")
out=[]
def f(chain, resi): out.append((chain,resi))
myspace={'f':f}
x.cmd.iterate("mysel and name CA", "f(chain, resi)", space=myspace)
print(out)
From: Zhou, Yingyao
Sent: Tuesday, May 28, 2024 3:57 PM
To: pymol-users@lists.sourceforge.net
Subject: How to ob
Hi,
In the example code below, there is a selection object "myself" within PyMOL, I
try to obtain the selected residues within Python.
The "out=x.cmd.do" prints the selection to stdout, but the variable out remains
None. What would be a good way to get the selection without going through disk
Hello Henrik,
your syntax is not correct:
select name_for_selection, selected_parts
https://pymolwiki.org/index.php/Select
eg.
select my_carbons, elem C & obj
will select atoms that are element C AND in obj and calls this
Dear Pymol users
Would anyone be able to help with the correct syntax used for selecting
specific elements within an object?
For example, I would like to be able to select only carbon or hydrogen.
select elem c (works but selects all the carbons in my project)
select elem c, obj (this selects
Thank you, it was really what I asked!
Em seg, 5 de ago de 2019 15:50, Christian "Cole" French <
christian.fre...@schrodinger.com> escreveu:
> select_with_filter allows you to make a selection as you would with the
> select command, so it supports all selection algebra including byres,
>
select_with_filter allows you to make a selection as you would with the
select command, so it supports all selection algebra including byres,
chain, organic, etc. Here's a modified example from the wiki:
# Select all residues within 5 Ang. of any organic small molecules whose
x-coordinate is at
Yes, one more question.
How to use all other "functions", like byres, "chain A" or "organic"?
Em seg, 5 de ago de 2019 12:36, Christian "Cole" French <
christian.fre...@schrodinger.com> escreveu:
> I see now. I updated the code at the link in my previous email to provide
> behavior which should
I see now. I updated the code at the link in my previous email to provide
behavior which should allow you to do what you want. Here are your examples
written using the command:
select_with_filter sele, flag 8, lambda s: len(cmd.get_chains(s)) < 2
select_with_filter sele, flag 8, lambda s:
I expressed myself wrong, I'm looking something like:
select peplength < 15 and chain A
Where peplength is an user defined function like:
def peplength(atom):
return compute_peplength(atom)
I'm looking for the availability of user defined functions on selection
expressions. How to?
Em
Edit: remove the cmd. part when running select_with_filter. (Since it's a
custom command, it doesn't belong to the cmd module.)
On Fri, Aug 2, 2019 at 2:41 PM Christian "Cole" French <
christian.fre...@schrodinger.com> wrote:
> Hi Pedro Lacerda,
>
> Here is a link to a script I wrote which adds
Hi Pedro Lacerda,
Here is a link to a script I wrote which adds a command which does what you
ask: https://gist.github.com/ColeFrench/6f68fa5f04a67bb6234f10c25debb865.
To use it, download the file to the directory where you run PyMOL from,
then open PyMOL and run run select_with_filter.py.
For
Hi Thomas,
I see! Is it supposed to work with other formats too? Or at least, is
it planned to be expanded? I'm trying to switch to PyMOL to view
GROMACS `.xtc` trajectories, and this feature would be a great
addition.
Cheers,
Lorenzo
___
PyMOL-users
Hi Lorenzo,
You are correct, it's doing nothing for most trajectory formats. Only the
implementation for AMBER .trj files uses it. It looks like it allows selecting
a subset of atoms.
Cheers,
Thomas
> On Jun 25, 2019, at 4:05 PM, Lorenzo Gaifas wrote:
>
> Dear pymol users,
>
> What is
: [PyMOL] selection of residues in protein using plane perpendicular
to Z-axis
Hi Divya -
It's not entirely clear what you're trying to do from your description. Are
you looking to select residues near the plane, or perhaps use the plane to
divide residues into "of interest" and "
Hi Divya -
It's not entirely clear what you're trying to do from your description. Are
you looking to select residues near the plane, or perhaps use the plane to
divide residues into "of interest" and "not of interest"? I think PyMOL can be
useful here, but the approach will likely be
Hi all,
I wanted to ask how to select a plane (perpendicular to zaxis) so that I can
select all residues of interest in a protein. Any help is greatly appreciated.
