Re: [PyMOL] Selections don't work on structures loaded using, 'fetch' command

[Timofey Tyugashev]

Thank you for prompt response. Now I recall that I've seen the mention 
of it in the release notes for 1.8, but paid no attention to it as I had 
no intent to install 1.8 so soon anyway being wary of probable bugs.
Probably earlier I just pedantically typed in the identifiers in capital 
letters, but yesterday was to tired to bother and got this unpleasant 
surprise.
I see that current versions already have it returned to work the old way.
Maybe it would be nice if all wiki pages with examples affected by 
case-sensitiveness get some kind of a note about it.
01.03.2016 03:54, pymol-users-requ...@lists.sourceforge.net пишет:
> Message: 7
> Date: Mon, 29 Feb 2016 08:35:13 -0500
> From: Thomas Holder<thomas.hol...@schrodinger.com>
> Subject: Re: [PyMOL] Selections don't work on structures loaded using
>   'fetch' command
> To: Timofey Tyugashev<tyugas...@niboch.nsc.ru>
> Cc:pymol-users@lists.sourceforge.net
> Message-ID:<73c4c9d6-c6b2-44b9-b508-f7c84b592...@schrodinger.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi Timofey,
>
> Seehttp://pymolwiki.org/index.php/ignorea _case
>
> Note: The wiki page mentions 1.8.0.0 (official release), but the SVN repo had 
> the change since 1.7.7.1 (https://sourceforge.net/p/pymol/code/4123/  ).
>
> Cheers,
>Thomas
>
> On 29 Feb 2016, at 06:23, Timofey Tyugashev<tyugas...@niboch.nsc.ru>  wrote:
>
>> >Sorry, it's actually part false alarm and part a completely different
>> >problem.
>> >
>> >For false alarm:Structure retrieved by 'fetch' simply lacked residue
>> >numbered 10, why my own file was already repaired and had it fine.
>> >
>> >For different problem: For some reason it turns out that 'select' is
>> >case-sensitive and it's not actually mentioned anywhere on the wiki, so
>> >selectors like 'resn' and 'name' simply silently failed.
>> >Is there a way to disable it?
>> >
>> >29.02.2016 17:10, Timofey Tyugashev ?:
>>> >>If I load my own pdb file and issue a simple select command like
>>> >>'select resi 10' it works fine, producing something like 'selection
>>> >>"sele" defined with 6 atoms'.
>>> >>However if I load the same structure using fetch command selections
>>> >>stop working,  'select resi 10'  results in 'selection "sele" defined
>>> >>with 0 atoms'.
>>> >>System is Linux. PyMOL is 1.7.7.2 version from svn.
> -- Thomas Holder PyMOL Principal Developer Schr?dinger, Inc.


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Re: [PyMOL] Selections don't work on structures loaded using 'fetch' command

[Thomas Holder]

Hi Timofey,

See http://pymolwiki.org/index.php/ignore_case

Note: The wiki page mentions 1.8.0.0 (official release), but the SVN repo had 
the change since 1.7.7.1 (https://sourceforge.net/p/pymol/code/4123/ ).

Cheers,
  Thomas

On 29 Feb 2016, at 06:23, Timofey Tyugashev  wrote:

> Sorry, it's actually part false alarm and part a completely different 
> problem.
> 
> For false alarm:Structure retrieved by 'fetch' simply lacked residue 
> numbered 10, why my own file was already repaired and had it fine.
> 
> For different problem: For some reason it turns out that 'select' is 
> case-sensitive and it's not actually mentioned anywhere on the wiki, so 
> selectors like 'resn' and 'name' simply silently failed.
> Is there a way to disable it?
> 
> 29.02.2016 17:10, Timofey Tyugashev пишет:
>> If I load my own pdb file and issue a simple select command like 
>> 'select resi 10' it works fine, producing something like 'selection 
>> "sele" defined with 6 atoms'.
>> However if I load the same structure using fetch command selections 
>> stop working,  'select resi 10'  results in 'selection "sele" defined 
>> with 0 atoms'.
>> System is Linux. PyMOL is 1.7.7.2 version from svn.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Selections don't work on structures loaded using 'fetch' command

[Timofey Tyugashev]

Sorry, it's actually part false alarm and part a completely different 
problem.

