Re: [PyMOL] Pymol license not found on cluster

hrodinger.com/ >> ) >> >> /lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol/license.lic >> $HOME/.pymol/license.lic >> >> I amstill getting the license not found watermark on my saved images. I >> checked the pymol path using the following code too:

Re: [PyMOL] Pymol license not found on cluster

t; watermark? > > Best > Nikhil Nambiar > > > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/l

[PyMOL] Pymol license not found on cluster

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 placed t

Re: [PyMOL] Pymol loading pdb files twice

e file >> once. I do not see this behavior in version 3.0.0. >> >> >> >> -- >> >> Kevin Jude, PhD >> >> Structural Biology Research Specialist, Garcia Lab >> >> Howard Hughes Medical Institute >> >> Stanford University School of

Re: [PyMOL] Pymol loading pdb files twice

e. I do not see this behavior in version 3.0.0. > > > > -- > > Kevin Jude, PhD > > Structural Biology Research Specialist, Garcia Lab > > Howard Hughes Medical Institute > > Stanford University School of Medicine > > Beckman B177, 279 Campus Drive

[PyMOL] Pymol loading pdb files twice

Using Pymol 3.1.3 (for mac from SBgrid) I notice that when I open pymol by double clicking a pdb file in finder or starting up from the command line with a pdb file, it appends a second state: % pymol ~/Downloads/4kc3.pdb PyMOL(TM) 3.1.3 - Incentive Product Copyright (C) Schrodinger, LLC This E

Re: [PyMOL] PyMOL 3.1.4

To add a bit to Engin’s message: under A when selecting “extract” I’m getting “copy” instead. I think it is a bug in 3.1.4. Thank you. Vaheh From: Engin Özkan Sent: Wednesday, March 19, 2025 8:02 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] PyMOL 3.1.4 Hi, In the latest version

Re: [PyMOL] PyMOL 3.1.4

instead. I think it is a bug in 3.1.4. > > > > Thank you. > > > > Vaheh > > > > *From:* Engin Özkan > *Sent:* Wednesday, March 19, 2025 8:02 PM > *To:* pymol-users@lists.sourceforge.net > *Subject:* [PyMOL] PyMOL 3.1.4 > > > > Hi, > > In

Re: [PyMOL] PyMOL 3.1.4

To:* pymol-users@lists.sourceforge.net *Subject:* [PyMOL] PyMOL 3.1.4 Hi, In the latest version of PyMOL, 3.1.4, I cannot see if an item in the list on the right-hand column is a selection or an object. The parantheses were really useful before. Is this intentional or an oversigh

Re: [PyMOL] PyMOL 3.1.4

>> >> >> >> Thank you. >> >> >> >> Vaheh >> >> >> >> *From:* Engin Özkan >> *Sent:* Wednesday, March 19, 2025 8:02 PM >> *To:* pymol-users@lists.sourceforge.net >> *Subject:* [PyMOL] PyMOL 3.1.4 >> >> &

Re: [PyMOL] PyMOL 3.1.4

strazeneca.com> wrote: > >> To add a bit to Engin’s message: under A when selecting “extract” I’m >> getting “copy” instead. I think it is a bug in 3.1.4. >> >> >> >> Thank you. >> >> >> >> Vaheh >> >> >> >&g

[PyMOL] PyMOL 3.1.4

Hi, In the latest version of PyMOL, 3.1.4, I cannot see if an item in the list on the right-hand column is a selection or an object. The parantheses were really useful before. Is this intentional or an oversight? But more urgently, for a selection I made, I no longer see the options under "A

Re: [PyMOL] [pymol] Assembly

Dear Matthias, use: set assembly, 1 set all_states, 1 fetch 7epp GUI "generate symmetry mates" does not work as the unit cell is defined as: CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1 resulting in symmetry mates shifted by 1.0 Ang. in x y z. We need a "generate biological assem

Re: [PyMOL] [pymol] Assembly

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 (7epp.pdb1) > into pymol

[PyMOL] [pymol] Assembly

To whom it may concern, I wanted to load a cryoEM structure of a virus-like particle (7epp.pdb1) into pymol 2.5.0. But instead of showing all the subunits, when I open the file, it makes a movie out of it with individual framesIs there a way to prevent this and just show the entire assembly?

