residue name matches the dictionary residue name?</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">If not, try File -Import CIF dictionary</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">Alternatively, did you check that</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"><FONT FACE="Consolas"> the atom names of the PDB file matches those of the restraints.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">Thank you very much for your help.</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Consolas">Georg</FONT></SPAN><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="en-us"></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"></SPAN><SPAN LANG="de"><FONT FACE="Consolas">-----Urspr�ngliche Nachricht-----<BR>
Von: phenixbb-bounces@phenix-online.org [<A HREF="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</A>] Im Auftrag von jonathan elegheert<BR>
Gesendet: Dienstag, 19. J�nner 2010 18:32<BR>
An: PHENIX user mailing list<BR>
Betreff: Re: [phenixbb] twin refinement in phenix-1.5-2</FONT></SPAN><SPAN LANG="de-at"></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">Hi Kelly,</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">I encountered the same with later nightlies than 1.5-2 also. The problem </FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">is the "fix_rotamers = True " command. You have to return it to its </FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">default value "None".</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">Apparently, some subroutines like that one don't work with twin_f_lsq </FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">algorithm. I believe because the fix_rotamers function depends on a map </FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">cc calculation which also in itself doesn't work with twin_f_lsq.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">At least that's my understanding.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">Jonathan Elegheert</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">PhD student</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">Ghent University</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">Kelly Daughtry wrote:</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> Hello all,</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> I am wondering if anyone has run across this problem and knows how to fix it.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> I have a twinned dateset and I am using phenix.refine to refine the dataset.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> I have the full 1.5-2 installation.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> When I include the twin law (-k, -h, -l) in the refinement, I get this error:</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> File "/usr/swr/phenix-1.5-2/cctbx_project/mmtbx/twinning/twin_f_model.py",</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> line 1651, in map_coefficients</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> "m_gradient"</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> AssertionError</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> If I do not include the twin law, I do not get the error and the</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> refinment continues as normal.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> When I downgraded to Phenix.1.4-3 (full install), And use the same</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> twin law, I am able to run phenix.refine without an error.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> I have attached my definition file for phenix.1.5-2 amd the log file.</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> Thanks in advance for any help you can provide,</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> Kelly Daughtry</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> *******************************************************</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> Kelly Daughtry</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> PhD Candidate</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> Department of Physiology and Biophysics</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> Boston University School of Medicine</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> 590 Commonwealth Ave</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> R 390</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> Boston MA, 02215</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> (P) 617-358-5548</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> *******************************************************</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> ------------------------------------------------------------------------</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">></FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="de-at"><FONT FACE="Consolas">> _______________________________________________</FONT></SPAN></P>
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