date:20100920

Re: [PyMOL] Sphere_quality

2010-09-20 Thread Vitaly Vostrikov

As a short follow up on my previous message: it appears to be possible to 
adjust the sphere quality for pseudoatom objects independently from the 
structure. Hopefully somebody will find this information useful (I know I did 
:-) ).

fetch 2kqt
pseudoatom pseudo, pos=[0,0,-12] 
show spheres, pseudo
zoom pseudo
set sphere_quality, 2, pseudo

Vitaly

- Original Message -
From: Vitaly Vostrikov 
Date: Sunday, September 19, 2010 1:16 am
Subject: Re: [PyMOL] Sphere_quality
To: Jason Vertrees 
Cc: pymol-users@lists.sourceforge.net

> Thank you, Jason! It would be nice if in one of the future releases 
> it would become a local property.
> 
> Vitaly
> 
> - Original Message -
> From: Jason Vertrees 
> Date: Saturday, September 18, 2010 11:41 pm
> Subject: Re: [PyMOL] Sphere_quality
> To: Vitaly Vostrikov 
> Cc: pymol-users@lists.sourceforge.net
> 
> > Hi Vitaly,
> > 
> > I haven't verified this by sifting through the code, but cursory
> > testing shows "sphere_quality" is a global setting.
> > 
> > Cheers,
> > 
> > -- Jason
> > 
> > On Sat, Sep 18, 2010 at 5:13 PM, Vitaly Vostrikov 
> >  wrote:
> > > Hello,
> > >
> > > Is it possible to apply sphere_quality to a particular 
> selection? 
> > I have tried the following, but it does not seem to work:
> > >
> > > fetch 1qvk
> > > set stick_ball, 1
> > > hide all
> > > show sticks
> > > set sphere_quality, 0, resn arg
> > > set sphere_quality, 2, resn trp
> > >
> > > Thank you.
> > >
> > > 
> --
> > 
> > > Start uncovering the many advantages of virtual appliances
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> users> > Archives: http://www.mail-archive.com/pymol-
> > us...@lists.sourceforge.net>
> > 
> > 
> > 
> > -- 
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schrodinger, LLC
> > 
> > (e) jason.vertr...@schrodinger.com
> > (o) +1 (603) 374-7120
> > 
> 
> 
> --
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Re: [PyMOL] cd in windows

2010-09-20 Thread Cun Zhang

cd "test space"

A nice way is,To Push down the TAB key(maybe need several times) after
inputing "test",the left will try complete all.

> cd test 

Cheers

Message: 1
> Date: Mon, 20 Sep 2010 11:20:10 -0400
> From: "David A.  Horita" 
> Subject: [PyMOL] cd in windows
> To: 
> Message-ID:
><
> 4ccfaf32fb7b2c449a189c82198e42653ce9b...@exchvs1.medctr.ad.wfubmc.edu>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
> How does one change directories in Windows when the directory name has a
> space in it?  I've tried double and single quotes as well as backslash
> space (I'd like to run a script that's in such a directory).
> Thanks
> David
>
> -
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine
> Winston-Salem, NC 27157-1016
> Tel: 336 713-4194
> Fax: 336 716-7671
> email:  dhor...@wfubmc.edu
> web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
> 
>
>
-- 
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Re: [PyMOL] cd in windows

2010-09-20 Thread Edward A. Berry

My apologies- having never written a pymol script in my life,
it never occurred to me that your "cd" was a pymol command.
All my examples were from the DOS shell.

Still it may be helpful that the DOS 8.3 (Progra~1) names work.
You can get the short name of your directory by DIR/x
(from the dos shell) in the directory above.

