select BONDS
does not ever report.
Why not just use the following?
Var x = connected({_N}, {_O}, "hbond")
then that's your bond set.
x.size is the number of bonds
x.length is the average length
x.atoms is the set of atoms involved.
select bonds @x
does the selection.
The reason it doesn't report is that it's very new that people are using
this. It could report.
Bob
On Wed, Sep 22, 2010 at 4:13 PM, Eric Martz <[email protected]>wrote:
> I want to count subsets of hbonds. My tests are in Jmol 12.0.14. My
> example is model 2 of 1lcd, after processing by Molprobity, which adds
> missing hydrogens and adjusts some hydrogen positions to correct bond
> lengths, and to optimize the hbond network.
>
> load 1lcdH_mod2.pdb
> calculate hbonds
> 116 hydrogen bonds
>
> OK, so there are 116 hbonds.
>
> hbonds 0.3
> select bonds @{connected({_H}, {_N}"hbond")}
>
> The above command generates no report. It works, because if I now do
> "hbonds 0.6" only the N-H hbonds are fat. (Most of the hbonds are O-H.)
>
> 1. Why doesn't the above command report the number of bonds selected? (I
> think it should.)
>
> 2. How do I generate a report of the number of bonds selected?
> -----------------
> print @{connected("hbond")}.size
> 211
>
> 3. Is this the number of atoms connected by hbonds? I think so. I think
> there are fewer than 2*116=232 because some atoms engage in two hbonds.
> -----------------
> print @{connected("hbond")}.bonds.size
> 134
>
> 4. What is "134" a count of?
>
> ----------------
> print @{connected("hbond")}
> ({5 18 33 47 63:65 78 95 96 110 114 128 129 142 148 149 161 175 179 213 214
> 241 245 272 278 279 302 303 308 335 342 343 358 363 369 382:384 397 403:405
> 415 416 420 427 428 433 434 445 446 460 464 478 479 489 495 496 508 523 527
> 551 552 557 558 585 589 621 652 680 771 773 775 776 785 790 804 814 825 829
> 830 837 841 853 855 863 869 887 901 910 920 932 934 935 943 952 953 964 968
> 970 986 995 999 1011 1013:1015 1030 1032 1033 1050 1066 1083 1084 1119 1121
> 1130 1138 1163 1167 1174 1184 1206 1211 1220 1228 1244 1250 1259 1265 1281
> 1285 1297 1303 1312 1314 1322 1324 1337 1351 1365 1374 1379 1416 1417 1428
> 1464 1467 1484 1486 1500 1502 1505 1506 1508 1510 1514:1518 1520 1524:1526
> 1529 1530 1532 1534 1536 1541 1548 1551 1556 1560 1562 1564 1568 1570
> 1572:1574 1576 1579 1580 1583 1587 1589:1591 1593:1596 1600 1602 1606 1609
> 1612 1615:1619 1622:1627})
>
> 5. How do I interpret the above syntax? What commands could use this
> report?
> -----------------
> print @{connected("hbond")}.bonds
> [{829 1073 1568 1569 1574 1580 1604 1607 1610 1618 1620 1621 1624 1634 1635
> 1637 1640 1641 1646:1761}]
>
> 6. How do I interpret the above syntax?
>
> Thanks, -Eric
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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