Best Regards,
Divya
___
PyMOL-users mailing list
Archives:
Dear PyMOL Users,
I have solved the problem by setting use_shaders to False. The problem
is probably caused by the incomplete/outdated OpenGL implementation of
the graphics driver/device.
Best regards,
Andras Wacha
On 07/03/2017 11:08 AM, András Ferenc WACHA wrote:
> Dear PyMOL Users,
>
> I'm
Dear PyMOL Users,
I'm using a Lenovo Thinkpad T410 notebook with the integrated intel
video card. I found that when I select something, the little purple
boxes are not shown.
The operating system is Arch Linux, and I use the most recent packages
available. Pymol v1.8.6.0 prints the following at
Dear Julian
You can also try the PDB plugin which places each chain into a selection
automatically for you.
https://pymolwiki.org/index.php/PDB_plugin
Regards
John
PDBe
On 12/06/2017 17:10, Thomas Holder wrote:
Hi Julian,
A one-liner to create chain selections looks like this:
for c
Hi Julian,
A one-liner to create chain selections looks like this:
for c in cmd.get_chains(): cmd.select("chain_" + c, "chain " + c)
PyMOL doesn't provide access to the PDB header fields. In principle PyMOL
provides a way to access everything inside mmCIF files, see:
Dear all,
I have a pdb-file with multiple chains (5N61).
Is there an easy way to create selections for all the chains that are
defined in the pdb-header (A to U) without doing it manually for every
chain (select A, chain A)?
Is it also possible to use the MOLECULE information from the header to
ly=1),chain,resi,resn)
>
> Thanks,
> Abhinav
>
> -Original Message-
> From: Thomas Holder [mailto:thomas.hol...@schrodinger.com]
> Sent: Wednesday, March 22, 2017 1:15 PM
> To: Kumar, Abhinav
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] select
(enabled_only=1),chain,resi,resn)
Thanks,
Abhinav
-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com]
Sent: Wednesday, March 22, 2017 1:15 PM
To: Kumar, Abhinav
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] selection of residues
Hi Abhinav,
You can
Hi Abhinav,
You can select by representation, e.g.:
iterate rep sticks, print(chain, resi)
or directly add labels on CA atoms:
label byca rep sticks, resi
Hope that helps.
Cheers,
Thomas
On 22 Mar 2017, at 15:43, Kumar, Abhinav wrote:
> Hi,
> Is there a way of
Hi,
Is there a way of extracting residue information from a session file in which a
few residues are shown in sticks representation?
I am interested in changing representation/adding labels to only those residues
with stick representation.
Thanks,
Abhinav
Abhinav Kumar, PhD
Senior Scientist,
Hi Yuxing,
We have released Incentive PyMOL 1.8.4.1, which fixes the ribbon coloring issue.
Cheers,
Thomas
On 21 Nov 2016, at 15:57, Thomas Holder wrote:
> Hi Yuxing,
>
> Thanks for reporting this. Yes it's a bug, luckily with a simple fix. We will
> provide
Hi Yuxing,
Thanks for reporting this. Yes it's a bug, luckily with a simple fix. We will
provide a bugfix release soon.
Cheers,
Thomas
On 21 Nov 2016, at 15:12, Yuxing Liao wrote:
> Hello All,
>
> I just updated Pymol from 1.8.0 to the latest 1.8.4. But I
Hello All,
I just updated Pymol from 1.8.0 to the latest 1.8.4. But I noticed when the
structure is rendered in ribbon and you try to color part of it, the behavior
changed at the boundaries. Instead of beginning and ending at the middle of the
bonds like before, now the colors start and end
Hi Lukas,
All operators:
https://sourceforge.net/p/pymol/code/4159/tree/trunk/pymol/layer3/Selector.cpp#l455
Operator types (e.g. number of arguments) and priority (order of operation):
https://sourceforge.net/p/pymol/code/4159/tree/trunk/pymol/layer3/Selector.cpp#l365
Hope that helps.
