On Mon, 3 Oct 2005, Terry Jones wrote:
> Is it possible to embed a pymol window into a bigger independent
> application?
"Embed"? No. At least, not if you want the pymol window to act as a
widget that can be embedded in a frame of some sort.
The last time I used pymol was vers
Greetings All,
I am a software developer starting a project for a biology lab doing
work in protein structure. I am not a biologist. We'll be using Pymol
as the basis for the visualization component of the application, and I
am at the beginning stages of understanding how pymol works and i
> improvements that I might like to make in the future (such as joining
> the gtk and rendering windows as you suggest). For now, I just thought
If you can figure out how to make pymol render into a passed in window
instead of creating its own toplevel, please let me know how you did
On Thu, 22 Jan 2004, Warren L. DeLano wrote:
> Where script.py contains the following sequence:
>
> import pymol
> pymol.finish_launching()
>
> [PS If there's anyone out there with a more elegant alternative for
> launching the PyMOL thread from a standalone Python
Hi
This is my first post to pymol-users lists. I have a problem regarding
usage of slerpy. Firstly i must admit that i have no clue of how to go
about using it in the first place. I know the pymol wiki has the list of
commands but do not know how to exploit them in a real case. If someone can
already
done that and share the ready made script for this purpose. This query may
be treated as a request for incorporation of this feature in PyMOL if it is
not available yet.
Thanks in advance.
Best wishes
Priyadarshan
Hi to everyone,
My apologies if the question is to naive. I was wondering if there was an
easier way to flip the puckering of ribose from endo to exo conformations
at 2' and 3' positions in pymol.
Thank you
Best wishes
Pr
uestion, not native at all. This is a perfect task for sculpting in PyMOL.
> You should fix the atoms which should not move, and limit the terms to bond
> length and angles (no torsion or VDW).
>
> The steps to do are best described in this short screencast:
> http://pymol.org/tmp/scul
Hi to everyone
Recently moved to latest pymol (from subversion r4050) on linux (ubuntu
12.10). Installation was fine and could launch pymol successfully. Using
builder crashes with a segmentation fault.
Has anyone encountered this? Please give suggestions to overcome this issue.
Thanks
Best
Hi
I have successfully installed pymol on linux using instructions from this
link <http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install> on
pymolwiki page and customized it to install to a path of my choice. Later I
started to add pymol-script-repo to the same folder, after sl
be
putting it in small letters or italicized etc. This would be like asking
pymol to read sequence from SEQRES section and compare it to sequence from
the section where coordinates are.
I am sorry if such a post/request has already been made but I could not
find it. Please suggest/direct.
Thank you
Thank you Thomas.
Best Regards
Priyan
On Thu, Sep 25, 2014 at 5:23 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:
> Hi Priyan,
>
> unfortunately PyMOL doesn't have such functionality to include missing
> atoms in the sequence viewer, neither does it read SEQ
Dear Steinberg
Thank you very much for the idea
Best Regards
Priyan
On Thu, Sep 25, 2014 at 7:33 PM, H. Adam Steinberg <
h.adam.steinb...@gmail.com> wrote:
> This is not as simple as you would like but PyMOL does have the ability to
> manually build in missing atoms. And this fe
; Hi Thomas et al,
> >>
> >> There was a recent question on the board about missing residues and the
> possibility of reading SEQRES headers and PyMOL being able to show the
> missing bits in the sequence view, perhaps with the amino acid letters
> grayed out to disti
Dear pymol-users
There is some trouble I end up with while using theseus from psico in
pymol. I am not sure what is causing this. Can anyone help me fix this one.
The log I get when executing theseus is given below.
thank you in advance,
Best Regards
Priyan
BEGIN THESEUS 3.0.0 >
Hi
I have a multi-state object loaded in PyMOL which represents transition of
a domain from one orientation to the other. I tried using "show_bumps.py"
to bring up clashes during the transition but the cgo that is written out
shows clashes only for the first state. Am I doing somethin
ymolwiki.org/index.php/Split_states>
> command to divide it into multiple objects, then run the script on each
> state individually.
>
> -Spencer
>
> On Thu, Jan 28, 2016 at 3:45 AM, ccp4 pymol wrote:
>
>> Hi
>>
>> I have a multi-state object loaded in PyM
t; generate your movie using some python loops to enable/disable the bumps for
> each frame, if you want to automate it.
> >
> > -Spencer
> >
> > On Thu, Jan 28, 2016 at 11:25 AM, ccp4 pymol
> wrote:
> > Dear Spencer
> >
> > Thank you for the suggest
Hi!
