Re: [PyMOL] ccmutate
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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Re: [PyMOL] Dynamic reloading of plugin
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. -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Autosave session Pymol
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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your business applications. It resolves application problems quickly and
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[PyMOL] morph issues
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 -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
