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 in
Dear all,
Could you please check this figure at the following link?
https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing
The structure in blue in this figure is prepared from chain A of pdb id 4gms.
Some residues are highlighted and look sharp ( as indicated in the
Dear all,
Could you please check this figure at the following link?
https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing
The structure in blue in this figure is prepared from chain A of pdb id 4gms.
Some residues are highlighted and look sharp ( as indicated in the
surrounding water). I think the command
you’re after is ‘set cartoon_transparency’
(https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels).
Depending on your choice of representation, see also ‘set sphere_transparency’
and ‘set stick_transparency’.
Cheers,
Paul
From: sunyeping via
transparency’
(https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels).
Depending on your choice of representation, see also ‘set sphere_transparency’
and ‘set stick_transparency’.
Cheers,
Paul
From: sunyeping via PyMOL-users
Sent: 03 December 2018 03:02
To: pymol-users
Subject: [PyMOL] how
ors.png
Hope that helps.
Cheers,
Jared
On December 5, 2018 at 3:33:35 AM, sunyeping via PyMOL-users
(pymol-users@lists.sourceforge.net) wrote:
Hi Paul,
Now I get closer to the final anwer!
After following your steps, I get the effect I want. However, afer I "ray" the
structure, a
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 illustrated in the ex
Dear everyone,
It there a way to show the boundary of each selected residues in surface
presentation with pymol?
Best regards
Arthur___
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ht
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 work. I know by u
via PyMOL-users
wrote:
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" comman
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 problem?
Best regards_
Dear all,
I color a protein as blue, display it by surface and cartoon simultaneously,
and set the surface transperant so that the cartoon representation inside the
surface can be seen. I display one residue as stick. I want to color the stick
by element, but keep the surface representation as
ayali
-
I’m protected online with Avast Free Antivirus. Get it here —
it’s free forever.
On Sat, Jul 6, 2019 at 2:29 PM sunyeping via PyMOL-users
wrote:
Dear all,
I color a protein as blue, display it by surface and cartoon simultaneously,
and set the su
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.___
PyMOL-u
the moment. So here, instead, is a
link to a few-years-old archive of that page.
Hope that helps.
Cheers,
Jared
On July 7, 2019 at 1:38:15 PM, sunyeping via PyMOL-users
(pymol-users@lists.sourceforge.net) wrote:
Dear all,
Is it possible to label secondary structures directly in pymol? I
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 pa
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 the
0
Email: akus8...@uni.sydney.edu.au
From: sunyeping via PyMOL-users
Reply-To: sunyeping
Date: Tuesday, 9 July 2019 at 12:41 pm
To: pymol-users
Subject: [PyMOL] The 'select' command for complex residue selection
Dear all,
In pymol I loaded two protein: protein_A and protein_B. I want to m
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" command, the two structures al
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 some
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 o
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 command
If you compile it, you can use the RMSD this way:
mda_load systemX.gro
mda_load_traj systemX.xtc
mda_rmsd
Kind Regards,
Mateusz
On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users
wrote:
Dear everyall,
I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and
a ref
branch https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
If you compile it, you can use the RMSD this way:
mda_load systemX.gro
mda_load_traj systemX.xtc
mda_rmsd
Kind Regards,
Mateusz
On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users
wrote:
Dear everyall,
I
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 bars generated with
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
Dear all,
I am trying to use APBS TOOLs 2.1 to calculate electrostatic potential of
proteins. After I finish "set grid", I press the "set grid" button, I get the
following error,
(, ImportError('No module named pdb2pqr',),
)
In show error 2
Could you tell what is the cause of the error and h
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 setu
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 thing
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.
--
pymol binaries
Sent: Friday, February 14, 2020 at 7:47 AM
From: "sunyeping via PyMOL-users"
To: "Thomas Holder"
Cc: pymol-users
Subject: Re: [PyMOL] How to compile pymol with --glut?
Hi Thomas,
Thank you and I know this has been asked before, but following the suggestion
po
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 molecules look very similar, there
- ED C2MP
Université de Lorraine
CRM² - UMR CNRS 7036
julien.capp...@univ-lorraine.fr
Tel: (+33)6 99 18 59 03
-
Le mer. 17 juin 2020 à 05:06, sunyeping via PyMOL-users
a écrit :
Dear pymol users,
I am trying to align two very similar trimeric molecule
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 regards,
Yeping S
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 selection and st
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
____________
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?
Best regards
Y
Dear all,
I wish to label residue name on top of sphere representation, but I find it is
difficult.
I tried the following command
select sele, c. A & resi 47 & name CB
show sphere, c. A & resi 47
lable sele, "Y47"
I and the "Y47" label is hidden inside the sphere and cannot be seen.
Even if I
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
running build_py
running bu
Dear all,
Now I revised Line 4 in the SceneView.cpp file from "#include
" to "#include ".
The error "layer1/SceneView.cpp:4:41: fatal error:
glm/ext/vector_relational.hpp: No such file or directory" disappeared, but a
now error appeared:
layer1/SceneView.cpp:31:55: error: no matching function
al` on lines 31
and 32 of that source file.
Hope that helps,
Jarrett J
On Sun, Sep 12, 2021 at 4:41 AM sunyeping via PyMOL-users
wrote:
Dear all,
Now I revised Line 4 in the SceneView.cpp file from "#include
" to "#include ".
The error "layer1/SceneView.cpp:4:41: fa
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 pandas" command will
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
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 fr
ays.
# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA
# Give Label Them as (Residue Name+Residue Number)
label CAs, "(%s%s)" % (resn, resi)
# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs
Regards,
sunyeping via
n now are fomatted as "(THR339)",
"(SER308)", etc.
I wonder how to show them as single-letter codes plus the numbers without the
parentheses, like "T339", "S308".
Thank you again.
Best,
-------------
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 th
Dear all,
I want to label residues with the resn+resi, and I tried the following command
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',
Dear all,
I want to label residues with the resn+resi, and I tried the following command
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',
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