I must develop a program in language C, in which I
have to execute Pymol
and to invocate functions as select
or translate
inside my program.
I am writing to enquire how can I do it,
how can I invocate the Pymols functions.
Thanks
Here is some info on a new project that may be interesting to some of your
users.
>> ProgPorts <<
http://progports.sourceforge.net
>> Project Description <<
ProgPorts provides a robust method for the adminstration and use of
the many computer programs that are interestin
Hello everyone
The number of plugins has become long and hence can not see the one listed
at the end. Is there a way to reorganise the list of plugins in the plugin
window of pymol or have a scroll bar to browse downwards.
Thank you
Best Regards
Priyan
efault.php?page=join.php&p=sourceforge&CID=DEVDEV
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I am a student. I applied for a free download voucher on the website, but I
haven't sent an email to me. I hope you can reply as soon as possible. Thank
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haven't received the license email yet? Why is this?I sincerely hope to receive
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Dear pymol users,
I am trying to intall pymol on my centos 7 system from source using the mothed
discribed at pymolwiki
(https://pymolwiki.org/index.php/Linux_Install)Everything was ok until I run
install script:
#!/bin/bash -e
prefix=/opt/pymol-svn
modules=$prefix/modules
# If you want to
Hello everyone!
I have a pdb file of a protein structure solved by NMR. It consists of 120
states/models/conformations depending on which term you prefer. Pymol refers to
them as states.
My question is, if I want to select atom 'CD' of residue number 11 (which is an
arginine) of sta
"set transparency" command:
set transparency, 0.8, sele
but it doesn't work.
Could anyone help me figure it out？ With sincere thanks.
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"set transparency" command:
set transparency, 0.8, sele
but it doesn't work.
Could anyone help me figure it out？ With sincere thanks.
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ng" problem?
Best regards,
Yeping
--
From:Smith, Paul
Send Time:2018 Dec 3 (Mon) 20:38
To:孙业平 ; pymol-users
Subject:RE: [PyMOL] how to make selected residues blurry?
Hi,
The ‘set transparency’ command will set the transparency of a surface (e.g. the
interface between a protein and the
rive.google.com/file/d/1Au0LUkRKMCBCtN7XM_O0WlGKLhmtnyMV/view?usp=sharing).
How does that happen and how to fix it?
Thank you again and best regards.
Yeping
--
From:Smith, Paul
Send Time:2018 Dec 4 (Tue) 21:00
To:孙业平 ; pymol-users
Sub
k you very much and best regards.
Yeping
--
From:Jared Sampson
Send Time:2018 Dec 6 (Thu) 12:09
To:孙业平
Cc:pymol-users ; "Smith, Paul"
Subject:Re: [PyMOL] how to make selected residues blurry?
Hi Yeping -
I had replie
Dear all,
I have a protein-ligand complex and I wish to make the protein looks blur but
keep the ligand clear and sharp with pymol. I find a "focalblur" script
(https://pymolwiki.org/index.php/FocalBlur) which seems to be able to do this.
However I can get the fancy effect illustra
Dear everyone,
It there a way to show the boundary of each selected residues in surface
presentation with pymol?
Best regards
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Dear pymol user,
I wonder why sometimes the secondary structure of a protein can not be
displayed incorrect in pymol. I have a structure, some residues are predicted
to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only
typing "dss" command in pymol doesn't
Thank you for the reply.
Do alter and rebuild commands really change the secondary structure of the
specific residues or they just change the display? I saved the structure
altered bt the alter and rebuild commands, but when I open the structure agian
in pymol, the residues I changes are
Dear all,
I installed pymol according to guide at
https://pymolwiki.org/index.php/Linux_Install. When I launched pymol, and get
the "Qt not available, using GLUT/Tk interface" error and no pymol GUI
appeared. How could I deal with this prob
color stick representation of this Gln by element
but keep its surface representation as blue?
Thank you in advance
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Gayali
Sent At:2019 Jul. 6 (Sat.) 18:20
To:孙业平
Cc:pymol-users
Subject:Re: [PyMOL] How to color stick and surface representation separately
there are two ways to achieve this (might not be correct ways, but it will give
you results)
1. Open the molucule and choose show as Surface
[image.png
Dear all,
Is it possible to label secondary structures directly in pymol? I mean add a
text near local structures which tells the types and numbers of their secondary
structures, such as "α1", "β1", "α2", "β2", etc..
Thank you in advance._
Thank you, Jared.
