Yes thanks it works!
Now assuming that I want to make alitle complicated script based on
that template.
Assuming that I have 3 pdbs used as references defined in variables
ref1, ref2,ref3
now I need loop all of my pdbs from the array and superimpose each pdb
from the array agains each of referen
You need to add “,async=0” to your fetch calls.
http://pymolwiki.org/index.php/Fetch
> On Apr 28, 2016, at 4:51 AM, James Starlight wrote:
>
> Hi,
>
> My script is
>
> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
> pdb_array_store=$template/pymol
>
>
> # A simple FETCHER via PYMO
Hi,
My script is
pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
pdb_array_store=$template/pymol
# A simple FETCHER via PYMOL: download pdbs to the folder and pre-process them!
mkdir ${pdb_array_store}
for i in ${pdb_array[@]}; do
pdb_tit=$(basename "$i")
pymol -d "fetch $i; save ${pdb_ar
Hi,
You need
for i in ${pdb_array[@]}
do
...
done
Cheers,
Tsjerk
On Apr 27, 2016 4:44 PM, "James Starlight" wrote:
> so As I tried to do it but it was not worked :-O)
>
> #pdbs list
> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
> #where to save
> pdb_array_store=$template/pymol/
>
>
so As I tried to do it but it was not worked :-O)
#pdbs list
pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
#where to save
pdb_array_store=$template/pymol/
# A simple FETCHER: download pdbs to the folder and pre-process them!
#mkdir ${pdb_array_store}
for i in `cat ${pdb_array}` ; do wget
Please give me an example of the list of 3 pdbs instead of just cat $1 :)
as well as proper syntax of how to save each pdb after fetching in
pymol using same command line
Forgot to mention important points:
1) that list should be physically in my script like in python
2) I use pymol because I will
If you really want to use pymol, this works
#!/bin/bash
#myscript.bash
for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
Then on the command line
>chmod +x myscript.bash; ./myscript.bash mylist.txt
> On Apr 27, 2016, at 2:55 AM, Jordan Willis wrote:
>
> Must you use pymol?
>
>
> Try d
Must you use pymol?
Try directly from the PDB
#!/bin/bash
#myscript.bash
for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ; done
Then on the command line
>chmod +x myscript.bash; ./myscript.bash mylist.txt
J
> On Apr 27, 2016, at 2:41 AM, James Starlight wrote:
>
> D
Dear Pymol users!
I need to add a few strings to my simple bash script which will creat
a list of pdb files and than will call pymol without GUI from the
terminal to fetch all the pdbs and save it to the desired location.
For one pdb it should be smth like
pdbs="1f88"
pymol -c -q -d "fetch ${pdb