Re: [PyMOL] Pymol 3 Timeline issues

> >>> Has anyone encountered similar issues? >>> >>> Thanks, >>> >>>Istvan >>> ___ >>> PyMOL-users mailing list >>> Archives: http://www.mail-archive.com/pymol-users@lists.sour

Re: [PyMOL] Pymol 3 Timeline issues

>> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > _______ > PyMOL-users mailing lis

Re: [PyMOL] Pymol 3 Timeline issues

Hi Istvan, I have related but not the same problems with pymol3 when making the movies. Using the pymol script that works for pymol 2.5, pymol3 could only produce a movie for the first 240(?) frames and I could not find the setting to fix this issue. In addition, I believe they also changed the de

Re: [PyMOL] Pymol 3 Timeline issues

gt; Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http

Re: [PyMOL] Pymol 3 Timeline issues

t now, it takes 24-48 hours to produce a 3000 frame movie, which is >> only 100 seconds. >> >> Has anyone encountered similar issues? >> >> Thanks, >> >>Istvan >> ___ >> PyMOL-users mailing list >

[PyMOL] Pymol 3 Timeline issues

Hi, I have had these issues with the new timeline. It works fine with scenes and short multi-state objects (like those showcased in the Pymol 3 online visualization course) but when it comes to real life MD trajectories I found two "dealbreaker" issues. 1) With complex movies based on MD traject

[PyMOL] PyMOL 3 Webinar Recording and Online Course

Hello everyone, I recently covered many of the new features of PyMOL 3.0 during a webinar hosted by Schrödinger, the recording of which can be found here: Webinar Recording

Re: [PyMOL] Pymol not opening files

Thanks. I will try that. On Sun, 25 Feb 2024, 07:08 Jared Sampson, wrote: > Hi Shivani - > > PyMOL's defer_builds_mode > setting can improve > performance when loading large trajectories. > > You can type `set defer_builds_mode, 3` on the PyMOL

Re: [PyMOL] Pymol not opening files

Hi Shivani - PyMOL's defer_builds_mode setting can improve performance when loading large trajectories. You can type `set defer_builds_mode, 3` on the PyMOL command line or adjust it via the Settings > Edit All menu. Hope that helps. Cheers, J

Re: [PyMOL] Pymol not opening files

I would not use pymol for big trajectory analysis. On Fri, 23 Feb 2024 at 22:13, shivani godbole wrote: > Hello, > > This is Shivani Godbole. I use Pymol for the movie files generated using > MD simulations. I am trying to use Pymol to visualize one of the movie > files which is around 2 GB in

Re: [PyMOL] Pymol not opening files

mediately notify the sender by return email and delete this email from your devices. From: shivani godbole Sent: Friday, February 23, 2024 3:12:31 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol not opening files Hello, This is Shivani Godb

[PyMOL] Pymol not opening files

Hello, This is Shivani Godbole. I use Pymol for the movie files generated using MD simulations. I am trying to use Pymol to visualize one of the movie files which is around 2 GB in size, but Pymol keeps crashing every time I open it. I was hoping you could assist me with the same. My computer uses

Re: [PyMOL] Pymol Getting rid of the Colorbar

_ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > -- > > *Jarrett Johnso

Re: [PyMOL] Pymol Getting rid of the Colorbar

__ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL _

[PyMOL] Pymol Getting rid of the Colorbar

Dear colleagues, I am using Pymol electrostatic potential to surface mapping quite often. But I have the issue that if I use command line mode, I always get the colorbar. I would prefer to use custom colorbar, which I can make e.g. in photoshop, but to hide the colorbar by default. Whenever I

