Hi Jarrett,
The issue still persists with the latest PyMOL version (3.1.6.1). I made a
new conda environment and installed Pymol and also downloaded a new license
file, renamed it to license.lic and placed in the 2 locations described
earlier:
/lustre/isaac24/scratch/nnambia1/envs/pymol36env
Box 56, Dunedin 9054
New Zealand | Aotearoa
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Hi,
I'm working on a remote cluster and using pymol without GUI and am
currently getting the license not found error. I installed pymol in a
virtual conda environment. The version of pymol I am running is pymol
3.1.4.1. I downloaded an educational license and renamed it to license.lic
and p
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Hi everyone,
just got here. I’ll break the ice with what may be a bit of a trivial question:
is anyone experiencing issues with not-so-old plugins and newer versions of
PyMOL?
My very useful plugins, among which my dearest “PyVOL”, stopped working after I
have upgraded from PyMOL 2.5.4. I’ve
WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoefg6ZIm0$>
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.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoefg6ZIm0$>
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:43
To: Irwin Selvam
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Caver3 plugin failure to initialise
Hi Irwin,
I'll ask others to double check on their setups too, but this one should have
all imports of tkinter removed. Are you using the specific `pyqt` branch there
and not
Hi,
Unfortunately, I'm still getting the same error ("no module named tkinter") and
a failure to initialise. Any ideas?
Cheers,
Irwin
From: Jarrett Johnson
Sent: 17 February 2025 00:33:26
To: Irwin Selvam
Cc: pymol-users@lists.sourceforge.
Hi all,
I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia 15.3)
but it's failing to initialise due to the "tkinter" module being missing. I've
updated python to 3.13.2, which should come with tkinter 8.6. Does anyone have
a so
e iterate over objects that are not selection of
atoms?
(I'm doing this from python using the pymol-bundle, but even in pymol I can't
find a way to save these into a file or print them or save them in a variable
somehow)
Kind regards,
Csongor
DISCLAIMER
Prezentul mesaj ?i orice documente
Hey everyone,
I am trying to use pymol from python to have some repetitive tasks done. I've
managed to get some basic functions running but I'm running into walls
frequently. I couldn't find a tutorial or documentation about this. Am I
missing something? I know it's und
Hello,
Under the plugin menu option there is an included default plugin "alignment"
tool which will bring up an alignment GUI.
Best,
Franz
From: Giuseppa Cefalu
Sent: Saturday, January 11, 2025 11:21 PM
To: PyMOL-users@lists.sourceforge.net
Subject: [External Email][PyMOL] 2
Sorry to bother you, I have registered for EDU-PyMOL for two days, but I
haven't received the license email yet? Why is this?I sincerely hope to receive
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hi,
is it possible to use the local resolution maps from cryosparc
in pymol ?
specifically we want to color the primary map based on the
local resolution map.
thanks
jpd
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r expenses (including meals).
We hope to see you at the school.
Charles, Andrey, Garib and Qingping
From: Xu, Qingping
Sent: Monday, April 8, 2024 1:26 PM
To: ccp...@jiscmail.ac.uk ; pheni...@phenix-online.org
; pymol-users@lists.sourceforge.net
Subject: 16th A
Hi Matthias, try dragging the pdb file into the center of the Pymol Viewing
screen, thanks:)
On Sun, Sep 22, 2024 at 12:21 PM Matthias Mayer <
m.ma...@zmbh.uni-heidelberg.de> wrote:
> To whom it may concern,
>
> I wanted to load a cryoEM structure of a virus-like particle (7e
e. QM via ORCA.*
*Best,*
*Joel 🚀*
On Thu, Aug 15, 2024 at 10:04 PM Xu, Qingping via PyMOL-users <
pymol-users@lists.sourceforge.net> wrote:
> Please note that we are still accepting applications, interested students
> are encouraged to apply before the deadline. A draft program is a
UfLG0Rb7c0RUuFJW2bU$
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Jose, I have a few questions about the BCIF format. Adding pymol-users
because there might be interest there as well (at least among developers).
First, at PDBe, where is the link for downloading BCIF files for a given
structure?
I only see this, for example, at https://www.ebi.ac.uk/pdbe/entry
Thank you so much!
Best,
Urban
>>> Takanori Nakane 30/07/2024 13:01 >>>
Hi,
Open the map in Coot and select [File]-[Export Map].
This allows you to save the map in .ccp4 (= .mrc)
format, which PyMOL can read.
Best regards,
Takanori Nakane
On 7/30/24 20:17, Urban Leitg
Hi,
I calculated anomalous difference maps with shelx and got .phs files as output.