--
From:Jared Sampson
Sent At:2019 Jul. 8 (Mon.) 12:08
To:pymol-users ; 孙业平
Subject:Re: [PyMOL] How to label secondary structures in pymol
Hi sunyeping -
Yes, it is possible. You can pick one atom to label in
Dear all,
It is easy to evaluate the simularity of two proteins in pymol. We just need to
align them and a RMSD will be given in pymol. However, I want to compare the
strutural similiarity of multiple proteins. I can align two of them once and by
doing alignment many times, I can finally get
Dear all,
In pymol I loaded two protein: protein_A and protein_B. I want to make a
selection of some incontinuous residues from two chains of protein_A, for
example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from
chain C. How should I write the select command? I tried
Hi, Ali,
Your command format works well. Thank you.
--
From:Ali Kusay
Sent At:2019 Jul. 9 (Tue.) 11:11
To:孙业平
Cc:pymol-users
Subject:Re: [PyMOL] The 'select' command for complex residue selection
Hi Sunyeping,
I a
Dear all,
I am now trying to compare two structures by alignment in pymol. The two
proteins are similar structures from the same family with about 500 residues. I
find that the "cealign" command gives much better result that the "align"
command. With the "cealign&quo
Dear all,
I loaded a gromacs trajetory containing about 1000 frames by the following
command in pymol:
load protein.gro
load_traj protein.xtc
I want to use these frames to make a movie. However, I find that the position
of the protein in first frame is very different from the other frames
Dear everyone,
I am trying to use the APBS plugin in pymol to calculate protein electrostatic
potentials. My system is centos 7. The pymol was installed with python 3.7
(~/software/build/anaconda3/bin/python). When I try to lauch the APBS Tool 2.1
from the plugin menu of pymol, a window jumps
Dear everyall,
I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and
a reference structure (B.pdb) into pymol. I wish to get the rmsd value between
each state of the MD simulation trajectory and the reference structure, but I
don't know how. I can use the align co
Hello Mateusz,
Thank you very much for your reply to my inquiry. Before I try the PyMOL
extension you mentioned, I want to try scripting language in pymol. I wrote a
attemptive one (align.py):
cmd.load("A.gro")
cmd.load("A.xtc")
cmd.load("ref.pdb")
for i in range
coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
***[m
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regards.
Yeping
--
From:Istvan Kolossvary
Sent At:2019 Aug. 20 (Tue.) 00:29
To:Mateusz Bieniek
Cc:孙业平 ; pymol-users
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation
trajectory and a reference
coords: 39.000597, -77.102102
http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
***[m
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Dear all,
I am trying to compare the vacuum electrostatics of three related proteins. I
loaded them in pymol and use "Action>generate>vacuum electrostatics menu to
generate the vacuum electrostatics of the three proteins. I find that the lower
and upper limit of the gradient bar
o Hyvonen
Sent At:2019 Sep. 12 (Thu.) 15:58
To:pymol-users
Subject:Re: [PyMOL] How to manually define the lower and upper limit of vacuum
electrostatics?
Hi Yeping,
Click on the bar object "Action" > "Levels" for a few preset levels/scales.
hth, Marko
On 12/09/201
is the cause of the error and how to fix it?
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dear all,
I am trying to compile pymol from source
(https://github.com/schrodinger/pymol-open-source.git). Python 3 and python 2
both have been installed in my system. I first tried compile pymol with python 3
python3 setup.py install --prefix=~/pymol-install-py3
It can work.
python3
Dear Pymol users,
I wish to prepare a image which looks like the picture at the follow link:
https://drive.google.com/file/d/1HPwTCNqD7hlTPX9QDHif00YW5ZIv8PCa/view?usp=sharing
I have ckecked the pymolwiki for different mode for drawing nucleic acid ladder
and ring, but cannot find any
Dear All,
I load a molecular dynamics (gromacs) trajectory into Pymol and wish to make a
movie with it. The trajectory contains 2500 frames, corresponding to 200 ns
simulation time, so each frame represents 80 ps. I wish to print time stample
on each stample. For example, on the first frame
Hi Thomas,
Thank you and I know this has been asked before, but following the suggestion
posted by you does not solve the problem.
After run the two commands:
rm -rf build
python2 setup.py --glut install --prefix=~/pymol-install-py2
The same error still comes out
Using yum of centos or apt of Ubuntu cannot install the latest version.
