users-requ...@lists.sourceforge.net пишет:
> Message: 7
> Date: Mon, 29 Feb 2016 08:35:13 -0500
> From: Thomas Holder
> Subject: Re: [PyMOL] Selections don't work on structures loaded using
> 'fetch' command
> To: Timofey Tyugashev
> Cc:pymol-users@lists.sourcef
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 a
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" def
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-sensi
Hi Pawel,
Pawel wrote, On 08/01/13 13:32:
> If it's not too much to ask: can you clarify the first paragraph of your
> response or point me to some place on the Wiki that explains it. Not
> sure what you mean by "state sensitive selection criteria" and by
> "operators".
I'm talking about the s
Hi Thomas,
That helps greatly. I wasn't aware of the PSICO package and it will
surely be useful for more than just helix angles. By the way, before you
responded I found the way to do what I wanted using the old
anglebetweenhelices script: using "frame i" command. Setting frame to
the desired
Hi Pawel,
the state argument of the select command is only for state sensitive
selection criteria (like around or within operators). The selection will
always be on all states (exception: discrete objects).
The angle_between_helices command itself needs a state argument. Since I
wrote that script
Hello,
I am having trouble running scripts which vary selections on different
states of a PyMOL object. I've converted an MD trajectory into a pdb
with 500 models that PyMOL loads as 500 states of 1 object. For example,
I would then like to run the anglesbetweenhelices.py script (from PyMOL
w
--
> 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 [2004-0
Hi Jason,
* Jason Vertrees [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 onl
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&#
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.ucalgar
Due to the degeneracy of the PyMOL selection language, there are many
ways.
Say we want 79 to 85 and 89 to 94 in chain A...
# the most concise way is
select name2, a/79:85+89:94/
# but alternatives include:
select name2, ( a/79:85/ or a/89:94/ )
select name2, ( chain a and (resi 79:85 or resi
Hi, I am new to pymol. I was wondering if someone could help me with
selecting multiple noncontinuous residues with the same name. For example,
I have tried the following:
select name1, a/79/ .# to select a single residue,
select name2, a/79:85/ ..# to select a continuous string of resid
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