[PyMOL] morph issues

[harold steinberg]

Hi all,

I need to generate a morph from 3J5R to 3J5Q. When I load both files and 
generate the morph, it’s all messed up. When I generate a morph of other 
structures it works just fine.

In the structures that do not morph correctly a sample selection is:
/3j5r/A/B/ILE`573/CD1
/3j5q/C/E/ILE`573/CD1

Notice that these files have an extra letter (“A” and “C” before the chain 
identifier).

In files that the morph does work this letter is missing (it’s a blank space):
/3lut//D/GLY`338/CA

Is that what is messing up the morph?


H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] Autosave session Pymol

[Thomas Holder]

Hi Matic,

As a proof of concept, the following snippet would save a session file every 30 
seconds. You can put this in your pymolrc file.

python
import os
import threading
import time
from pymol import cmd
def _auto_save():
filename = os.path.expanduser(time.strftime('~/pymol-auto-save-%s.pse'))
while True:
time.sleep(30) # interval in seconds
cmd.save(filename, quiet=0)
_auto_save = threading.Thread(target=_auto_save)
_auto_save.setDaemon(1)
_auto_save.start()
python end

Saving session files is not very fast, so with larger molecules, the 
interruption will be very noticeable. There is a new experimental setting in 
PyMOL 1.8.2 which can improve this: pse_binary_dump

Cheers,
  Thomas

On 22 Apr 2016, at 02:31, Matic Kisovec  wrote:

> Dear PyMOL users,
> 
> I would just like to bump this question again.
> I would be glad to see some replies either from users or developers.
> 
> Best regards,
> Matic
> 
> 
> On 31. 03. 2016 08:02, Matic Kisovec wrote:
>> Dear Pymol users,
>> 
>> a quick google search returned empty regarding the ability of Pymol to
>> autosave the session at a specified time interval.
>> The feature is available in different programs from text to vector
>> editors etc.
>> I would find it useful to have the ability to automatically save a
>> couple of recent checkpoints while I am using Pymol.
>> 
>> My question is if this would be interesting/useful for anybody and a
>> question to the developers if this can be implemented?
>> 
>> Best regards,
>> Matic

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Dynamic reloading of plugin

[Thomas Holder]

Hi Martin,

how about:

set_key F1, run script.py; function_from_script()

Reduces step 3) and 4) to hitting "F1" on the keyboard.

Cheers,
  Thomas

On 24 Apr 2016, at 06:36, Martin Hediger  wrote:

> Hi all
> 
> When working on a PyMOL extension script, my workflow is currently something 
> like this:
> 
> 1) Start PyMOL
> 2) Work on script
> 3) PyMOL> run script.py
> 4) PyMOL> function_from_script()
> 5) See if function works, go back to 2)
> 
> Is it possible to have PyMOL automatically re-run the script everytime i save 
> it?
> 
> Thanks and best regards
> Martin
>  
> -- 
> Martin R. Hediger, PhD
> Mittlere Strasse 65
> 4056 Basel

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] ccmutate

[Thomas Holder]

Hi Martin,

short answer: Your PyMOL version is too old, this script works with PyMOL 1.8.

PyMOL 1.8 can download fragments from PDBeChem with type=cc, e.g.:

PyMOL> fetch ALA, type=cc

I assume you found the ccmutate script on my user page. It's an experimental 
script to provide a mutation command with all the fragments which are available 
from PDBeChem.

Cheers,
  Thomas

On 23 Apr 2016, at 18:15, Martin Hediger  wrote:

> I found the ccmutate script on the pymol wiki
> 
> I tried it but I receive a weird error:
> 
> PyMOL>ccmutate "ALA", resi 112
> Traceback (most recent call last):
>   File 
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/parser.py",
>  line 254, in parse
> self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>   File "021_scripts/ccmutate.py", line 47, in ccmutate
> cmd.fetch(code, tmp_frag, type='cc', zoom=0)
>   File 
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/importing.py",
>  line 1417, in fetch
> r = _multifetch(*args)
>   File 
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/importing.py",
>  line 1352, in _multifetch
> discrete, multiplex, zoom, type, path, file, quiet, _self)
>   File 
> "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/importing.py",
>  line 1263, in _fetch
> raise ValueError('type')
> ValueError: type
> 
> 
> What could be going on? The PyMOL mutagenesis wizard in any case works when I 
> do the mutation by hand.
> 
> Thanks for hints
> Martin
>  
> --
> Martin R. Hediger, PhD
> Mittlere Strasse 65
> 4056 Basel

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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