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 <emartz@microbio.umass.edu> 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