Re: [PyMOL] Shell utilities for structural bioinformatics

Hi Small correction to Gianlucas suggestion ">" will direct the output to a file, overwriting the contents ">>" will direct the output to a file, appending the contents Venlig hilsen Folmer Fredslund Den 05/09/2014 19.16 skrev "Gianluca Santoni" : > Don't even need cat > simply do > > grep PPC

Re: [PyMOL] Access to pymol commands from the terminal

Hi James, adding my 2 cents to this conversation. Save the bash script below as "pymolsuper.sh". - pymolsuper.sh - #!/bin/bash if [[ $# < 2 ]]; then echo "usage: $0 mobile.pdb target.pdb [out.pdb]" exit 1 fi script="python names = cmd.get_object_list() c

Re: [PyMOL] Shell utilities for structural bioinformatics

Don't even need cat simply do grep PPC ref.pdb > tar_i.pdb redirecting std out with > appends it directly to the file (after the last line) Cheers On 9/5/14 6:48 PM, James Starlight wrote: > Dear Pymol users! > > I've decided to open new topic focused on the implementation of the > common shel

Re: [PyMOL] Access to pymol commands from the terminal

Hi Jed! thanks for the advise! As I understood some commands like FIT and WRITE should be provided being INSIDE of the profit to obtain pdb output. Does it possible to do it in one line style from bash like profit ref tar output etc ? BTW profit send errors when I try to fit mob to ref and w

[PyMOL] Shell utilities for structural bioinformatics

Dear Pymol users! I've decided to open new topic focused on the implementation of the common shell utilities like grep awk and sed for the structural bioinformatics tasks like processing and editing of the large sets of pdbs. In my current task I need to copy all lipids from one pdb (called it re

Re: [PyMOL] Access to pymol commands from the terminal

BTW using python script given by Matthew i've obtained error >>> execfile ('pymol.py') Traceback (most recent call last): File "", line 1, in File "pymol.py", line 2, in import pymol File "pymol.py", line 4, in pymol.finish_launching() AttributeError: 'module' object has no attrib

Re: [PyMOL] Access to pymol commands from the terminal

Thanks Tsjerk! Today I've tried some software of pairs alignment (like ce, tmalign and mammoth) and found that it's not good for me because the positions of reference and target are both altered as the result of the alignment by means of the rotational matrix superimposition method. In my case I n

[PyMOL] label unit cell

Hi, I can display the unit cell by typing 'show cell'. How can I label the unit cell? I want to see the origin and unit cell axes a, b, c. Looking forward to hearing from you..., hena -- Slashdot TV. Video for Nerds. Stu

Re: [PyMOL] Access to pymol commands from the terminal

Hi James, I have a light version for fitting gromacs' gro files. No time to adapt that now for PDB, but it's not too hard. ./qfit.py source.gro target.gro > output.gro Hope it helps, Tsjerk On Fri, Sep 5, 2014 at 12:31 PM, James Starlight wrote: > should to add > > than I've used both TMali

Re: [PyMOL] Access to pymol commands from the terminal

should to add than I've used both TMalign and mammoth utilities but didn't understand how to obtain superimposed output as the full-atomic pdb's. I will be thankful if someone could share with me its experience :) James 2014-09-05 12:00 GMT+02:00 James Starlight : > Thanks Matthew, > > > I'll

Re: [PyMOL] Access to pymol commands from the terminal

Thanks Matthew, I'll try to use this opportunity! BTW does anybody knows some simple Linux utility to perform structural superimposition of 2 pdbs and obtain the superimposed (target.pdb) in separate pdb file? This time I'm writing big docking script where I need to superimpose each receptor agai