VMD-L Mailing List

From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Wed Mar 19 2014 - 08:44:01 CDT

Hi John,

That is what I was looking for. I did not know that you could call "altloc".

So, in conclusion, this is the tcl that I am using in the end:

mol new 4HBC.pdb
set myprotein [atomselect 0 "protein and (altloc \"\" or altloc \"A\")"]
$myprotein writepdb 4HBC_p.pdb
quit

Notice that generation of the corresponding psf files will come later and
therefore this thread is unrelated to psfgen. I mistakenly assumed that it
would be. The record is now rectified.

Thank you.

Ivan

Ivan Gregoretti, PhD
Bioinformatics

On Tue, Mar 18, 2014 at 6:12 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> Here is an example for you:
> mol new 4hbc
>
> atoms that are members of all conformations:
> set allconf [atomselect top "altloc \"\""]
> $allconf num
> output of the 'num' query is: 3528
>
> atoms that are only in conformation A, and not any others:
> set aconf [atomselect top "altloc \"A\""]
> $aconf num
> output of the 'num' query is: 63
>
> all atoms that are in conformation A:
> set allAconf [atomselect top "altloc \"\" or altloc \"A\""]
> $allAconf num
> output of the 'num' query is: 3591
>
> You can see what altloc fields exist using the "Selections"
> tab of the graphical representations window, and selecting
> the "altloc" field in the "Keyword" list in the bottom left pane.
>
> Let us know if you have further questions on this...
>
> Cheers,
> John
>
>
> On Tue, Mar 18, 2014 at 02:53:18PM -0400, Ivan Gregoretti wrote:
> > Hello everybody,
> >
> > The 4HBC structure from www.pdb.org contains some atoms with
> alternate
> > locations.
> >
> > "Alternate location indicator" is documented here:
> > http://www.wwpdb.org/documentation/format33/sect9.html#ATOM
> >
> > Could somebody show an example tcl script to show how to select only
> one
> > of the alternate location?
> >
> > To make it more clear for everybody and for posterity, this is the
> > specific case of 4HBC. It has two Glutamates in position 4 and 5 but
> the
> > one at position 4 has atoms with alternate locations. See an excerpt
> of
> > 4HBC.pdf below
> >
> > ...
> > ATOM 23 N GLU H 4 -18.496 13.736 -4.183 1.00
> > 15.67 N
> > ANISOU 23 N GLU H 4 1974 1712 2266 -240 -130
> > -234 N
> > ATOM 24 CA AGLU H 4 -19.388 14.888 -4.131 0.50
> > 16.69 C
> > ANISOU 24 CA AGLU H 4 2047 1755 2537 -198 83
> > -300 C
> > ATOM 25 CA BGLU H 4 -19.411 14.883 -4.050 0.50
> > 16.19 C
> > ANISOU 25 CA BGLU H 4 1921 1779 2449 -254 135
> > -337 C
> > ATOM 26 C GLU H 4 -18.582 16.106 -3.757 1.00
> > 17.44 C
> > ANISOU 26 C GLU H 4 2129 1850 2645 -409 69
> > -49 C
> > ATOM 27 O GLU H 4 -17.847 16.090 -2.749 1.00
> > 16.19 O
> > ANISOU 27 O GLU H 4 2098 1487 2563 -451 125
> > -315 O
> > ATOM 28 CB AGLU H 4 -20.547 14.696 -3.145 0.50
> > 20.39 C
> > ANISOU 28 CB AGLU H 4 2213 2491 3041 -473 251
> > 61 C
> > ATOM 29 CB BGLU H 4 -20.363 14.711 -2.860 0.50
> > 17.05 C
> > ANISOU 29 CB BGLU H 4 1827 1976 2672 -890 118
> > -296 C
> > ATOM 30 CG AGLU H 4 -21.763 15.525 -3.538 0.50
> > 20.47 C
> > ANISOU 30 CG AGLU H 4 2244 2203 3330 -299 617
> > 42 C
> > ATOM 31 CG BGLU H 4 -21.391 13.611 -3.001 0.50
> > 16.46 C
> > ANISOU 31 CG BGLU H 4 2070 1310 2875 -662 301
> > -564 C
> > ATOM 32 CD AGLU H 4 -22.702 15.816 -2.392 0.50
> > 26.30 C
> > ANISOU 32 CD AGLU H 4 2917 3370 3704 -99 1106
> > 151 C
> > ATOM 33 CD BGLU H 4 -22.387 13.818 -4.137 0.50
> > 18.00 C
> > ANISOU 33 CD BGLU H 4 1901 1926 3010 -474 336
> > -524 C
> > ATOM 34 OE1AGLU H 4 -22.562 15.182 -1.330 0.50
> > 33.40 O
> > ANISOU 34 OE1AGLU H 4 4469 4323 3897 301 589
> > 351 O
> > ATOM 35 OE1BGLU H 4 -22.569 14.950 -4.604 0.50
> > 19.11 O
> > ANISOU 35 OE1BGLU H 4 2342 2121 2795 -217 233
> > -484 O
> > ATOM 36 OE2AGLU H 4 -23.576 16.695 -2.558 0.50
> > 29.87 O
> > ANISOU 36 OE2AGLU H 4 2647 3962 4740 -163 1014
> > 1053 O
> > ATOM 37 OE2BGLU H 4 -23.021 12.822 -4.538 0.50
> > 20.78 O
> > ANISOU 37 OE2BGLU H 4 2060 2331 3501 -511 275
> > -1045 O
> >
> > ATOM 38 N GLU H 5 -18.726 17.150 -4.589 1.00
> > 15.93 N
> > ANISOU 38 N GLU H 5 1889 1443 2719 116 120
> > -308 N
> > ATOM 39 CA GLU H 5 -18.049 18.406 -4.374 1.00
> > 16.04 C
> > ANISOU 39 CA GLU H 5 1953 2033 2107 -277 81
> > -454 C
> > ATOM 40 C GLU H 5 -18.937 19.321 -3.565 1.00
> > 16.42 C
> > ANISOU 40 C GLU H 5 1938 2160 2140 -296 9
> > -635 C
> > ATOM 41 O GLU H 5 -20.179 19.262 -3.616 1.00
> > 18.96 O
> > ANISOU 41 O GLU H 5 1998 2422 2783 -619 -28
> > -523 O
> > ATOM 42 CB GLU H 5 -17.673 19.112 -5.679 1.00
> > 16.38 C
> > ANISOU 42 CB GLU H 5 2052 1832 2339 -159 121
> > -316 C
> > ATOM 43 CG GLU H 5 -16.912 18.255 -6.701 1.00
> > 17.54 C
> > ANISOU 43 CG GLU H 5 2275 2182 2205 191 -327
> > -544 C
> > ATOM 44 CD GLU H 5 -17.793 17.402 -7.584 1.00
> > 16.66 C
> > ANISOU 44 CD GLU H 5 1966 1865 2497 -2 -304
> > -256 C
> > ATOM 45 OE1 GLU H 5 -19.019 17.248 -7.320 1.00
> > 17.80 O
> > ANISOU 45 OE1 GLU H 5 2167 2177 2419 -16 -252
> > -609 O
> > ATOM 46 OE2 GLU H 5 -17.227 16.890 -8.585 1.00
> > 18.14 O
> > ANISOU 46 OE2 GLU H 5 2213 2270 2408 -43 -249
> > -110 O
> > ...
> >
> > Thank you,
> >
> > Ivan
> >
> > Ivan Gregoretti, PhD
> > Bioinformatics
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/