For false alarm:Structure retrieved by 'fetch' simply lacked residue 
numbered 10, why my own file was already repaired and had it fine.

For different problem: For some reason it turns out that 'select' is 
case-sensitive and it's not actually mentioned anywhere on the wiki, so 
selectors like 'resn' and 'name' simply silently failed.
Is there a way to disable it?

29.02.2016 17:10, Timofey Tyugashev пишет:
> If I load my own pdb file and issue a simple select command like 
> 'select resi 10' it works fine, producing something like 'selection 
> "sele" defined with 6 atoms'.
> However if I load the same structure using fetch command selections 
> stop working,  'select resi 10'  results in 'selection "sele" defined 
> with 0 atoms'.
> System is Linux. PyMOL is 1.7.7.2 version from svn. 


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Re: [PyMOL] Selections

[Michael George Lerner]

 For example, I found a PDB online called 'pope.pdb' (a cool lipid
 bilayer; http://moose.bio.ucalgary.ca/Downloads/) and simply wanted to
 select all the hydrophobic tails and hydrophilic heads so that I may
 apply different attributes to each.  If I need to select the tails,
 which in the PDB are labeled from C10 (or so) to C50 depending on the
 molecule, can I use something like c10-c50 (experience tells me no) or
 must I do c10+c11+c12...c50?

I don't know an easy way to do this .. like almost does what you want,
but not quite.  You could do something like

select sol, resn sol
select heads, name 
N4+C5+C6+O7+O9+O10+O11+C12+C13+O14+C15+O16+C32+O33+C34+O35+P8+H1+H2+H3
select tails, not sol and not heads

Or .. even easier .. drop this in a file called something like
select_names.py

---
#!/usr/bin/env python
from pymol import cmd,stored

def select_names(newSelectionName,selection):

Makes a new selection called newSelectionName comprised of
everything that has the same atom name as something in selection.

stored.selected_names = []
cmd.iterate(selection,'stored.selected_names.append(name)')
cmd.select(newSelectionName,'name %s'%'+'.join(stored.selected_names))

cmd.extend('select_names',select_names)
---

and type run selected_names.py from within PyMOL.
Now use the mouse to select one of the heads (I use shift+lb to put things
into the selection (lb).
Now type select_names heads, lb and you'll have a selection called
heads that has all of the heads.

Maybe someone who knows more about selections will know a better way,
though.


 So, it comes down to: do you prefer the macro method or standard; and,
 do you have any hints or tips for more accurate or powerful selections?

If you're going to be using PyMOL a lot, it's definately worth your time
to learn how to write Python scripts.  I'd also recommend looking through
the PyMOL source itself.  I don't have anything much to say about
selections, though .. I've always been quite happy with simple PyMOL
selections.

-michael

 As an example, how could I select just the tails or just the heads in
 the aforementioned pope.pdb file?

 Thanks.

 --
 Jason Vertrees
 BSCB Graduate Student @ UTMB, Galveston
 javer...@utmb.edu :: http://www.bscb.utmb.edu


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Re: [PyMOL] Selections

[Robert Campbell]

Hi Jason,

* Jason Vertrees javer...@utmb.edu [2004-04-14 22:55] wrote:
 Master Users,
 
 I'm a bit new to PyMol and still trying to master selections.  I've read
 the documentation and played with quite a few macromolecules now and
 still have some problems with selections.
 
 For example, I found a PDB online called 'pope.pdb' (a cool lipid
 bilayer; http://moose.bio.ucalgary.ca/Downloads/) and simply wanted to
 select all the hydrophobic tails and hydrophilic heads so that I may
 apply different attributes to each.  If I need to select the tails,
 which in the PDB are labeled from C10 (or so) to C50 depending on the
 molecule, can I use something like c10-c50 (experience tells me no) or
 must I do c10+c11+c12...c50?