David A. Horita wrote:
> Thanks for the replies/suggestions.  Looks like I may need to upgrade from 
> v1.1, but:
>
> cd \"program files", "\program files", and \program?files give a variant of
>
> PyMOL>cd \"program files"
> Traceback (most recent call last):
>File "C:\Program Files\DeLano 
> Scientific\PyMOL/modules\pymol\externing.py", line 46, in cd
>  os.chdir(dir)  # raises on error
> OSError: [Errno 22] Invalid argument: '\\"program files"'
>
>
> cd \progra~1 does work, however.
> Pymol 1.1r1 running on Vista (32-bit) Business.
>
> -David
>
> -Original Message-
> From: Edward A. Berry [mailto:ber...@upstate.edu]
> Sent: Mon 9/20/2010 2:03 PM
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] cd in windows
>
> David A. Horita wrote:
>> Hi,
>> How does one change directories in Windows when the directory name has a
>> space in it? I've tried double and single quotes as well as backslash
>> space (I'd like to run a script that's in such a directory).
>> Thanks
>> David
>
> These all work for me:
>   >cd \"program files"
>
>   >cd "\program files"
>
>   >cd \program?files
>
>   >dir/x \prog*
> 06/05/2010  10:02p   PROGRA~1
>   >cd \progra~1
>
> Or run in your data directory using full path of the executable:
>   >\"program files"\seamonkey\seamonkey.exe
>
> (seamonkey is artemia the brine shrimp, you understand.
> Diminutive alternative to thunderbird and firefox)
>
> --
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> and start using them to simplify application deployment and
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>
>
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>


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Re: [PyMOL] cd in windows

2010-09-20 Thread David A. Horita

Thanks for the replies/suggestions.  Looks like I may need to upgrade from 
v1.1, but:

cd \"program files", "\program files", and \program?files give a variant of

PyMOL>cd \"program files"
Traceback (most recent call last):
  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\externing.py", 
line 46, in cd
os.chdir(dir)  # raises on error
OSError: [Errno 22] Invalid argument: '\\"program files"'


cd \progra~1 does work, however.
Pymol 1.1r1 running on Vista (32-bit) Business.

-David

-Original Message-
From: Edward A. Berry [mailto:ber...@upstate.edu]
Sent: Mon 9/20/2010 2:03 PM
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] cd in windows
 
David A. Horita wrote:
> Hi,
> How does one change directories in Windows when the directory name has a
> space in it? I've tried double and single quotes as well as backslash
> space (I'd like to run a script that's in such a directory).
> Thanks
> David

These all work for me:
 >cd \"program files"

 >cd "\program files"

 >cd \program?files

 >dir/x \prog*
06/05/2010  10:02pPROGRA~1
 >cd \progra~1

Or run in your data directory using full path of the executable:
 >\"program files"\seamonkey\seamonkey.exe

(seamonkey is artemia the brine shrimp, you understand.
Diminutive alternative to thunderbird and firefox)

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Re: [PyMOL] cd in windows

2010-09-20 Thread Edward A. Berry

David A. Horita wrote:
> Hi,
> How does one change directories in Windows when the directory name has a
> space in it? I've tried double and single quotes as well as backslash
> space (I'd like to run a script that's in such a directory).
> Thanks
> David

These all work for me:
 >cd \"program files"

 >cd "\program files"

 >cd \program?files

 >dir/x \prog*
06/05/2010  10:02pPROGRA~1
 >cd \progra~1

Or run in your data directory using full path of the executable:
 >\"program files"\seamonkey\seamonkey.exe

(seamonkey is artemia the brine shrimp, you understand.
Diminutive alternative to thunderbird and firefox)

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Re: [PyMOL] cd in windows

2010-09-20 Thread Roger Rowlett



  
  
David,
  
  Use double quotes or start typing and autocomplete with the
   key.
  
  Cheers.