Cheers,
Dear PyMOL users,
I am trying to add support for pymol-like selection algebra into one of your
software tools. Therefore, I was wondering, if there is any formal
description of the language available in for example as context-free
grammar. I was trying to find something in the source code
Hi Leila,
Have a look at selection syntax (help selections), in particular 'within
... of ...'
Hope it helps,
Tsjerk
On Mar 2, 2016 06:46, "leila karami" wrote:
> Dear all
>
> I have a complex (protein-ligand). I want to have only those residues
> (from protein) with
Dear all
I have a complex (protein-ligand). I want to have only those residues (from
protein) with special distance relative to ligand.
How to do that?
Any help will highly appreciated
--
Site24x7 APM Insight: Get Deep
Hi Alireza -
For renumbering a chain, the program PDBSET in the CCP4 suite is my tool of
choice. If your protein is chain A, the command would look something like this:
pdbset xyzin my_protein.pdb xyzout my_protein_renumbered.pdb EOF
renum 1 chain A
EOF
To remove the extraneous stuff within
Dear All,
I would like to colour different regions of a protein in different colour;
say region one, amino acid number 1 to 100 and region two amino acid 101 to
150; However, when I look into a pdb file using pymol; by displaying the
residuals, I see the residue number 1, does not correspond to
Hi,
There is a script available on the pymol wiki called zero_residues. This
will allow you to easily renumber any AA sequence.
As far as other heteroatoms are concerned you could consider removing them
(remove hetatm), or extract them into a second object.
Another alternative is to simply adjust
Thanks for your prompt answer,
numbers resets in every chain - and there is a lot of nucleobases in the
beginning (A,C,U,G) and MG at the end and these atoms mess up the residues
number additionally !
can I remove them via pymol ? Thank you
http://en.wikipedia.org/wiki/Nucleobase
On Sat, Dec 13,
Hi all,
I'm trying to write a script to data mine the pdb. I'm want to look at the
ligands in a pdb file and fish out those that meet a certain criteria. I've
got a script that can look at the ligands all at once but I need to assess
each ligand individually. Since I'm looking at 40,000+ pdbs I
constituents, by either chain Id and resid.
Hope this helps a bit.
Carsten
From: Katherine Sippel [mailto:katherine.sip...@gmail.com]
Sent: Friday, December 13, 2013 10:28 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selection algebra issue
Hi all,
I'm trying to write a script to data
Id and resid.
Hope this helps a bit.
Carsten
*From:* Katherine Sippel [mailto:katherine.sip...@gmail.com]
*Sent:* Friday, December 13, 2013 10:28 AM
*To:* pymol-users@lists.sourceforge.net
*Subject:* [PyMOL] Selection algebra issue
Hi all,
I'm trying to write a script to data
this helps a bit.
Carsten
From: Katherine Sippel [mailto:katherine.sip...@gmail.com]
Sent: Friday, December 13, 2013 10:28 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selection algebra issue
Hi all,
I'm trying to write a script to data mine the pdb. I'm want to look
Hello Pymolers
I think this is an easy one, but I can't seem to get this to work.
I'd like to select residues with a bfactor equal to a certain value, say 0.
However something like:
select aa, b = 0
does not work
although
select aa, b 0.5
does work.
Cam someone show me how to do this?
Cheers
Hi Mike,
We didn't implement the equals operator, but the less than and greater than
operators are strict comparisons so you can do the following:
select my_exact_b, not (b0.5 or b0.5)
Cheers,
-- Jason
On Thu, Oct 10, 2013 at 9:34 PM, Osborne Michael
michael.osbo...@umontreal.ca wrote:
select chain A and ss s worked great. I didn't know to put the 'and' there.
Thanks!
On Sat, Dec 31, 2011 at 7:53 PM, Takanori Nakane
t.nak...@mail.mfour.med.kyoto-u.ac.jp wrote:
Happy new year,
I have a structure of a protein composed of two
Corey,
PyMOL's ability to create precise atom selections can be very useful.