--
From:Robi Gus
Sent At:2020 Feb. 14 (Fri.) 22:00
To:孙业平
Subject:Re: [PyMOL] How to compile pymol with --glut?
much easier to use apt to install open source
Hi all,
I would like to get all the dihedral angles of a protein structure. I'm most
especially interested in the side-chain angles. I've only been able to get the
phi and psi angles using PyMOL, which is not exactly what I need. Does anyone
have a script to calculate the side-chai
Dear pymol users,
I am trying to align two very similar trimeric molecules. I tried different
alignment commands including "align", "cealign" and "super", but none of them
gives satisfying effect. Athough the backbone conformations and orientations of
two two mole
:2020 Jun. 17 (Wed.) 17:05
To:孙业平
Subject:Re: [PyMOL] Effect of different align method
Hello Sunyeping,
I would suggest you to try TM-align, and a very good way to use it for
multi-protein alignment is to use their server mTM-align. TM-align is a very
robust alignment tool that will in most o
Dear pymol user,
I select a series of atoms with the follow command in pymol:
select atoms, chian A within 4 of chain B
I wonder how to select the resides containing the selected "atoms", and how to
return the names and indexes of these residues.
Thank you in advance!
Best regar
Dear all,
I know that if you want to visualize b facotor of a objector in pymol, you can
use A>Present>b factor putty. However, how can show the b factor putty on a
certain selection of the object? Is there any command line to do this or do I
have to create a new object for the selecti
ing?
Best,
--
From:Mooers, Blaine H.M. (HSC)
Sent At:2020 Oct. 27 (Tue.) 18:09
To:孙业平 ; pymol-users
Subject:RE: [PyMOL] [EXTERNAL] present b factor putty on select
I am sorry. I am wrong. I should have tested by suggestion.
Irregardless of the selection that I specify, the entire chain
Dear all,
When you use "cartoon putty[, selection]" command in pymol, you will get the
cartoon putty representation of your selection. And the backbond of the
selection show different thickness. So dose the thickness of residues reflect
b-factor in cartoon putty representation?
Be
e and cannot be seen.
Even if I set the sphere to be 80 % transparency, the label cannot be seen yet.
So what the the correct way to make such a labelling?
Best regards,
Yeping Sun___
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Dear pymol users,
I am installing pymol in Centos 7 according to the guide in
https://pymolwiki.org/index.php/Linux_Install. I encounter an error of "error:
command 'g++' failed with exit status 1". A fill output of the install command
is as following:
running build
runn
.cpp:31:55: error: no matching function for call to
‘equal(const vec3&, const vec3&, float)’
Do you know how to deal with such an eorror?
With many thanks!
Best regards
--
From:pymol-users
Send Time:2021年9月12日(星期日) 15:39
Dear Mr. Jarrett,
Yes, with the glm of version 0.0.9, pymol can be installed successful.
Thank you very much:)
--
From:Jarrett Johnson
Send Time:2021年9月13日(星期一) 01:30
To:孙业平
Cc:pymol-users
Subject:Re: [PyMOL] pymol installation
Dear all,
I installed Pymol in CentOS from source following the guide in
"https://pymolwiki.org/index.php/Linux_Install";. I compiled Pymol with the
Python from anaconda, but I found that I cannot import anaconda packages (such
as pandas, numpy, etc.) in Pymol.
The "import
Dear Pymol users,
I wish to label the one-letter residue names for a bunch of selected resides on
surface representation of a protein, but I found the labels cannot be seen on
the image. It seems that these labels can been seen on cartoon representation
when the surface is hide.
Could you tell
Hello,
I wonder is there a way to contact the makers of Pymol for general question or
to request certain program features?
Regards,
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Dear pymol users,
I select a series of CA atoms in a structure in pymol and show them as sphere
in pymol and want to label them. If using the label menu at the up-right conner
of pymol, the labels shown overlaps with spheres and can not be seen. So I wish
to show the labels at a bit distance
"S308".
Thank you again.
Best,
--
From:Halil İbrahim Özdemir
Send Time:2022年1月18日(星期二) 18:50
To:孙业平
Subject:Re: [PyMOL] How to label atom at proper positions?
Hi Sunyeping,
You can easily apply the following script from PyMOL terminal. Have a nice d
321S"]
label CAs, mut.pop
but I found that the labels are put in the wrong positions. So what is the
correct way the show the labels for mutations?
Best regards
--
From:Halil İbrahim Özdemir
Send Time:2022年1月19日(星期三) 1
Dear pymol users,
I have a coordinate file (pdb) and a map file (mtz), and I want to make a image
that shows both the coordinate and the map. I generate a .map.ccp4 file using
fft in CCP4 program. However, when I open the pdb file and the .map.ccp4 in
pymol, I find the coordinates are out of
:'M', 'ALA':'A',\
'GLY':'G', 'PRO':'P', 'CYS':'C'}
select CAs, obj & n. CAs
label CAs, "%s%s" % (one_letter[resn],resi)
These work find. However, when I write these in a script and the last two
;M', 'ALA':'A',\
'GLY':'G', 'PRO':'P', 'CYS':'C'}
select CAs, obj & n. CAs
label CAs, "%s%s" % (one_letter[resn],resi)
These work find. However, when I write these in a script and the last tw
Hi need help with PyMOL rename command:
from https://pymolwiki.org/index.php/Rename :
Rename
rename creates new atom names which are unique within residues.
