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Subject:

Re: unexpected errors in LSQKAB

From:

Robbie Joosten <[log in to unmask]>

Reply-To:

Robbie Joosten <[log in to unmask]>

Date:

Mon, 10 Sep 2018 10:19:10 +0000

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text/plain

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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 <[log in to unmask]> On Behalf Of Eleanor 
> Dodson 
> Sent: Monday, September 10, 2018 12:03 
> To: [log in to unmask] 
> 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 
> <[log in to unmask] <mailto:[log in to unmask]> > 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 <[log in to unmask] 
> <mailto:[log in to unmask]> > 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. 
>  
>  
>  
>  
>  
>  
>  
>  
>  
>  
>  
>  
>  
> ________________________________ 
>  
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