[PyMOL] PyMol Education license

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

[PyMOL] Pymol education uses for thesis

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 ___ PyMOL-users mailing list Archives: http://www.mail-archive.com

[PyMOL] Pymol registration Problem

Hi, I wanted to register using giving my credentials and email id to Pymol for educational purpose on 25th December. I did not get any registration confirmation email. I checked my inbox and Junk Folder on outlook. No email from Pymol. Then I emailed Pymol regarding the problem @h...@schrodinger

Re: [PyMOL] pymol for educational purpose

_ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___

[PyMOL] pymol for educational purpose

Goodmorning, I am a student of the University of Pavia and i need pymol; I tried to register on the site for getting it free but the confirmation email didn't arrive. How can i fix this? Have a good day. Letizia Pizzorni. ___ PyMOL-users mailing list Arc

[PyMOL] PyMOL Announcements (Fellowship & Future of PyMOL)

PyMOL. Stay tuned for more details on our website about PyMOL 3.0 and our future roadmap later this year. Best, PyMOL Development Team -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol

Re: [PyMOL] "PyMOL-users" mailing list

ribe -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] "PyMOL-users" mailing list

To whom it may concern, I am sorry, but I wonder if this is the address I should write to if I have questions about PyMOL. Kind regards, ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: h

Re: [PyMOL] pymol education license

Wow, good to hear your advice. Thank you! -Original Messages- From:"EDUARDO JOSÉ AZEVEDO CORREA" Sent Time:2022-06-18 03:29:37 (Saturday) To: "Jarrett Johnson" Cc: "Xiang Zhang" , "Pymol User list" Subject: Re: [PyMOL] pymol education license

Re: [PyMOL] pymol education license

gt; I can't receive pymol education license in my mail box even though I >> tried 2 mail address. >> >> Best, >> Xiang Zhang >> >> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pym

Re: [PyMOL] pymol education license

_ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL _

Re: [PyMOL] pymol education license

-Original Messages- From:"Xiang Zhang" Sent Time:2022-06-17 12:13:07 (Friday) To: pymol-users@lists.sourceforge.net Cc: Subject: pymol education license Hi I can't receive pymol education license in my mail box even though I tried 2 mail address. Best, Xiang Zhang__

[PyMOL] PyMOL scripting issues

Hello, I have a problem with PyMOL. I am writing a more complex automation script, and I want to import pymol's cmd module. The problem is that the python interpreter on my linux system doesn't recognize pymol and it throws an ModuleNotFound Error. I have a Ubuntu system and I installed pymol

Re: [PyMOL] pymol cartoon for hexamer

Hi, You have to predict how six monomers assemble into a hexamer. This can be done by AlphaFold multimer or ColabFold notebook. Best regards, Takanori Nakane 差出人: vivek ambastha 送信日時: 2022年3月22日 12:56 宛先: pymol-users@lists.sourceforge.net 件名: [PyMOL

[PyMOL] pymol cartoon for hexamer

Hello all, I am naïve to pymol or even protein structure. I need help in creating the hexameric model of a protein whose structure is in predicted through alpha folds. I can download the monomer. My objective is to develop a cartoon for the hexamer using these six individual monomers. Is this po

Re: [PyMOL] Pymol-Alignment Module

Hi Ecem - If I understand correctly, you first want to align on one set of residues and calculate their RMSD, then to calculate the RMSD for the remaining residues without moving the structures. This is straightforward using PyMOL's internal command line. ``` # Create two selections called "sel1

[PyMOL] Pymol-Alignment Module

Dear Pymol community, I have a question about alignment module of Pymol. I have two different pdb ids and each have about 100 amino acid long. I would like to align the specific parts of these proteins and see both how the rest of the proteins and also these specific parts superimpose with each ot

