[gmx-developers] Coordinate scaling in pdbio.c

[David van der Spoel]

On 2012-04-10 21:10, Anton Feenstra wrote:
> On 09/04/12 21:47, Justin A. Lemkul wrote:
>>
>>
>> Radhakrishna Bettadapura wrote:
>>> All,
>>>
>>> I'm trying to figure out why a pdb input to pdb2gmx results in
>>> coordinates that are scaled by a factor of 0.1. That is, if a line in
>>> the PDB file reads
>>>
>>>
>>> ATOM 1 N ALA B 3 -1.221 20.481 12.450 1.00 34.64 N
>>>
>>> then the corresponding line in the .gro file reads
>>>
>>> 3ALA N 1 -0.122 2.048 1.245
>>>
>>> The culprit seems to be the following lines in pdbio.c:
>>>
>>> static int read_atom(t_symtab *symtab,
>>> char line[],int type,int natom,
>>> t_atoms *atoms,rvec x[],int chainnum,gmx_bool bChange)
>>> {
>>>
>>> // do stuff
>>>
>>> x[natom][XX]=strtod(xc,NULL)*0.1; /*all coordinates scaled by 0.1...
>>> why?*/
>>> x[natom][YY]=strtod(yc,NULL)*0.1;
>>> x[natom][ZZ]=strtod(zc,NULL)*0.1;
>>>
>>> //do more stuff
>>>
>>> }
>>>
>>>
>>> There's also a line in the output function that multiplies all
>>> incoming coordinates by 10 before writing it to output:
>>>
>>> void write_pdbfile_indexed(FILE *out,const char *title,
>>> t_atoms *atoms,rvec x[],
>>> int ePBC,matrix box,char chainid,
>>> int model_nr, atom_id nindex, atom_id index[],
>>> gmx_conect conect, gmx_bool bTerSepChains)
>>> {
>>>
>>>
>>> //do stuff...
>>>
>>>
>>> fprintf(out,pdbform,pdbtp[type],(i+1)%100000,nm,resnm,ch,resnr,
>>> (resic == '\0') ? ' ' : resic,
>>> 10*x[i][XX],10*x[i][YY],10*x[i][ZZ],occup,bfac,atoms->atom[i].elem);
>>> // do more stuff...
>>>
>>> }
>>>
>>>
>>> Can someone tell me why this coordinate scaling occurs? And why the
>>> scale factor is a single hard-coded number than, say, something that
>>> depends on the input?
>>>
>>
>> PDB coordinates are in Angstrom, while .gro coordinates are in nm. Hence
>> the conversion factor of 0.1.
>
> What happened to A2NM and NM2A?
> In my (4.0.5, yes that is very old) includes/physics.h I still see:
>
> #define A2NM (ANGSTROM/NANO) /* NANO */
> #define NM2A (NANO/ANGSTROM) /* 10.0 */
>
> Why aren't these still used for that?
>
>
At some stage macros were removed from the code, even though these seem 
rather harmless. I agree that it is confusing to hard code these 
numbers. If we cannot use macro's like this we should probably replace 
them by
static const real ANGSTROM=1e-10;
static const real NANO=1e-9;

etc.

Comments?


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se