The latter is correct, unfortunately.  You can certainly do a selection
like:

select tails1, r. pop  n.
c17+c18+c19+c20+c21+c22+c23+c24+c25+c26+c27+c28+c29+c30+c31+ca1+ca2+c36
+c37+c38+c39+c40+c41+c42+c43+c44+c45+c46+c47+c48+c49+c50

(where I've wrapped the line)

or you could do the shorter selection first:

select heads, r. pop  n.
c5+c6+c12+c13+c15+c32+c34+n4+o7+o9+o10+o11+o14+o16+o33+o35+p8+h1+h2+h3

and then do:

select tails2, r. pop ! heads

If you don't want to go to the trouble of picking every atom to see its
name, just select one atom in the residue (ctrl-middle-click) and show
the atom name labels for the residue (use the pkresi selection in the
right menu and labels are under L)

 So, it comes down to: do you prefer the macro method or standard; and,
 do you have any hints or tips for more accurate or powerful selections? 
 As an example, how could I select just the tails or just the heads in
 the aforementioned pope.pdb file?

I found clicking on each atom to add them to the lb selection as
Michael suggests less simple, but then I type quickly!

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

RE: [PyMOL] Selections

[Warren DeLano]

  must I do c10+c11+c12...c50?

Yes, unfortunately.  However, this long selection: 

 select tails1, r. pop  n.
 c17+c18+c19+c20+c21+c22+c23+c24+c25+c26+c27+c28+c29+c30+c31+ca
1+ca2+c36
 +c37+c38+c39+c40+c41+c42+c43+c44+c45+c46+c47+c48+c49+c50

Can be replaced with some Python code in your script:

   my_list = map( lambda x: c%2d%x, range(10,51) )
   my_str = string.join( my_list, '+' )
   cmd.select( tails1, resn pop  name  + my_str )

   show lines, tails1

Which allows you to adjust the range manually by changing the values in the
range call.

FYI:

   print my_str

gives

 
c10+c11+c12+c13+c14+c15+c16+c17+c18+c19+c20+c21+c22+c23+c24+c25+c26+c27+c28+
c29+c30+c31+c32+c33+c34+c35+c36+c37+c38+c39+c40+c41+c42+c43+c44+c45+c46+c47+
c48+c49+c50

Cheers,
warren

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Robert Campbell
 Sent: Thursday, April 15, 2004 8:39 AM
 To: PyMol Users List
 Subject: Re: [PyMOL] Selections
 
 Hi Jason,
 
 * Jason Vertrees javer...@utmb.edu [2004-04-14 22:55] wrote:
  Master Users,
  
  I'm a bit new to PyMol and still trying to master selections.  I've 
  read the documentation and played with quite a few 
 macromolecules now 
  and still have some problems with selections.
  
  For example, I found a PDB online called 'pope.pdb' (a cool lipid 
  bilayer; http://moose.bio.ucalgary.ca/Downloads/) and 
 simply wanted to 
  select all the hydrophobic tails and hydrophilic heads so 
 that I may 
  apply different attributes to each.  If I need to select the tails, 
  which in the PDB are labeled from C10 (or so) to C50 
 depending on the 
  molecule, can I use something like c10-c50 (experience 
 tells me no) or 
  must I do c10+c11+c12...c50?
 
 The latter is correct, unfortunately.  You can certainly do a 
 selection
 like:
 
 select tails1, r. pop  n.
 c17+c18+c19+c20+c21+c22+c23+c24+c25+c26+c27+c28+c29+c30+c31+ca
1+ca2+c36
 +c37+c38+c39+c40+c41+c42+c43+c44+c45+c46+c47+c48+c49+c50
 
 (where I've wrapped the line)
 
 or you could do the shorter selection first:
 
 select heads, r. pop  n.
 c5+c6+c12+c13+c15+c32+c34+n4+o7+o9+o10+o11+o14+o16+o33+o35+p8+h1+h2+h3
 
 and then do:
 
 select tails2, r. pop ! heads
 
 If you don't want to go to the trouble of picking every atom 
 to see its name, just select one atom in the residue 
 (ctrl-middle-click) and show the atom name labels for the 
 residue (use the pkresi selection in the right menu and 
 labels are under L)
 
  So, it comes down to: do you prefer the macro method or 
 standard; and, 
  do you have any hints or tips for more accurate or powerful 
 selections?
  As an example, how could I select just the tails or just 
 the heads in 
  the aforementioned pope.pdb file?
 
 I found clicking on each atom to add them to the lb 
 selection as Michael suggests less simple, but then I type quickly!
 
 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
 
 
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