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',
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 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
':'S', 'THR':'T', 'MET':'M', 'ALA':'A',\
'GLY':'G', 'PRO':'P', 'CYS':'C'}
# 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" % (one_letter[resn],resi)
# Set Label Positions for
"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
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
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 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
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: fatal error:
glm/
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
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
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 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
20 4:54 AM
To: sunyeping; pymol-users
Subject: Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi sunyeping,
You are right; there is a way via the command line:
preset.b_factor_putty(selection='all')
Replace "all" with your selection.
Best regards,
Blaine
Blaine Mooers, Ph.D.
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
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
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
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
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
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.
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, "
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 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 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
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 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
iek
Sent At:2019 Aug. 19 (Mon.) 20:32
To:孙业平
Cc:pymol-users
Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD simulation
trajectory and a reference structure?
Hi Sunyeping,
Besides using the scripting language in pymol, you might want to consider the
experimental PyMOL
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
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 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 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
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 am not sure
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
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,
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.___
-
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 surface
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
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
the same command but just change the “S” to an “H”. Or you can use a “L”
if you want a loop (unstructured).
alter 3-10/, ss=‘H’
You also need to enter the command: rebuild, to redraw the structure on your
screen. Use rebuild after you enter the alter command.
On Jun 4, 2019, at 10:37 PM, sunyeping
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
Dear everyone,
It there a way to show the boundary of each selected residues in surface
presentation with pymol?
Best regards
Arthur___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:
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
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 small part of the structu
ld prevent the your molecule from appearing 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 transparenc
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
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
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
Dear all,
I am trying to install pymol on my centos 6 system from source following the
guide on the pymolwiki ("https://pymolwiki.org/index.php/Linux_Install)". The
installation process seemed to be successful but when I initialized pymol, I
got the following error:
import _tkinter # If this
Dear all,
Do you have any idea of how to judge the favorability of a residue to another
residue and a group of residues. I mean I conceptually know that two
hydrophobic residue repel each other, and two residues with the same charge
repel each other, but is there any comprehensive and precise
Dear all,
If we show surface of an object in pymol, the surface appears to wrap the
object all around. But whether is it possible to show a surface that cover only
one side of certain part of that object？ For example, when I draw a surface of
the active site that contacts a drug, I wish the
Dear all,Could it be possible to move or rotate a subdomain of one peptide
chain around a hinge manually in pymol?Thanks in advance! Yeping SunInstitute
of Microbiology, Chinese Academy of Sciences--
Dear all,
I wish to make a movie which shows the following scenary: firstly two subunits
of a complex form the complex, and then another protein appears, competitively
bind to one subunit of that complex and substitutes the other subunit. I guess
only pymol might not be able to do these.
Dear pymol user,
I find my pymol install in win7 system have some problems on the right button
of the mouse. It cannot change the size of the the image in the Pymole viewer
window; instead, when I click right botton of the mouse and drag, the size of
the pymol viewer window changes: dragging
Dear pymol user,
I find my pymol installed in win7 system have some problems on the right button
of the mouse. It cannot change the size of the the image in the Pymol viewer
window; instead, when I click right botton of the mouse and drag, the size of
the pymol viewer window changes: dragging
Dear pymol users,
I wish to highlight the interactions between two proteins consituting the
complex. I want to make these interacting residues clear but other residues
obscure as the background in Pymol. Which would be the skill?
Thanks a lotYeping Sun
Institute of Microbiology, Chinese Academy
Dear all,
I have a protein complex which has a ring-like shape; and another protein
complex which forms a long filament. Is there a way in Pymol to measure the
angle between the ring plane and the filament?
Best regards. Yeping Sun
Institute of Microbiology, Chinese Academy of
Dear all,
I now have some problems in naming the chains in PDB files. If a PDB file
contains more than 26 chains, say, 40 chains, I can name the first 26 chains
with the letters A to Z, but how should I name the rest 14 chains？ It seems
that they can not be named with repeated letters which
Dear all,In order to emphasize local interactions of several residues within a
protein, I want to highlight these studied residues but make other residues
vague and being as background. The setting set fog, on doesn't help much
because the constrast between the studied residues and other
Dear all,
I find that when I show the protein as cartoon representation in pymol, and
select some residues to show as sticks, then the sticks do not connect to the
backbone shown by the cartoon but looks as floating over the backbone. How to
make the sticks connect to the backbone?
With many
Dear pymol user,I have a homoligomer protein composed of several same subunits.
How can I know the symmetry of it (whether it has 2, 3 or 6-fold symmetry)? Can
pymol determine this property of the protein?Best regards,Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
Dear all,I have a protein complex which contains two subunit. How can I measure
the angle between these to subunit? Thanks
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
Dive into the World of
Dear pymol user,Could you tell me how to color a polypeptide continuously from
N- to C-terminal by continuous spectrum such as red to blue?