On 9/20/2010 11:20 AM, David A. Horita wrote:

  
  
  Hi,
  How
does one change directories in Windows when the directory
name has a space in it?  I've tried double and single quotes
as well as backslash space (I'd like to run a script that's
in such a directory).
  Thanks
  David
   
  -
  
  David A. Horita, Ph.D.
  Department of Biochemistry
  Wake Forest University School of Medicine
  Winston-Salem, NC 27157-1016 
  Tel: 336 713-4194
  Fax: 336 716-7671 
  email:  dhor...@wfubmc.edu
  web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
   
  

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-- 
  

Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
  

  


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[PyMOL] cd in windows

2010-09-20 Thread David A. Horita

Hi,
How does one change directories in Windows when the directory name has a
space in it?  I've tried double and single quotes as well as backslash
space (I'd like to run a script that's in such a directory).
Thanks
David
 
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
 
 
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Re: [PyMOL] Mutagenesis How many rotamers per amino acid

2010-09-20 Thread Jason Vertrees

Hi Martin,

> atoms within less than VdW distance. Is there an easy, very low-level, PyMOL
> way of fixing this? Can the sculpting wizard be used for this?


Yes, after you place the sidechain and have the new structure (via the
"apply" function) you can then apply sculpting.  It would look
something like this:

# pause the UI
cmd.set("suspend_updates",1)

# reset the sphere scale
cmd.set("sphere_scale","1.0")

# go back to frame 1 (if you changed it)
cmd.frame(1)

# enable sculpting
cmd.set("sculpting",1)

# sculpt for 100 cycles
cmd.sculpt_activate("myProtein")
cmd.set("sculpting_cycles",100)

# resume the UI
cmd.set("suspend_updates",0)

# write coords
cmd.sculpt_iterate("myProtein")

#quit sculpting
cmd.unset("sculpting")


Load a small protein and call it "myProtein".  Then, copy/paste the
above code into PyMOL to see what happens.

Cheers,

-- Jason



On Mon, Sep 20, 2010 at 5:35 AM, Martin Hediger  wrote:
>  Dear All
> Just one little thing, say I obtain a couple of rotamers by mutating a
> sidechain. It happens that some of them are sterically not favourable, i.e.
> atoms within less than VdW distance. Is there an easy, very low-level, PyMOL
> way of fixing this? Can the sculpting wizard be used for this?
>
> Thanks a lot for any suggestions.
>
> Martin
>
>
>
>
>
>
>
> Am 19.09.10 19:00, schrieb Jason Vertrees:
>>
>> Martin,
>>
>>> I am wondering, are there any scripts/ plugins for PyMOL out there that
>>> facilitate the generation of a large amount of rotamers for different
>>> mutants? I might take the effort and start building this into a plugin.
>>
>> I'm not aware of any.  Some of our other seasoned PyMOLers might,
>> though.  If you need help w/the plugin there's a simple tutorial on
>> the PyMOLWiki (http://www.pymolwiki.org/index.php/Plugins_Tutorial)
>> and TKinter/PMW are very easy to develop with.  Good luck!
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Sat, Sep 18, 2010 at 6:48 PM, Martin Hediger  wrote:
>>>
>>>  This is great. Thanks a lot.
>>> I am wondering, are there any scripts/ plugins for PyMOL out there that
>>> facilitate the generation of a large amount of rotamers for different
>>> mutants? I might take the effort and start building this into a plugin.
>>>
>>> Martin
>>>
>>>
>>>
>>>
>>>
>>>
>>> Am 16.09.10 19:51, schrieb Jason Vertrees:

 Hi Martin,

 This took a bit of work to figure out, but the following code solves
 your problem (above).  It will download a PDB (I coded "1RSY") and
 select a residue (I coded 236).  I will then mutate that residue to
 all possible residues given what the rotamer library knows about, and
 write that out to N-files called "stateXYZ.pdb", where XYZ is the
 mutation number.  Instead of rewriting the code, it turns out you can
 hack the wizard through the API to do what you want:

 # begin a python block of code;
 python
 org = "1rsy"
 cpy = "1rsy_cpy"

 # fetch a PDB
 cmd.fetch(org, async=0)

 # make a copy on which to operate
 cmd.create(cpy,org)
 res = cpy + " and i. 236"

 # focus no the residue, if you want
 cmd.zoom(res, 3)

 # start the wizard to count the number of rotamers for this residue
 cmd.wizard("mutagenesis")

 # this was the painful part: if you just write "res" instead of "(res)"
 # pymol will delete your residue.  "(res)" make it an anonymous
 selection
 cmd.get_wizard().do_select("("+res+")")
 nStates = cmd.count_states("mutation")

