Re: [PyMOL] (small) Pymol feature request--filter for edit settings window
Hello Michelle,
You can also edit the SetEditor.py file. The file is in the
'/usr/lib/python2.3/site-packages/pmg_tk' directory on linux and add the
feature. It can be done by adding to small portion of add-on code to the
file. If you do so:
Keep a copy of the original file in a safe place !
Here is a part of the modified file:
###
class SetEditor:
def __init__(self,app):
self.app = app
self.list = []
for a in pymol.setting.get_index_list():
self.list.append(%-30s %s%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.index = {}
c = 0
for a in pymol.setting.get_name_list():
self.index[a] = c
c = c + 1
self.dialog = Pmw.SelectionDialog(self.app.root,title=Settings,
buttons = ('Edit', 'Done'),
defaultbutton='Edit',
scrolledlist_labelpos=N,
label_text='Double click to edit',
scrolledlist_items = self.list,
command = self.command)
self.dialog.geometry(500x400)
# start of the add-on
interior = self.dialog.interior()
self.filter = Pmw.EntryField(interior,
labelpos = 'w',
label_text= 'Filter:',
validate = None,
command = self.filter_list)
self.filter.pack()
# end of the add-on
self.listbox = self.dialog.component('scrolledlist')
self.listbox.component('listbox').configure(font=app.my_fw_font)
self.dialog.protocol('WM_DELETE_WINDOW',self.cancel)
app.my_show(self.dialog)
# start of the add-on
def filter_list(self):
self.list = []
for a in pymol.setting.get_index_list():
if self.filter.getvalue() in pymol.setting._get_name(a):
self.list.append(%-30s %s%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.dialog.setlist(self.list)
self.dialog.update()
# end of the add-on
def cancel(self,event=None):
self.command(result='Done')
###
This code works fine on my linux box. If you have some problem, don't hesitate
to ask me !
Cheers,
Jerome Pansanel
Le Mardi 18 Avril 2006 18:02, Michelle Gill a écrit :
While we're discussing ways to make our favorite program a little
better, I had an idea I thought I'd throw out there...
While making some figures the other day, I found myself scrolling
endlessly through the edit settings menu (under Setting -- Edit All) a
number of times, mostly to locate a relatively small number of settings
related to ray tracing. This got me thinking about a way to improve
access to the many wonderful features that have been added to PyMOL.
The solution I came up with is a filter line which could be placed
directly above the window listing all the settings. Users could then
type a word, say ray or cartoon, and only the settings containing
this word would be shown.
The best example of a program containing this feature is the
about:config window in Firefox. When you open a browser and type
about:config instead of an address, a window containing hundreds of
settings appears. At the top is a filter bar which you can use to pare
down the number of settings listed below.
I think this would be a great addition to PyMOL and would help users
familiarize themselves with the many new settings which have been (and
will be) implemented. :)
Perhaps others have even better solutions to this problem. The use of a
filter is just the first idea which came to my mind. I think it would be
relatively easy to implement, although my python programming skills are
somewhat limited.
Thanks,
Michelle Gill
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Re: [PyMOL] (small) Pymol feature request--filter for edit settings window
Hello Michelle,
You can also edit the SetEditor.py file. The file is in the
'/usr/lib/python2.3/site-packages/pmg_tk' directory on linux and add the
feature. It can be done by adding to small portion of add-on code to the
file. If you do so:
Keep a copy of the original file in a safe place !
Here is a part of the modified file:
###
class SetEditor:
def __init__(self,app):
self.app = app
self.list = []
for a in pymol.setting.get_index_list():
self.list.append(%-30s %s%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.index = {}
c = 0
for a in pymol.setting.get_name_list():
self.index[a] = c
c = c + 1
self.dialog = Pmw.SelectionDialog(self.app.root,title=Settings,
buttons = ('Edit', 'Done'),
defaultbutton='Edit',
scrolledlist_labelpos=N,
label_text='Double click to edit',
scrolledlist_items = self.list,
command = self.command)
self.dialog.geometry(500x400)
# start of the add-on
interior = self.dialog.interior()
self.filter = Pmw.EntryField(interior,
labelpos = 'w',
label_text= 'Filter:',
validate = None,
command = self.filter_list)
self.filter.pack()
# end of the add-on
self.listbox = self.dialog.component('scrolledlist')
self.listbox.component('listbox').configure(font=app.my_fw_font)
self.dialog.protocol('WM_DELETE_WINDOW',self.cancel)
app.my_show(self.dialog)
# start of the add-on
def filter_list(self):
self.list = []
for a in pymol.setting.get_index_list():
if self.filter.getvalue() in pymol.setting._get_name(a):
self.list.append(%-30s %s%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.dialog.setlist(self.list)
self.dialog.update()
# end of the add-on
def cancel(self,event=None):
self.command(result='Done')
###
This code works fine on my linux box. If you have some problem, don't hesitate
to ask me !