USAGE
CURRENT
rename object-name [ ,force ]
force = 0 or 1 (default: 0)
PROPOSED
rename object-or-selection,force
NOTES
Thank You a lot indeed explanation ways more clear than the wiki one
https://pymolwiki.org/index.php/Rename https://pymolwiki.org/index.php/Rename
I know I should have tried more
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Hello,
This might be a naive question as I am new to PyMol.
I recently installed MacPyMol and followed the instructions on Plugins -
PyMOLWiki to install the plugin Caver.
After successfully installing Caver, I loaded the trajectory I want to analyze
to compute tunnels, I get the following
A short how-to
https://www.macinchem.org/reviews/3D/augmented.php
<https://www.macinchem.org/reviews/3D/augmented.php>
Cheers
Chris
>
> Message: 1
> Date: Fri, 31 Aug 2018 12:26:03 -0400
> From: Abel J Baerga Ortiz
> To: pymol-users@lists.sourceforge.net
> Subject:
Inviato da iPad
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After optimizing the structure the coordinates transforms to another frame,
what I need to do is to transfer back to the original coordinates by getting
the transformation matrix when I tried to get this matrix using pymol, I got an
error and I can't figure out the problem because I am n
right what
should I do in order to apply it to the post-processing object ? should I apply
it as it is or the inverse of it?
Thank you, Fedaa Ali
On Saturday, December 1, 2018, 5:59:37 PM GMT+2, Fedaa Nada via PyMOL-users
wrote:
After optimizing the structure the coordinates transforms
choice of representation, see also ‘set sphere_transparency’
and ‘set stick_transparency’.
Cheers,
Paul
From: sunyeping via PyMOL-users<mailto:pymol-users@lists.sourceforge.net>
Sent: 03 December 2018 03:02
To: pymol-users<mailto:pymol-users@lists.sourceforge.net>
Subject: [PyMOL]
to be broken.
Cheers,
Paul
From: sunyeping
Sent: Tuesday, December 4, 2018 3:23:00 AM
To: pymol-users; Smith, Paul
Subject: Re: [PyMOL] how to make selected residues blurry?
Hi, Paul,
Thank you for your reply. I think the ‘set transparency’ command is on the
d I need to find the transformed
structure, how I could do it ?
Thank you, Fedaa Ali
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g the
lodging reservations at the Argonne Guest House. The workshop will cover all
other expenses (including meals).
We hope to see you at the school.
Charles, Garib and Qingping
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cover all
other expenses (including meals).
We hope to see you at the school.
Charles, Garib and Qingping
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ons at the Argonne Guest House. The workshop will cover all
other expenses (including meals).
We hope to see you at the school.
Charles, Garib and Qingping
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U
To whom it may concern,
I am writing to you in the hopes of knowing how to upload a PyMol plugin that I
developed on the page PyMolWiki ?
Best regards,
Wael Azzam
B.S in Bioinformatics
Lebanese American University, Beirut
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ou have used PyQt in your plugin.
>
> Nowadays, people usually upload released code onto repositories like GitHub.
> But I'm not sure which open source license we need to use if PyQt is used.
>
> Hope anyone who is familiar with this issue could help.
>
> Many thanks
Hi all,
I am a beginner of the PyMol script. I have 200 pdbs(names, C_1, C_2,
…..C_200), and all of them contain 2 domains(resi 1-80, or resi 92-160). I want
to calculate the rotation angle between the two domains. I do this calculation
with the orientation.py in batch mode. Do someone know
nd Qingping
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Dear Pymol-users support,
I want to compare the sizes of different virus and IgG in Pymol. But they
are exhibiting similar sizes. how can i change that?
the commands I enter are as below:
fetch 1igt, type=pdb1
fetch 1s58, type=pdb1 set all_states, on
fetch 3j3i, type=pdb1 set all_states, on
bulletin board. In the meantime, the
registration site remains open. We are sorry for the inconvenience.
The CCP4/APS school organizers
From: Xu, Qingping
Sent: Monday, January 6, 2020 12:04 PM
To: ccp...@jiscmail.ac.uk; pheni...@phenix-online.org;
pymol-users@lists.sourceforge.net
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