I can open them in coot, but not in pymol.
I have read that I have to convert them to .mtz or rather calculate a map. Can
anyone tell me how to do that?
Thanks,
Urban
At
https://pymolwiki.org/index.php/Windows_Install
the process fails for
3. Download the appropriate wheel files
<http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol-open-source>,
which is a dead link.
Does anyone know how to run open source PyMOL on Windows OS?
Bob
Seeing as MMTF is being deprecated, I am wondering if efforts are underway
to allow PyMOL to read the BinaryCIF format?
Bob Hanson
>From July 2024 the PDB file archive will not be offered in the compressed
> MMTF format anymore. Users are strongly encouraged to switch to the BinaryCIF
&g
I want to ask for your help.
The circumstances is I want to download a license file, but when I click it, it
appears a error,just like the picture shows.So how can I solve that?<>
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O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUuFJW2bU$
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Here is the solution. Wonder if someone can help explain why the line below
gives an error about print is not defined:
out=x.cmd.do("iterate mysel and name CA, print(resi)")
Thanks!
import pymol2
x=pymol2.PyMOL()
x.start()
x.cmd.do("fetch 1crn; select mysel, /1crn//A/10-20
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 withou
Hi,
I'm currently trying out the improved movie functions of PyMOL 3.03
(timeline, scenes) which I think are a great improvement. However, I
noticed when I want to write out a composition as single frames (PNG) using
the 'Export movie' function only one frame gets written (the f
Hi
Am using pymol 3. Am I correct in thinking that you can't use the 'label'
dialogues to label nucleotides in a nucleic acid? Only proteins?
Thanks
Joel
-
<https://url.au.m.mimecastprotect.com/s/0-PhCE8wmrt130Xr6Sp2TTu?domain=mackaymatthewslab.org>
From: Jarrett Johnson
Sent: Tuesday, April 2, 2024 2:57 PM
To: Joel Mackay
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] create new object from selection - version 3.0
Hi Joel,
Thanks for y
wmrt130Xr6Sp2TTu?domain=mackaymatthewslab.org>
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Dear All,
I am wondering what parameters (cutoff distance, angles, side chains relative
orientations) are used by the functions implemented in pymol (distance (mode =7
and A>find>pi-cation))to define cation-pi interaction. I didn’t find it in the
documentation. Is there any way to even
Dear all,
I would like to compare two crystal structures of the same protein, one
obtained by X-ray diffraction and the other by neutron diffraction. I used the
Align command in PyMOL with zero cycles of refinement to align these structures
and obtain a rmsd between all non-H/D protein atoms
Hello, all.
My name is Alex Zatuchney, and I am a full-time high school student that is
looking to use PyMOL to generate renders for both self-study and a possible
research paper for the AP Research program. At some point, I would like to
publish this research. Since I am a full-time student
Hello,
I installed PyMol 2.5.7 and ran APBS electrostatic. However, I got the error:
Error encountered: No heavy atoms found. You may also see this message if
PDB2PQR does not have parameters for any residue in your protein.
The point is: I am evaluating molecules (acesulfame potassium, in this
Hello,
I am using Version 2.5.0, if I not mistaken, I installed it via apt-get:
sudo
apt-get
-y
install
pymol
In the legacy tab, there is nothing...
Thank you
On Saturday, November 25th, 2023 at 6:38 PM, Mooers, Blaine H.M. (HSC)
wrote:
> Hi Luigi ,
>
> Please include the v
Hello,
I tried to install APBS by launching Plugin manager and giving the URL of the
app:
http://www.pymolwiki.org/index.php/apbsplugin
The file has been written in ~/.pymol/startup but I got the error:
Plugin "apbsplugin" has been installed but initialization failed.
How do I prope
axis. How can I move along the x/y axis?
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I can find the polar contact between my target and a ligand, but is it possible
to get a table with all the bound residues and for all the poses, instead of
manually finding the involved residues one by one?
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Hello,
I have several poses from a docking to a protein and I have different ligands
to compare.
I can load on PyMol the different ligands on a same protein file, and I can
look at each pose for the different ligands but only, let's say, in sync: pose
1 of ligand 1 together with pose
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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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
Hello,
I am teaching at the Hanze University Groningen and I have used PyMol in two
courses (Bioinformatics and Biochemistry) for a couple of years now without any
problems. However, this year I have tried twice to get the educational license,
but I did not receive the file with the license as
Hello Everyone,
I am trying to find a way to calculate the buried surface area in a complex
with 2 molecules using pymol. Can anyone direct me to the correct way to do it?