Cheers,
Jerome Pansanel
Le Mardi 18 Avril 2006 18:02, Michelle Gill a écrit :
While we're discussing ways to make our favorite program a little
better, I had an idea I thought I'd throw out there...
While making some figures the other day, I found myself scrolling
endlessly through the edit settings menu (under Setting -- Edit All) a
number of times, mostly to locate a relatively small number of settings
related to ray tracing. This got me thinking about a way to improve
access to the many wonderful features that have been added to PyMOL.
The solution I came up with is a filter line which could be placed
directly above the window listing all the settings. Users could then
type a word, say ray or cartoon, and only the settings containing
this word would be shown.
The best example of a program containing this feature is the
about:config window in Firefox. When you open a browser and type
about:config instead of an address, a window containing hundreds of
settings appears. At the top is a filter bar which you can use to pare
down the number of settings listed below.
I think this would be a great addition to PyMOL and would help users
familiarize themselves with the many new settings which have been (and
will be) implemented. :)
Perhaps others have even better solutions to this problem. The use of a
filter is just the first idea which came to my mind. I think it would be
relatively easy to implement, although my python programming skills are
somewhat limited.
Thanks,
Michelle Gill
---
This SF.Net email is sponsored by xPML, a groundbreaking scripting language
that extends applications into web and mobile media. Attend the live
webcast and join the prime developer group breaking into this new coding
territory!
http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642
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Re: [PyMOL] mutations
I follow the method outlined by Nick with one additional step, after selecting the new residue you can run through a sidechain rotamer library using the forward arrows at the bottom of the window. You also have a choice to use backbone dependant or backbone independant rotamers. Andrew On 4/18/06, Noinaj noi...@uky.edu wrote: Orla, This is simply, for the most part. Here is what I do. Load your *.pdb file. Then under WIZARD in the menu bar, select MUTAGENESIS. Then pretty much, follow directions. In the PyMOL VIEWER window, it will ask you to ' pick a residue.' Once you pick a residue, select the type of residue you want to mutate to by left clicking on [No Mutation] button and holding down (under Mutagenesis). This brings up a list of residues that you can then select from. Once you select the residue you want, hit APPLY, then DONE. If everything was done correctly, you should see your mutated residue. There are probably other ways to do this, but I hope this helps. If you would like screenshots of the steps, just let me know. Cheers, Nick - Original Message - From: Orla O'Sullivan To: pymol-users@lists.sourceforge.net Sent: Tuesday, April 18, 2006 11:31 AM Subject: [PyMOL] mutations Hi all I'm a newbie to Pymol and so far have been very impressed. However I have tried to mutate some residues in my structure and have hit a brick wall. Has anyone done this with pymol and let me know how to do it? Regards Orla Dr.Orla O'Sullivan Research Officer Biotechnology Moorepark Food Research Centre Teagasc Moorepark Fermoy, Co. Cork Ireland Tel: +353 - (0)25 - 42344
Fw: [PyMOL] translation
orla, not actually had to do this, but I think you can try the translate command. -- translate DESCRIPTION translate can be used to translate the atomic coordinates of a molecular object. Behavior differs depending on whether or not the object parameter is specified. If object is None, then translate translates atomic coordinates according to the vector provided for the selection and in the state provided. All representation geometries will need to be regenerated to reflect the new atomic coordinates. If object is set to an object name, then selection and state are ignored and instead of translating the atomic coordinates, the object's overall representation display matrix is modified. This option is for use in animations only. The camera option controls whether the camera or the model's axes are used to interpret the translation vector. USAGE translate vector [,selection [,state [,camera [,object PYMOL API cmd.translate(list vector, string selection = all, int state = 0, int camera = 1, string object = None) EXAMPLES translate [1,0,0], name ca NOTES if state = 0, then only visible state(s) are affected. if state = -1, then all states are affected. - This seems like a pain, probably a better option somewhere, not sure? Hope this hopes. Cheers,Nick - Original Message - From: Orla O'Sullivan To: pymol-users@lists.sourceforge.net Sent: Thursday, April 20, 2006 6:56 AM Subject: [PyMOL] (no subject) Hi all This probably a very stupid question but its driving me mad. I have produced two Raster 3D scences using molscript and have loaded them into pymol. What I want to do is to be able to move them on screen independent of each other. Is this possible? Regards Orla Dr.Orla O'Sullivan Research Officer Biotechnology Moorepark Food Research Centre Teagasc Moorepark Fermoy, Co. Cork Ireland Tel: +353 - (0)25 - 42344
