Re: [Jmol-users] 11.3.47 - cross-model bonds

[Bob H. <ha...@st...>]

Pretty good for an amateur! ;)
yes, sure enough, Jmol has flagged the improper coordinates of groups 
around C2C and C3C in that heme.
same problem with C7 in the PT structure.

OK, so Jmol is vindicated!

You need the -o option to divert the output from the Java console to 
sysout, and on the PC you need something like:

java -Xmx512m -jar "Jmol.jar" -o > logfile.txt

Bob









Egon, what do you have to do to write to sysout for Unix?





Rolf Huehne wrote:

>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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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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