How to count number of unique values of a field in a tab-delimited text file?

http://stackoverflow.com/questions/3502177/how-to-count-number-of-unique-values-of-a-field-in-a-tab-delimited-text-file

sed - how to do several consecutive substitutions but process file only once?

http://unix.stackexchange.com/questions/97428/sed-how-to-do-several-consecutive-substitutions-but-process-file-only-once

How to remove a column or multiple columns from file using shell command?

http://unix.stackexchange.com/questions/222121/how-to-remove-a-column-or-multiple-columns-from-file-using-shell-command

Remove full path from terminal

http://askubuntu.com/questions/232086/remove-full-path-from-terminal

Converting vertical items into Horizontal

Converting vertical items into Horizontal



paste -d, -s mylist2 >testml1
paste -sd' ' mylist2


http://www.unix.com/shell-programming-and-scripting/116537-converting-vertical-items-into-horizontal-plz.html

http://www.linuxquestions.org/questions/linux-newbie-8/bash-to-print-words-lines-horizontally-4175450926/

How to grep for a pattern in the files in tar archive without filling up disk space

http://stackoverflow.com/questions/13041068/how-to-grep-for-a-pattern-in-the-files-in-tar-archive-without-filling-up-disk-sp

calculate the rmsd of all ligands loaded in the pymol with reference to a reference ligand using a script

[unformatted]

Hi There,

I am trying to calculate the rmsd of all ligands loaded in the pymol with reference to a reference ligand using a script. My current script looks like this,

myobjects = cmd.get_object_list()

print myobjects

cmd.select('sele', "F60_target_14 and resn UNK")

cmd.create('obj01', 'sele')

for i in myobjects:

    i = i.strip()

    cmd.sele('sele', i +'and resn UNK')

    cmd.create ('obj02', 'sele')

    cmd.rms_cur ('obj02', 'obj01')

    cmd.delete ('obj02')

obj01 will be my reference and I want to use rms_cur to all objects loaded.

The problems here are, 

(1) My obj02 selection part is not working properly. I know I am not calling the myobject list in the correct way. Could somebody help me fix this?

(2) I want to write the rmsd values to a file. How can I do it?

Thanks for the help.

Regards,

Subha

Looks like you’re missing a space in the string ‘and resn UNK’, it should be: i + ‘ and resn UNK’

I figured out the rms_cur part too.

Using 'python' and 'python end' in pymol scripts

Using 'python' and 'python end' in pymol scripts

Dear Users,

I am trying to implement a script which uses a mix of pymol and python scripting. I enclosed the main portion within the 'python' and 'python end' commands. This runs perfectly fine in Pymol GUI mode, however when I tried it with 'pymol -cg my_script.py', it generates an error:

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 338, in parse
    parsing.run_file(path,self.pymol_names,self.pymol_names)
  File "/usr/lib/python2.7/dist-packages/pymol/parsing.py", line 452, in run_file
    execfile(file,global_ns,local_ns)
  File "/usr/lib/python2.7/dist-packages/pymol/parsing.py", line 447, in execfile
    b.execfile(filename, global_ns, local_ns)
  File "bondH.py", line 122
    python end
             ^
SyntaxError: invalid syntax

How do I overcome this problem?

Answer: 

Rename the script from .py to .pml

Run JavaScript from command line in Linux

https://fixmynix.com/run-javascript-from-command-line-linux/