Bob Hanson wrote:
> Rolf Huehne wrote:
>> Sorry, I don't remember the ID. I noticed it while investigating the
>> "Chemical Component Dictionary" of the wwPDB and it will be difficult to
>> find it again within about 7000 structures. Since I have to use bonding
>> information from the dictionary in order to be able to color the bond
>> types individually I didn't pay much attention to it.
>> But as far as I remember it were plain C-H bonds and one of the carbons
>> had five bonds because of this. And the dictionary also showed different
>> bonds. (The distance of the hydrogen to the carbons was nearly identical.)
>>
>>
>>
> Well, it would be good to find that. Something almost certainly was odd
> about the positions of the H atoms in that file.
>
I would guess they were added computationally.
It would be quite easy to find if it would be possible to get something
other than just coordinates/images/states out of Jmol during batch
processing.
I couldn't figure out any way to get a specific information into
standard output or at least standard error. Neither "message" nor
"print" output is showing up there.
But while writing this I checked the documentation again and found a
rather unhandy way of achieving it:
write VAR [variable name] "fileName"
It is quite unhandy to end up with thousands or hundreds of thousands of
individual output files. And it might also become a memory problem if
the information must be stored in a variable first.
(An "APPPEND" option for "write" might be a first step, although it
would be much easier and more flexible to have something like "write
STDOUT" and "write STDERR".)
So I searched now with a script containing the following command
sequence for each "Chemical Component Dictionary" file (converted to CIF
format):
load 001.cif;
x={connected(2) and hydrogen}.size;
if (x > 0);
y=getProperty("fileName") + ".txt";
write VAR x @y;
end if;
And after about 10 minutes I got 2 entries as a result:
http://remediation.wwpdb.org/pyapps/ldHandler.py?query=1FH
http://remediation.wwpdb.org/pyapps/ldHandler.py?query=2PT
(Note: I also tried to put all the filenames into an array and use a
loop but I got the error message "too many parentheses".)
Regards,
Rolf
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