Hi Martin -
I've also experienced this kind of tedium. Depending on the type of extension
it is, you could also consider writing tests for your function that can be run
by either:
a) importing PyMOL commands into a python (.py) script and running e.g.
`nosetests` or other unit testing softwa
Hi Ankita,
set depth_cue, 0
http://pymolwiki.org/index.php/Depth_cue
Cheers,
Thomas
On 27 Apr 2016, at 11:06, H. Adam Steinberg wrote:
> Scrolling the mouse will not move the molecule, it will reduce the fog that
> pymol puts in the image, making it less gray.
>
> Sent from my iPhone
>
>
Hi Christoph,
This sounds like a serious picking bug, possibly related to your graphics
driver. Please send further details directly to me (I'll send an update to the
list once we've figured it out).
Thanks,
Thomas
On 27 Apr 2016, at 05:24, Christoph Parthier wrote:
> Hi,
>
> I have a str
Scrolling the mouse will not move the molecule, it will reduce the fog that
pymol puts in the image, making it less gray.
Sent from my iPhone
> On Apr 27, 2016, at 6:45 AM, ankita mehta wrote:
>
> No, I can not do this becos i have to show the complex that is protein in a
> fix orientation.
>
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
No, I can not do this becos i have to show the complex that is protein in a
fix orientation.
Suggest some alternative..
Thanks!
On Wed, Apr 27, 2016 at 4:01 PM, Dheeraj Prakaash wrote:
> Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and
> down!
> Usually (if you have
Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and
down!
Usually (if you have not changed any settings), SCROLLING UP should solve
your problem.
Cheers.
On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta
wrote:
> Hii,
> I want to save the image in pymol
> I am using white back
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
Hii,
I want to save the image in pymol
I am using white background but it gives me dull colouring of the protein
which is at the background than the protein part at foreground.
I want a unified sceme for all protein .
pls suggest.
thanks!
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
Hi,
I have a strange issue with (incentive) PyMOL version >= 1.8 for Linux
running under Scientic Linux 6.x (64-bit, current OPENGL driver for
NVIDIA Quadro graphics cards).
Independent of the mouse mode in PyMOL (2-Button/3-Button) selecting
(left mouse button), ID-ing (right mouse button) or
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