VMD-L Mailing List
From: Ashar Malik (asharjm_at_gmail.com)
Date: Sat Jan 17 2015 - 21:14:19 CST
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Thanks for all the answers.
Makes perfect sense now. :)
On Sun, Jan 18, 2015 at 4:18 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> Hi Ashar,
>
> Its not hidden data, its the limitations of floating point arithmetic. VMD
> reads in the decimal number, and stores it internally as the nearest double
> precision floating point number. Since floating point uses base 2, not base
> 10, many decimal numbers cannot be cleanly expressed, and are rounded
> internally to their closest floating point representation. Tcl returns this
> floating point representation converted back to decimal, which usually
> means a number with 15-16 digits after the decimal place.
>
> -Josh Vermaas
>
>
> On 01/17/2015 05:57 AM, Michail Palaiokostas Avramidis wrote:
>
> My initial answer was based on the following:
>
>
> A PDB file is a txt file with a special structure, interpreted as a
> coordinate file by special programs. Other than that, it does not include
> any "hidden" data. What you see is what you get apart maybe from some
> special format characters such as \t, \n etc.
>
>
> Having said that, the "problem" must be on the interpretation program
> (so in this case VMD). As you can also see in the TCL wiki:
> http://wiki.tcl.tk/11969 ,what you observe is normal.
>
> Just to be safe however, try to initialize the variables first.
> Alternatively, try the example of the wiki. Make two variables, 0.1 and
> 0.3, print them, sum them and see if what you get is exactly
> 0.400000000000.
>
>
> Best,
>
> Michalis
>
>
> -------------------------------------------------------------------
> Michail (Michalis) Palaiokostas-Avramidis
> PhD Student
> School of Engineering and Materials Science
> Queen Mary, University of London
> United Kingdom
> LinkedIn Profile
> <https://www.linkedin.com/pub/michalis-palaiokostas-avramidis/31/ba/312>
> -------------------------------------------------------------------
> ------------------------------
> *From:* Ashar Malik <asharjm_at_gmail.com> <asharjm_at_gmail.com>
> *Sent:* Saturday, January 17, 2015 11:01 AM
> *To:* Michail Palaiokostas Avramidis; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: Is a PDB file hiding something ???
>
> I would disagree with that.
>
> here is why:
>
> This is in the pdb:
> 71.696 112.940 -84.327
>
> after using the code the output is:
>
> {71.69599914550781 112.94000244140625 -84.3270034790039}
>
> If you observe the x-coordinates -- 71.696 is in the PDB which is being
> read into TCL by the script i sent earlier and it shows 71.695999 .,.. that
> means that PDB TEXT file was displaying a rounded off number. Where as --
> somehow when the TCL script read the PDB TEXT file ... it produced --
> 71.69599.. which is the un-rounded off number.
>
> On Sat, Jan 17, 2015 at 11:23 PM, Michail Palaiokostas Avramidis <
> m.palaiokostas_at_qmul.ac.uk> wrote:
>
>> Hi Ashar,
>>
>> I think that a coordinate is stored as a double precision number in the
>> memory. However the PDB file contains only a fraction of a double number's
>> decimals. Therefore the rest are filled with what the memory had before. If
>> it is important for you to have zero's in that level, I suppose you can
>> find a way to initialize the variables in a way that gives 0 for all digits.
>>
>> Hope that helps.
>>
>> Best,
>> Michail Palaiokostas
>>
>>
>> ---- Ashar Malik wrote ----
>>
>>
>> Hi,
>>
>> The coordinates in the PDB file of an atom are:
>>
>> 75.146 114.983 -86.817
>>
>> using
>>
>> for {set i $first} {$i < $last} {incr i} {
>> set sel3 [atomselect top "resid $i and name C1'"]
>> puts [$sel3 get {x y z}]
>> }
>>
>> they are returned as:
>>
>> {75.14600372314453 114.98300170898438 -86.81700134277344}
>>
>> Question:
>>
>> Maybe I am missing some understanding of something here:
>>
>> How does VMD/TCL script get the higher precision??
>>
>> Any comments anyone ??
>>
>> --
>> Best,
>> /A
>>
>
>
>
> --
> Best,
> /A
>
>
>
-- Best, /A
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