Thank you Robbie! A bit clearer now to me..
On 10 September 2018 at 11:19, Robbie Joosten <[email protected]> wrote: > Hi Eleanor, > > You point out two major problems with PDB files. The TER record nightmare > is pretty bad. Although it seems that at least now they are written by > programs, they end op at the weirdest places due to aggressive addition of > the TERs. At the same time, they are sometimes missing when there are for > instance (mono/di)peptide ligands. The problem is that most programs that > write PDB files are not aware of the sequence of entire protein. That, or > they just blatantly ignore it. This should work better in mmCIF as long as > programs enforce the presence of a sequence for the macromolecular > entities. > > The charges thing has been getting on my nerves lately because most of the > time it is a load of dingo's kidneys. There is no localized integral charge > on the NH atoms of ARG! Neither is there for ASP and GLU sidechains, > especially not a 1+. The PDB is aware of the problem now, but the source of > these charges is not obvious. They do not seem to come from refinement > programs, but these programs do use the charges to modify the scattering > factors and write them out again. One hopes that this problem is solved > soon. > > Sorry for straying off topic. > > Cheers, > Robbie > > > -----Original Message----- > > From: CCP4 bulletin board <[email protected]> On Behalf Of Eleanor > > Dodson > > Sent: Monday, September 10, 2018 12:03 > > To: [email protected] > > Subject: Re: [ccp4bb] unexpected errors in LSQKAB > > > > Eugenere - are you responsible for mmdb? Could these features cause > > problems? > > Eleanor > > > > > > The PDB file Thern_tRNA has some anomalies - > > > > 1) several unneeded TER cards > > > > TER 399 LYS A 52 - there is a chain break here but not a > chain > > termination > > TER 3219 GLY A 421 > > > > > > TER 3343 GTP C -1 - Never sure about these but GTP is not part > of chain > > > > TER 4163 G C 37 > > TER 4967 A C 76 > > > > > > 2) Some of the atom types are unusual > > > > eg N1+ here instead of N > > > > I am not sure whether that is important of not. > > > > ATOM 22 NH1 ARG A 4 24.496 181.121 132.218 1.00103.17 > N1+ > > ANISOU 22 NH1 ARG A 4 15732 10019 13448 1911 785 -419 > N1+ > > > > > > > > > > On 10 September 2018 at 10:36, Eleanor Dodson > > <[email protected] <mailto:[email protected]> > wrote: > > > > > > Charlie - I will try to check this, but cant read your pse file - > can you > > find another format? > > > > Thanks Eleanor > > > > > > On 8 September 2018 at 12:28, Carter, Charlie <[email protected] > > <mailto:[email protected]> > wrote: > > > > > > Hi folks, > > > > > > I continue to use lsqkab because it offers unique > flexibility > > and features appropriate to what I do. > > > > > > Currently, I’ve a project that requires such superposition > and > > for that I created from the original pdb files a set of monomeric pdb > files that > > have already been superposed by POSA. The POSA alignment used all the > > residues, and I want to orient only a subset that is structurally > invariant, in > > order to identify possible interdomain motions. > > > > > > There are ten such files; eight appear to work properly and > > have aligned. The other two give one or another of two pathologies. The > first > > appears simply to get confused and output a rotated coordinate file that > > appears to be ~90 degrees off, despite the fact that the residue > numbering is > > correct (see attached .pse file in which three _Urz coordinate sets are > > illustrated, which were superimposed on Ecoli_Urz. The Ttherm_H file is > > correctly rotated; the Stau_LF file is not.). > > > > > > I decided to try to rotate the two files into an > intermediate > > orientation that gave a satisfactory result, i.e. Ttherm_H. The first > attempt at > > this involved a second problematic file, Ttherm_tRNA. LSQKSB gave the > > following error message, which instructs me to contact the developers. > The > > problematic pdb file, Ttherm_tRNA.pdb, is also attached. > > > > > > > > > > *** RWBROOK error: point code unit function > > *** 1 -102 2 MMDB_F_Atom > > *** file : Ttherm_tRNA_rot.pdb > > *** reason : internal error #2 -- report to developer > > *** Execution stopped. > > > > > > I should note that I am still using the following version > of the > > software: > > > > > > source /usr/local/bin/ccp4-7.0/include/ccp4.setup > > > > > > The commands in my script are: > > > > > > > > #source /usr/local/bin/ccp4-7.0/include/ccp4.setup > > lsqkab XYZINM $1 XYZINF $2 XYZOUT $1_rot.pdb << END- > > lsqkab > > FIT RESIDUE MAIN 8 TO 82 > > MATCH 10 to 84 > > FIT RESIDUE MAIN 83 TO 111 > > MATCH 85 to 113 > > FIT RESIDUE MAIN 122 TO 129 > > MATCH 124 to 131 > > OUTPUT XYZ > > END > > END-lsqkab > > > > > > Many thanks in advance for any help. > > > > > > > > > > > > > > > > > > > > > > > > > > > > ________________________________ > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