I am currently trying out the following method, and I need to find out if there
is anything else I need to do to do this
then delete it from your system.
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chain of base. I understand this.
However, why “not /base//H+L” returns an empty selection?
Thanks!
From: Jarrett Johnson
Sent: Thursday, June 29, 2023 6:31 AM
To: Zhou, Yingyao
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Help with selecting interface residues between two
str
I am a relatively new PyMOL user and would like to get some helps from the
community.
I have two structures for the same antibody-antigen complex (with three chains:
light chain L, heavy chain H, and an antigen chain A) .
Structure "base" is the experimental true structure, structure
Hi,
I am currently a master of philosophy student and am using Pymol education. I
will need to write a thesis and was wondering if I can use this within my
thesis or not.
Thanks
Lauren
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Hi Jarrett,
Thank you very much for your kind and comprehensive advice, really appreciate
it!
I will try it out.
Kind regards,
Jessica Lim
From: Jarrett Johnson
Sent: Thursday, May 18, 2023 8:32 PM
To: #JESSICA LIM JIAYING#
Cc: pymol-users
the command gyradius as
part of the psico package in PyMOL but it only outputs a single value, and I
would have to click manually to the next state and re-enter the command to get
the next value. Hence, I would like to be able to obtain a list of values
without having to click through 100
Hi, I try to open grd files from the Open3DQSAR program.I do not see some
significant errors, but I see nothing in the visualization window.
Here is the text log from Pymol program:https://pastebin.com/qqCHDzUjHow can I
resolve this issue
<https://aka.ms/o0ukef>
From: Jarrett Johnson
Sent: Monday, March 27, 2023 4:23:30 PM
To: Kyle Moorman
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] PLEASE HELP
EXTERNAL EMAIL : Exercise caution when responding, opening
lin
To whom it may concern,
While I am a licensed user of PyMol,
h...@schrodinger.com<mailto:h...@schrodinger.com> has still not responded to
me. I have some very technical installation questions which upon trying to
solve on my own is only making the problem worse.
Below is all the informa
Hello PyMOL support team,
I am unable to install the post-translational modification (PyTM) plugin in
my PyMOL. If I try to copy-paste the PyMOLwiki or the respective repository
URL in the given box under the "Install new plugins" tab (Plugin manager),
it shows some error (...sscl:504
l.ac.uk/CCP4BB, a
mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
available at https://www.jiscmail.ac.uk/policyandsecurity/
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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
you??___
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During mutagenesis dashed yellow lines appear from the main chain of the new aa
with distances attached and they remain when moving through the various rotamer
states. Is there a way of hiding these lines and labels?
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Newbie here. Is there a way to script hiding the main chain for a named
selection as per the GUI (H-main chain)?
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would be really useful if you could guide me to do this.
Thank you,
Tanaya
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structure with the complex or the adduct-removed structure the RMSD values are
0.47 and 0.52, respectively.
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:'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
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
, January 24, 2022 10:07 AM
To: ccp...@jiscmail.ac.uk ;
pymol-users@lists.sourceforge.net ;
pheni...@phenix-online.org ; Ahrens, Kristin
Subject: Virtual Annual CCP4/APS Crystallographic School (2022) in the US
Dear Colleagues,
We are pleased to announce the virtual annual CCP4/APS
I have been using VMD for most of my MD analysis, but I am trying to learn
PyMol now. I know how to load a pdb and a dcd onto that pdb. But how do I
measure the RMSD of each frame in the DCD aligned to the starting structure,
and then output a graph like of RMSD vs frame? Doing this through
Fees: There is no fee for attending the virtual school for the chosen
applicants.
We hope to see you at the school.
Charles, Andrey, Garib and Qingping
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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
27;br. poly within 4 of resn XXX')
> > ^ Where 4 is the distance and XXX should be substituted with the
residue name of the ligand
> >
> > Cheers,
> >
> > Ali
> >
> > On 27/1/22, 10:12 pm, "Enrico Martinez" wrote:
> >
w('sticks','br. poly within 4 of resn XXX')
^ Where 4 is the distance and XXX should be substituted with the residue name
of the ligand
Cheers,
Ali
On 27/1/22, 10:12 pm, "Enrico Martinez" wrote:
Dear Pymol Users!
I am working on the visualization of the
drey, Garib and Qingping
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Hello Professor,
That's great. Finally, is it possible to show mutation information in the
labels, like "T389S", "R201E", etc.?