Please see the 'select' command
(http://pymolwiki.org/index.php/Select). On that page, please be sure
to see the two topics under the See Also heading. Those will
illustrate how powerful 'select' can really be. Let me
I have a structure of a protein composed of two monomers A and B. I
want to select the beta sheets in monomer A only. I know I can select all beta
sheets with, select ss s, but I haven't been able to find a simple way to
make a selection within a selection.
Happy new year,
I have a structure of a protein composed of two monomers A and B.
I want to select the beta sheets in monomer A only.
I know I can select all beta sheets with, select ss s,
but I haven't been able to find a simple way to make a selection
within a selection.
select
Dear All:
One of our crystals contains a dimer in the asymmetric unit, with chains
labeled A and B.
If I want to display chain b, I can first select chain a and remove the
atoms, using the commands:
select a, chain a
( (a) action menu: remove atoms)
Result: atoms removed
However, if after
: Tue 6/2/2009 2:08 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selection/remove bug?
Dear All:
One of our crystals contains a dimer in the asymmetric unit, with chains
labeled A and B.
If I want to display chain b, I can first select chain a and remove the
atoms, using the commands
Hello
I would like know, how can i show the electron density map of the only
selcted part along with my ligand in pymol. I donot like to show the extra
density. I guess isomesh map, selction site may help, but i would be
interested in detail of it. I would appreciate the suggestions.
Thanks in
How to list residues within given selection? E.g. if I have selection:
select name, resi 134 around 4.0
How to get details about atoms, residues which could be used by extrenal
code or just copied to text file?
Wiktor
Hi there,
i have the following problem: selecting all ca atoms in chain A of 1ao0
the amino acids in the selection are disordered with respect to their
occurrence in the protein.
After loading the protein i tried the following:
numbers=[]
iterate (chain a)(name
pymol-users-ad...@lists.sourceforge.net wrote on 01/19/2006 06:55:11 AM:
Hi there,
i have the following problem: selecting all ca atoms in chain A of 1ao0
the amino acids in the selection are disordered with respect to their
occurrence in the protein.
(snip)
So the 56th amino acid is
: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Frank Dressel
Sent: Thursday, January 19, 2006 7:36 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] selection disordered
Hi there,
i have the following problem: selecting
Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of James Puckett
Sent: lundi, 31. octobre 2005 00:27
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selection of DNA backbone or base pairs
I am trying to color the DNA
I am trying to color the DNA backbone and DNA base pairs uniquely en
masse for several crystal / NMR structures. Is there a simple way to
select solely the DNA phosphate backbone or solely the DNA bases or
DNA bases + sugars, etc? I know how to select atoms individually,
but am wondering
.pdb, a2
load 3.pdb, b1
load 4.pdb, b2
I wanted to create two new selections:
one = a1 a2
two = b1 b2
I've tried many different combinations of PyMOL selection
syntax, but I cannot get the objects to add to the same
selection (using 'create' or
'select'):
create one, a1 + a2
of PyMOL selection
syntax, but I cannot get the objects to add to the same
selection (using 'create' or
'select'):
create one, a1 + a2
create one, a1 and a2
create one, object a1 + object a2
create one, a*
From what I've read in the manual, I think these commands
are not working because
Dear fellows
I try to select the atoms surround a PHE ring and I use the 'around'
expression. With a value of 4 selects almost the whole molecule and
with a value of 1 selects considerably less atoms but with a random
distribution through the molecule. What actually I'm looking for is to
If you have the molecules mol01 and mol02 open, you can type mol_list
= cmd.get_names() to get the list of molecules put into the variable
mol_list: ['mol01' ,'mol02'].
Now let's say you've got those two molecules open and you've made some
selections within those two molecules. The GL window
Hi All-
I cannot make PyMOL make selections of residues with negative
(sequence) numbers. Any quick way around this?
ex. that works:
PyMOLshow sticks, //mod1//10/
ex. that fails:
PyMOLshow sticks, //mod1//-4/
Selector-Error: Invalid Range.
( s; mod1 i; :4 )--
I found this post on the
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Douglas Kojetin
Sent: Thursday, July 15, 2004 8:23 AM
To: pymol
Subject: [PyMOL] selection of residues with negative numbers
Hi All-
I cannot make PyMOL
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