 # foreach state, make the change and write to disk
 for i in range(1,nStates+1):
   print "State ", i, "/", nStates
   cmd.get_wizard().do_select("("+res+")")
   cmd.frame(i)
   cmd.get_wizard().apply()
   cmd.save("state" + str(i) + ".pdb", cpy)
   cmd.delete(cpy)
   cmd.create(cpy,org)

 # end the python block
 python end

 # quit the wizard
 cmd.set_wizard()

 Cheers,

 -- Jason

 On Tue, Sep 14, 2010 at 6:33 PM, Martin Hediger
  wrote:
>
>  I'm beginning to see things.
> When I issue:
>
> for value in rot_lib[('ASP', 40, -100)]:
>    rl.write(str(value) + '\n')
>
> rot_lib is being initiated by
>
> rot_lib =
>
>
> pickle.load(open("/Applications/PyMOLX11Hybrid.app/pymol/data/chempy/sidechains/sc_bb_dep.pkl",'r'))
>
>
> I get the following output:
> {('N', 'CA', 'CB', 'CG'): -169.69, 'FREQ':
> 0.477356998,
> ('CA', 'CB', 'CG', 'OD1'): 3.6001}
> {('N', 'CA', 'CB', 'CG'): -173.5, 'FREQ': 0.191343999, ('CA',
> 'CB',
> 'CG', 'OD1'): 56.797}
> {('N', 'CA', 'CB', 'CG'): -72.094, 'FREQ':
> 0.119497999,
> ('CA', 'CB', 'CG', 'OD1'): -12.9}
> {('N', 'CA', 'CB', 'CG'): -167.81, 'FREQ': 0.108205, ('CA',
> 'CB', 'CG', 'OD1'): -55.5}
> {('N', 'CA', 'CB', 'CG'): -64.594, 'FREQ':
>

Re: [PyMOL] Mutagenesis How many rotamers per amino acid

2010-09-20 Thread Martin Hediger

  Dear All
Just one little thing, say I obtain a couple of rotamers by mutating a 
sidechain. It happens that some of them are sterically not favourable, 
i.e. atoms within less than VdW distance. Is there an easy, very 
low-level, PyMOL way of fixing this? Can the sculpting wizard be used 
for this?

Thanks a lot for any suggestions.