Best
--
From:Halil İbrahim Özdemir
Send Time:2022年1月19日(星期三) 14:05
To:孙业平
"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
tle>
Chris
> On 14 Jan 2022, at 12:03, pymol-users-requ...@lists.sourceforge.net wrote:
>
> Send PyMOL-users mailing list submissions to
> pymol-users@lists.sourceforge.net
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.sourcefor
Hi Enrico,
This is actually quite simple, see the PyMOL wiki:
https://pymolwiki.org/index.php/Aa_codes
Paste this python dictionary into PyMOL:
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN&#x
when I do the surface calculations using bash
script operating with the command lines of the pymol it produces
correctly pse session with the surfaces. BUT if I save an image using
png, the surface is totally absent. Here are my commands directly from
the shell script:
$pymol -c
ealth
424, Brain and Mind Centre | The University of Sydney | NSW 2050
On 10/1/22, 10:10 pm, "Enrico Martinez" wrote:
Dear Pymol users!
Working on the vizualisation of the protein-ligand interactions I
would like to switch from cartoon to the surface representation of the
3 to align to, this uses
the "super" alignment method but you can also use "align", "cealign", "fit",
etc. Depending on what gives the best results. Just a note, this will align all
PyMOL objects to your selected object, you can make sub selections as need
. Is there
another way achieve what I described above.
Looking forward to any suggestions
Many thanks in advance and all the best for 2022
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Hi,
I installed pymol on Ubuntu 20.04 on WSL (Windows 10) using:
sudo apt-get install -y pymol
However, when I run pymol on the command line, I get this error:
:1: DeprecationWarning: the imp module is deprecated in favour of
importlib; see the module's documentation for alternative
ch is operated by Leidos
Biomedical Research, Inc. for the National Cancer Institute.
--
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Hi,
Thanks all will give it a try
Cheers,
Chris
> On 6 Dec 2021, at 06:08, Jarrett Johnson
> wrote:
>
> IIRC when we tried with Rosetta2, PyMOL was still faster (about 2x I think)
> than the previous x86. Your mileage may vary.
>
> Best,
> Jarrett J
>
> O
Hi,
Is there a build of PyMOL for M1 Macs yet?
Cheers,
Chris
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Hi Gret,
No worries,
In regards to the selection: “resi 25 and object”
Its more so to ensure that you don’t accidently select “resi 25” from multiple
chains or objects
Like if you load two pdb files into PyMOL (say obj01 and obj02) and both have a
resi 25, then resi 25 from both objects will
e multiple chains or
objects with "resi 25", all will be included in the selection. Doing something
like resi 25 and object is safer, object is the name in the object list in PyMOL
To remove the unwanted water atoms, do:
remove other_waters
Cheers,
Ali
Ali Kusay | BPharm (Hons) |
Hello,
I wonder is there a way to contact the makers of Pymol for general question or
to request certain program features?
Regards,
K. Zeghida.___
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Thank you both for the suggestions.
I tried to upgrade. I get “pymol” is already at the latest version
All the best
George
> On 28.10.2021, at 14:40, Jarrett Johnson
> wrote:
>
> Hi George,
>
> This issue should've been addressed in PyMOL 2.5.1. I would consider
the control key pymol
crashes.
I’m using
PyMOL(TM) 2.5.0 - Incentive Product
Thanks in advance
George
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is assigning the same chain ID to multiple
> chains. Can you give each protein (open, closed) unique chain IDs and see if
> the problem persists?
>
> best,
> Zuben
> From: Brown, Zuben
> Sent: Thursday, October 14, 2021 4:42 PM
> To: George Tzotzos
> Cc: pymol-us
Apologies if this is trivial but I’m rather new to Pymol.
I’m loading a script (x.py) that allows me to visualise correlations in the
atomic movements of my protein. I have no problems with this.
My next task is to load the native pdb file (e.g y.pdb) of the same protein but
in a different
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
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
.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 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
I know this has been asked before, but
for older versions of pymol.
I just updated my pymol version to 2.5 by installing from sbgrid. I
installed on a Macbook Pro using OSX 10.15.7. The font size in the GUI is
extremely small now and I cannot find a setting to change this to a
readable size.
Any
Dear Thomas Holder,
Thank you for helping out PyMOL users like myself. Also putting up user
friendly advise for the over the years who use PyMOL.
I tend to read your email correspondence with other users, since they seem to
be more thought through than my few emails I asked in these forums
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___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/p
Dear all,
I hope you are keeping safe and well.
I am a new user to PyMOL and had a query that I hope someone can help me with.
I have performed an alignment of two homologs with the super command on PyMOL,
I have generated a rmsd value for this alignment using the C-alpha atoms as
comparison
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