Re: [PyMOL] PyMOL for M1 macs

sers >>> >> <mailto:pymol-users@lists.sourceforge.net>> wrote: >>> Hi, >>> >>> Is there a build of PyMOL for M1 Macs yet? >>> >>> Cheers, >>> >>> Chris >>> >>> >>> ____

Re: [PyMOL] PyMOL for M1 macs

>> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] PyMOL for M1 macs

t;> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> > > > -- > > *Jarrett Johnson* | Senior Developer, PyMOL > > _

Re: [PyMOL] PyMOL for M1 macs

ing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > -- > Jarrett Johnson | Senior Developer, PyMOL > >

Re: [PyMOL] PyMOL for M1 macs

ol/lists/pymol-users/unsubscribe > -- *Jarrett Johnson* | Senior Developer, PyMOL ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] PyMOL for M1 macs

Hi, Is there a build of PyMOL for M1 Macs yet? Cheers, Chris ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] PyMOL-users Digest, Vol 185, Issue 11

> -- > > Message: 1 > Date: Sun, 24 Oct 2021 12:32:19 + > From: Xiao Yin Lee > To: "pymol-users@lists.sourceforge.net" > > Subject: [PyMOL] show cartoon mode failed > Message-ID: <1635078740242.19...@kuleuven.be> > Con

Re: [PyMOL] pymol installation error

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

Re: [PyMOL] pymol installation error

amp;, 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 > To:pymol-users > Subject:[PyMOL] pymol i

Re: [PyMOL] pymol installation error

.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

[PyMOL] pymol installation error

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

[PyMOL] PyMol warning while loading mmcif file

Hi Everyone, I have a structure of protein ligand complex generated using CCP4. While trying to load the mmcif file of the structure , I am getting this warning *mmCIF- Warning: no coordinates found in data_comp_list* *mmCIF- Warning: no coordinates found in data_comp_DRG* The structure has two

[PyMOL] PyMOL 2.5.1 Released

Greetings all, A maintenance release for 2.5 (as 2.5.1) has been uploaded to https://pymol.org/. Details of maintenance releases for 2.5 can be found at the bottom of https://pymol.org/dokuwiki/doku.php?id=media:new25. We will continue to address feedback and bug reports and expect to have 2.5.2 o

Re: [PyMOL] PyMOL 2.5 released

Hi, Open-source features are typically added on a rolling basis as they're implemented (for example, support for curved helices have been in open source since last October), so many of the features listed here (the non-Incentive Only ones) should have already applied. If they aren't, feel free to

Re: [PyMOL] PyMOL 2.5 released

very good. When will this migrate to github.com/schrodinger/pymol-open-source.git? On 05/10/2021 12:27 PM, Jarrett Johnson wrote: Greetings, We are happy to announce the release of PyMOL 2.5. Download ready-to-use bundles from https://pymol.org/ or update your installation with "conda instal

[PyMOL] PyMOL 2.5 released

Greetings, We are happy to announce the release of PyMOL 2.5. Download ready-to-use bundles from https://pymol.org/ or update your installation with "conda install -c schrodinger pymol". New features include: - Multiple-level undo for PyMOL actions (Incentive Only) - Curved cartoon cylindrical he

Re: [PyMOL] Pymol in conda-forge osx-arm64 for new M1 Macs

Hi Florian, This is an eventual goal for the *schrodinger *channel. First I'd like to have conda-forge's qt/pyqt support osx-arm64 and our CI runner which provides the mac builds support M1 too. Best, Jarrett J. On Mon, May 3, 2021 at 11:34 AM Florian Nachon wrote: > Hello, > > I want to inst

[PyMOL] Pymol in conda-forge osx-arm64 for new M1 Macs

Hello, I want to install a native version of Pymol for the new M1 Mac with conda but Pymol is not yet in the new osx-arm64 platform in conda-forge (https://conda-forge.org/blog/posts/2020-10-29-macos-arm64/ ) Is there any work to put