Martin







Am 19.09.10 19:00, schrieb Jason Vertrees:
> Martin,
>
>> I am wondering, are there any scripts/ plugins for PyMOL out there that
>> facilitate the generation of a large amount of rotamers for different
>> mutants? I might take the effort and start building this into a plugin.
> I'm not aware of any.  Some of our other seasoned PyMOLers might,
> though.  If you need help w/the plugin there's a simple tutorial on
> the PyMOLWiki (http://www.pymolwiki.org/index.php/Plugins_Tutorial)
> and TKinter/PMW are very easy to develop with.  Good luck!
>
> Cheers,
>
> -- Jason
>
> On Sat, Sep 18, 2010 at 6:48 PM, Martin Hediger  wrote:
>>   This is great. Thanks a lot.
>> I am wondering, are there any scripts/ plugins for PyMOL out there that
>> facilitate the generation of a large amount of rotamers for different
>> mutants? I might take the effort and start building this into a plugin.
>>
>> Martin
>>
>>
>>
>>
>>
>>
>> Am 16.09.10 19:51, schrieb Jason Vertrees:
>>> Hi Martin,
>>>
>>> This took a bit of work to figure out, but the following code solves
>>> your problem (above).  It will download a PDB (I coded "1RSY") and
>>> select a residue (I coded 236).  I will then mutate that residue to
>>> all possible residues given what the rotamer library knows about, and
>>> write that out to N-files called "stateXYZ.pdb", where XYZ is the
>>> mutation number.  Instead of rewriting the code, it turns out you can
>>> hack the wizard through the API to do what you want:
>>>
>>> # begin a python block of code;
>>> python
>>> org = "1rsy"
>>> cpy = "1rsy_cpy"
>>>
>>> # fetch a PDB
>>> cmd.fetch(org, async=0)
>>>
>>> # make a copy on which to operate
>>> cmd.create(cpy,org)
>>> res = cpy + " and i. 236"
>>>
>>> # focus no the residue, if you want
>>> cmd.zoom(res, 3)
>>>
>>> # start the wizard to count the number of rotamers for this residue
>>> cmd.wizard("mutagenesis")
>>>
>>> # this was the painful part: if you just write "res" instead of "(res)"
>>> # pymol will delete your residue.  "(res)" make it an anonymous selection
>>> cmd.get_wizard().do_select("("+res+")")
>>> nStates = cmd.count_states("mutation")
>>>
>>> # foreach state, make the change and write to disk
>>> for i in range(1,nStates+1):
>>>print "State ", i, "/", nStates
>>>cmd.get_wizard().do_select("("+res+")")
>>>cmd.frame(i)
>>>cmd.get_wizard().apply()
>>>cmd.save("state" + str(i) + ".pdb", cpy)
>>>cmd.delete(cpy)
>>>cmd.create(cpy,org)
>>>
>>> # end the python block
>>> python end
>>>
>>> # quit the wizard
>>> cmd.set_wizard()
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>> On Tue, Sep 14, 2010 at 6:33 PM, Martin Hedigerwrote:
   I'm beginning to see things.
 When I issue:

 for value in rot_lib[('ASP', 40, -100)]:
 rl.write(str(value) + '\n')

 rot_lib is being initiated by

 rot_lib =

 pickle.load(open("/Applications/PyMOLX11Hybrid.app/pymol/data/chempy/sidechains/sc_bb_dep.pkl",'r'))


 I get the following output:
 {('N', 'CA', 'CB', 'CG'): -169.69, 'FREQ':
 0.477356998,
 ('CA', 'CB', 'CG', 'OD1'): 3.6001}
 {('N', 'CA', 'CB', 'CG'): -173.5, 'FREQ': 0.191343999, ('CA',
 'CB',
 'CG', 'OD1'): 56.797}
 {('N', 'CA', 'CB', 'CG'): -72.094, 'FREQ':
 0.119497999,
 ('CA', 'CB', 'CG', 'OD1'): -12.9}
 {('N', 'CA', 'CB', 'CG'): -167.81, 'FREQ': 0.108205, ('CA',
 'CB', 'CG', 'OD1'): -55.5}
 {('N', 'CA', 'CB', 'CG'): -64.594, 'FREQ':
 0.0753029995,
 ('CA', 'CB', 'CG', 'OD1'): -50.0}
 {('N', 'CA', 'CB', 'CG'): 62.399, 'FREQ': 0.013899, ('CA',
 'CB',
 'CG', 'OD1'): 1.3}

 I understand these are dictionaries containing the phi, psi values for a
 rotamer. Now this would mean in this case there are six rotamers for this
 situation. Starting to get closer to what i want.
 Still, if there is a easy way to get PDB files of every rotamer, that
 would
 solve my problem.
 So the thing left to figure out is how to find the right key for the
 rot_lib
 to give me the rotamers of the residue i am actually interested in.

 Thanks again for the support.

 Martin






 Am 14.09.10 01:01, schrieb Jason Vertrees:
> Hi Martin,
>
> Try replacing
>
>> (phi, psi) = cmd.phi_psi("br. first my_res")
> with
>
> (phi, psi) = cmd.phi_psi("br. first my_res").values()[0]
>
>
> Here's what I have now, for the script (I fixed one more bug):
> import pickle
>

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