Re: [PyMOL] ..and rotate
orla, If in fact you actually have to move molecules independently using the 'dirty' method that I have suggested, you will probably need the rotate command too, for more flexibility in setting things up. rotate DESCRIPTION rotate can be used to rotate the atomic coordinates of a molecular object. Behavior differs depending on whether or not the object parameter is specified. If object is None, then rotate rotates the atomic coordinates according to the axes and angle for the selection and state provided. All representation geometries will need to be regenerated to reflect the new atomic coordinates. If object is set to an object name, then selection and state are ignored and instead of translating the atomic coordinates, the object's representation display matrix is modified. This option is for use in animations only. USAGE rotate axis, angle [,selection [,state [,camera [,object [,origin] PYMOL API cmd.rotate(list-or-string axis, string selection = all, int state = 0, int camera = 1, string object = None) EXAMPLES rotate x, 45, pept NOTES if state = 0, then only visible state(s) are affected. if state = -1, then all states are affected. -Cheers,Nickreference:http://pymol.sourceforge.net/newman/ref/S1000comref.html - Original Message - From: Orla O'Sullivan To: pymol-users@lists.sourceforge.net Sent: Thursday, April 20, 2006 6:56 AM Subject: [PyMOL] (no subject) Hi all This probably a very stupid question but its driving me mad. I have produced two Raster 3D scences using molscript and have loaded them into pymol. What I want to do is to be able to move them on screen independent of each other. Is this possible? Regards Orla Dr.Orla O'Sullivan Research Officer Biotechnology Moorepark Food Research Centre Teagasc Moorepark Fermoy, Co. Cork Ireland Tel: +353 - (0)25 - 42344
RE: [PyMOL] importing pymol modules in a python script
Alan, The only sure way to get this to work is to build into a local Python interpreter from PyMOL source code using distutils. Otherwise, you're likely better off with pymol -qc Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Alan Sent: Thursday, April 20, 2006 5:37 AM To: Pymol Subject: [PyMOL] importing pymol modules in a python script Hello List! I want a python script likewise: #!/usr/bin/python -O import sys, tempfile from pymol import editor from pymol import cmd However, even defining 'export PYTHONPATH=/usr/local/pymol/modules' I got this error: from pymol import editor File /usr/local/pymol/modules/pymol/__init__.py, line 353, in ? import _cmd ImportError: No module named _cmd Is there a way to run the python script with pymol stuff imported or only via 'pymol -c'? Many thanks in advance. Alan -- Alan Wilter S. da Silva, D.Sc. - Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=kkid0709bid3057dat1642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] pymol transitions recorded as movie?
Hi Eva, If you save your scenes (conformations) as a psw file (under save as) you can then use a hyperlink in powerpoint and this will launch pymol in presentation mode and you can just use page down to scroll through the scenes. Pymol is still active so you can rotate the molecules in the presentation. Hope this helps J Eva Vanamee wrote: I regularly use the F function keys in PyMol to store conformations and call them back in a presentation. I really like the transition effects. Is it possible to record those transitions as a movie and use them in a Powerpoint presentation? Thanks in advance, - Eva --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034
Re: [PyMOL] a scaling question
Hi Fei, * Fei Xu f...@rutchem.rutgers.edu [2006-04-19 11:55] wrote: Hi!: I met a scaling problem. I created many pdb files along one trajectory of DNA movement. I loaded each pdb file in pymol to create a picture, that is, one frame of the trajectory. Pymol shows each molecule in an optimal size automatically according the general shape of the molecular. The shape of the molecule along trajectory kept changing so that the size of the molecule also kept changing. When I connected all the time frames together, I saw the funny effect that the molecule was jumping back and forth. How can I put the molecule in the different time frames in exactly the same size? What you are experiencing is the auto_zoom feature of pymol. I have this turned off in my .pymolrc file. You can type: set auto_zoom, 0 to disable this feature. Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