Re: [PyMOL] PyMOL-users Digest, Vol 177, Issue 5

In case anyone has a similar problem, here is my solution from pymol import cmd from glob import glob cmd.do("run list_hb.py") for file in glob("model*.pdb"): print(file) cmd.load(file) obj=cmd.get_object_list('all') print(obj) #hydrogen bonds cmd.do("list_hb all, all, write_distances_file=hb_"+s

[PyMOL] pymol from no-gui mode

Dear PyMol users, I would like to integrate pymol in my scripting workflow in order to save images/pymol sessions of different protein-ligand complexes. Notably I have a typical autodock output in multi-model format of 20 ligand poses and 1 snapshot of the protein. I need to execute from the termi

Re: [PyMOL] Pymol install on CentoOS7

Hi Yanni, What's your Python version? You need at least Python 3.6. If you don't have Python 3.6 available, you can try the legacy Python 2 branch: https://github.com/schrodinger/pymol-open-source/tree/py2 Cheers, Thomas > On Oct 6, 2020, at 2:53 PM, Yanni G wrote: > > Hello everyone > > I

Re: [PyMOL] Pymol install on CentoOS7

Hi Yanni, If you have root access (su), it might be easier to try "Open-Source PyMOL in Linux Distros" ( https://pymolwiki.org/index.php/Linux_Install#Open-Source_PyMOL_in_Linux_Distros). This approach saves the process of compiling the code manually. Best, Y. Tao Yanni G 于2020年10月7日周三 上午5:21写

[PyMOL] Pymol install on CentoOS7

Hello everyone I'm having difficulty installing pymol on my Centos7 machine. I have followed the instructions on the Pymol wiki page but when I try to build+install, I get this error: python3 setup.py build install --home=/opt/pymol-osbuild File "setup.py", line 227 out.write(f'set PYMOL_

[PyMOL] Pymol course

Hi All, I am preparing a simple intro for pymol for my students at my university and I am wondering if its fine to copy some part and take pics from the pymol manual and the wiki. Or I have to paraphrase first and ask first for the copyright permission. Again it is only for educational purposes in

[PyMOL] Pymol Will Not Open PDBs on a New HDD

Hi, I recently moved my documents to a new hard drive disk. Interestingly, Pymol will not open any pdb's in the new location. When the same file was moved outside the new disk the problem goes away. Other visualization programs, e.g. Chimera, work fine. I'm working on Ubunut 20.04, and I'm usi

Re: [PyMOL] PyMOL-users Digest, Vol 169, Issue 9

> On Jun 7, 2020, at 17:28, 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.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] PyMOL 2.4 released

Greetings, We are happy to announce the release of PyMOL 2.4. Download ready-to-use bundles from https://pymol.org/ or update your installation with "conda install -c schrodinger pymol". Highlights: - Incentive PyMOL only: - Support for https://lookingglassfactory.com/schrodinger - Pi-Pi

Re: [PyMOL] Pymol Rendering

Hi Seán, Enabling multi-layer transparency should do the trick. From the menu: Setting > Transparency > Multi-Layer From the command line: PyMOL> set transparency_mode, 1 Hope that helps. Cheers, Thomas > On Feb 24, 2020, at 10:32 PM, Seán Downey wrote: > > Hi all, > > I am trying to r

[PyMOL] Pymol Rendering

Hi all, I am trying to render an image of a protein structure with a transparent surface and a slightly less transparent cartoon structure, of the same colour, in order to show both the cartoon structure and a ligand (non-transparent) bound within as well as the surface. Using the ray option, the

[PyMOL] PyMOL crashes when building a nanotube

Hi, I'm building a nanotube by adding some polymer side chains to a nanotube that I already have (pdb files). I've been able to do about 1/2 of adding the side chains but now when I open the pse file or the saved project as a pdb to continue editing it, PyMOL crashes as soon as I open the builder