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
Dear all
I want to display structures which contains numerous chains such as viruses in
pymol. I find these sturctures can be displayed normally as line
representation. However, when I show them as cartoon, usually only one chain
can be displayed, and usually it is cartoon loop rather than the
:
fetch 3j2v, type=pdb1, async=0
set all_states, 1
orient
as cartoon
I am using Open Source PyMOL 1.6.0.0.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Sep 2, 2014, at 6:20 AM, sunyeping sunyep...@aliyun.com
Dear all,Please see the figure (surface1.tif) I deposited in dropbox
(https://www.dropbox.com/home, Account sunyep...@aliyun.com, Password:
pymolusers). A is taken from a literature, and B is prepared by myself. In A,
the stick representation of the side chains of residues P3, D156, R97, etc.,
Dear pymol users,
I want to operate a structure whose crystal structure has one molecule in one
asymmetry unit. I try to display its polymer. I loaded the structure and used
generate command in the pymol GUI interface: Ageneratesymmetry mates4A,
and then many copies of this molecure appeared
. So what is the proper way to obtain the effects in the sample
figure?Best Regards.Yeping
On 7/10/14 12:40 PM, sunyeping wrote:
Dear all,
Could anyone tell me how the figure attached to the following web site
or the attach file is drawn? In What pymol repersentation of the
residues is shown
the hints you need.
:)
Gian
On 7/11/14 8:27 AM, sunyeping wrote:
发送时间：2014年7月10日(星期四) 21:20
收件人：pymol-users pymol-users@lists.sourceforge.net
主 题：Re: [PyMOL] what is the pymol representation in this figure?
It should be a solid surface with transparency on,
if I'm not getting it wrong.
Dear
Dear all,how can I paste pictures on this pymol mail list? Thanks.
Yeping Sun
--
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community
://kong.med.nyu.edu/
On Apr 27, 2014, at 8:50 AM, sunyeping sunyep...@aliyun.com wrote:
Dear proessor Holder and pymol users,
I previously tried to color a protein structure accord to a set of customer
data. I replaced the b factor of individual Ca atoms and colored the structure
,
Thomas
On 10 Dec 2013, at 01:04, sunyeping sunyep...@aliyun.com wrote:
Hi, professor Holder,
Thank you for the reply, but how can I do this on the level of individual
amino acids in stead of atom? I have two homolog stuctures and I want to map
the difference between the b factors
Dear all,
I am trying to map b factor onto a structure by gradually changing color. I use
the following command:
pymolspectrum b, blue_white_red, byres=1It seems to work. But I don't know how
to make pymol show a color bar presenting the range of b factor. Could you help
me? Thanks.Yeping Sun
Dear all, I want to show my protein in cartoon_tube or cartoon_loop described
in pymolwiki ( http://www.pymolwiki.org/index.php/Cartoon), but when I type the
command
show cartoon_tube, allit returns error information:Error: unknown
representation: 'cartoon_tube'. Choices: angles cgo
Dear all,If I have the structures representing two conformations of one
protein, then could I make a animation movie that shows how the protein
transforms from one conformation to the other conformation using pymol? Thanks.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
Dear all,I want to draw CA atoms of a peptide as circles, but not spheres. How
can I do that? Thanks
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
Rapidly troubleshoot problems before they affect
Dear all,I want to show amino acids in a structure according to their
flexibility (B factor) by gradually changed colors. Can pymol do this? Thanks.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
, at 11:30, sunyeping sunyep...@aliyun.com wrote:
Dear all,
I want to show amino acids in a structure according to their flexibility (B
factor) by gradually changed colors. Can pymol do this? Thanks.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
Dear pymol users,
Pdb files give B factor of each atom. How can I get B factor of the individual
residues? Thanks.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences--
November Webinars for C, C++,
Dear all,
I want to set transparecy of selected residues which are shown as sticks and I
use the command:
set stick_transparency, 0.8, sele
but it doesn't work. If I use the command:
stick_transparency, 0.8
then all sticks become transparency, including the residues I
Dear pymol users,
Could anyone tell me how to show the coordinate of a selected atom?
Regards,
Yeping Sun
--
See everything from the browser to the database with AppDynamics
Get end-to-end visibility with application
Dear pymol users,
Does anyone use the caver plugin of pymol to analyze a ion channel? I don't
know how to specify selection for the starting of plugin. Should the starting
point be at the center of the channel where there is empty and no atoms in the
molecule? or should it be certain atom of
Dear pymol users,
I want to make a cross-section on a ion tunnel protein to cut it in half and
observe the intenal characters of the tunnel. According to materials on web, I
runed the following commands:
hide all
show surface
set ray_trace_mode, 0
set two_sided_lighting, off
set
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