[PyMOL] Pymol, qt organization question

Greetings, I built Pymol 2.4.0.0a from the open source under mingw64 on W10(64 bit) and also have another variant from Christoph Gohlke's site here: https://www.lfd.uci.edu/~gohlke/pythonlibs/ When run in cmd.exe and access to the mingw64 directories is allowed mine starts right up in qt m

Re: [PyMOL] PyMOL 2.3.2 - GUI not printing/returning values when running get, count_atoms etc

Did you try: ` print(cmd.get("light_count"))`? On Sun, Jan 5, 2020 at 12:02 AM Joe Kaczmarski wrote: > Hi all, > > Pymol is not returning/printing values in the GUI command line window > after I run any command that is supposed to return/print a value (e.g. get, > count_atoms, get_viewport). > >

[PyMOL] PyMOL 2.3.2 - GUI not printing/returning values when running get, count_atoms etc

Hi all, Pymol is not returning/printing values in the GUI command line window after I run any command that is supposed to return/print a value (e.g. get, count_atoms, get_viewport). For example, if I run >get light_count, nothing is returned. However, I can get the value to print by running

Re: [PyMOL] Pymol APBS plugin error

Also, keep in mind that pdb2pqr isn't python3 friendly so you will have to use an externally generated pqr file. The current mechanism for calling pdb2pqr from within the APBS Tool results in pdb2pqr running under the same python as pymol. Jack On Mon, Dec 2, 2019 at 5:58 PM Jack Howarth

Re: [PyMOL] Pymol APBS plugin error

You need more patches in your installed Pmw 2.0.0. On MacPorts, we use... https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2-py36.diff and https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2.diff applied over Pmw_2_0_0. Jack

[PyMOL] Pymol APBS plugin error

Dear all, I get the following errors when trying to launch the APBS plugin from the plugins menu Traceback (most recent call last): File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py", line 322, in command = lambda s=self: APBSTools2(s)) File "/home/quyen/Pymol/i

Re: [PyMOL] Pymol Qt Wayland

Hi Thomas, Yes that appears to work wiith qt5-wayland package installed. I run pymol in a container so the command is #!/bin/bash -e export LC_LANG="en_US.utf8" toolbox -v run --container pymol bash -exec 'QT_QPA_PLATFORM=xcb ~/Pymol/install/bin/pymol' Best, Quyen On Tue, Nov 5, 2019 at 10:12

Re: [PyMOL] Pymol Qt Wayland

Hi Quyen, This works for me: export QT_QPA_PLATFORM=xcb pymol Hope that helps. Cheers, Thomas On Sun, Nov 3, 2019 at 6:15 AM RDirective wrote: > > Dear all, > > I have a slight problem with Pymol on Fedora 31. The vanilla distribution > runs Gnome on Wayland. Pymol complains that [q

[PyMOL] Pymol Qt Wayland

Dear all, I have a slight problem with Pymol on Fedora 31. The vanilla distribution runs Gnome on Wayland. Pymol complains that [qt.qpa.plugin: Could not find the Qt platform plugin "wayland" in ""]. The GUI and 3D render will still work but if I were to install qt5-qtwayland-devel to provide the

Re: [PyMOL] PyMol: incomplete replacement of b- and q-factors

Hi Joe, There can be atoms without coordinates. In particular, when loading mmCIF files, PyMOL fills in dummy-CA atoms for missing residues, to provide a complete sequence display in the sequence viewer. "alter" iterates over all atoms, including those without coordinates. "iterate_state" only

[PyMOL] PyMol: incomplete replacement of b- and q-factors

Hello all, I am trying to color several proteins by different factors, e.g., distance from a given point (here the origin). To do this, I replace the q-factor (or b-factor) with my variable of choice. However, most of my files have one or a few residues that are for some reason not affected by

Re: [PyMOL] PyMOL-users Digest, How to download and install (Pedro Lacerda)

Hi Pedro For Windows, you can get precompiled open source PyMOL from http://www.lfd.uci.edu/~gohlke/pythonlibs/. Dr. Annemarie Honegger Dept. of Biochemistry Zürich University Winterthurerstrasse 190 8057 Zürich Switzerland e-mail:

Re: [PyMOL] PyMOL-users Digest, Vol 158, Issue 13

Dear sunyeping The critical step in calculating a 3D superposition is the decision of which atom in one structure to fit on which atom in the second structure. Actually fitting the transformation matrix is trivial in comparison. In PyMOL you have different ways to determine what you fit: If you

Re: [PyMOL] PyMOL-users Digest, Vol 158, Issue 6

Dear Yeping You can color the surface independent of the atom color with the command set surface_color, (color), (selection) similarly, you color the cartoon representation dependent of the atom color with the command set cartoon_color, (color), (selection) best regards Annemarie __

Re: [PyMOL] pymol in no-gui mode

thank you very much, Ali! I only changed the quotes in your script because I have integrated it to my shell script in order to use with the varibables: # run pymol to align the snapshots and save it to the session pymol -c -d " from pymol import cmd cmd.load('${sim}/${simulation}_after_min

Re: [PyMOL] pymol in no-gui mode

Hi James, Just a follow up, I would still recommend you use the script in a file to do this as it is less messy but it can be done: pymol -c -d ' from pymol import cmd cmd.load("A.pdb") cmd.load("B.pdb") cmd.load("C.pdb") cmd.super("C*","A*") cmd.super("B*","A*") cmd.bg_color("white") cmd.save("

[PyMOL] pymol in no-gui mode

hello there, As a part of my scripting routine, I would like to use pymol in no-gui mode (directly in the linux shell) to do the following things: 1) load in pymol 3 conformations of the same protein, which are defined as A.pdb B.pdb C.pdb 2) superimpose C to A using "super" or alternatively (whic

Re: [PyMOL] PyMOL-users Digest, Vol 157, Issue 6

Dear Annemarie, Thank you very much it worked !!! Stéphane -- Stéphane Abel, Ph.D. Commissariat à l’Energie Atomique et aux Energies Alternatives Centre de Saclay DSV/ISVFJ/SB2SM Bat 528, Office 138C Gif-sur-Yvette, F-91191 FRANCE Phone (

Re: [PyMOL] PyMOL-users Digest, Vol 157, Issue 2

Dear Hao In PyMOL bonds are essentially drawn based on a distance cut-off: Two atoms are considered bonded if distance <= connect_cutoff + (vdw1 + vdw2)/2 You can generally adjust the sensitivity of bond recognition by adjusting the connect_cutoff global variable ( https://pymolwiki.org/index.

Re: [PyMOL] [pymol] Wrong Visualization of set Spheres

Hi Julian, I think the problem is that you format the radius as an integer: # wrong (%d) cmd.alter("helix%d" % i, expression="vdw=%d" % vdw_a) # correct (%f) cmd.alter("helix%d" % i, expression="vdw=%f" % vdw_a) # also correct: cmd.alter("helix%d" % i, "vdw=vdw_a", space={'vdw_a': vdw_a}) Hope t

Re: [PyMOL] Pymol Activation

Hi Julia, As a student, you can register for a free educational license: https://pymol.org/edu/ Cheers, Thomas > On Apr 4, 2019, at 8:54 PM, Julia Garcia wrote: > > Hello, > > I am currently a student and I am using pymol in one of my classes. I was > able to download the software, but

Re: [PyMOL] Pymol recolour B factors

Hi Mark, In that data2bfactor.py script (which I wrote) you need to provide the molecular object name, not a file name. In other words in your example you should load the 1d3z.pdb file as an object (defaults to 1d3z as object name). Then after using the run command to load the script into you

[PyMOL] Pymol recolour B factors

Hello, I'm trying to recolour the B factors in a pymol file with chemical shift differences (from NMR data). There's a nice script here for this http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ (data2bfactor.py) and also a simpler one here https://figshare.com/articles/Pymol_script_loadB

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