Re: [PyMOL] Questions about licenses
I would suggest you to use the PyMol open Source version for Research Publications. https://github.com/schrodinger/pymol-open-source Regards, Saurabh Gayali -- *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] saurabh.gay...@gmail.com / +91 8800412916 <http://example.com/>Bangalore, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> 14/01/24, 01:19:07 am On Sun, Jan 14, 2024 at 12:56 AM ALEX ZATUCHNEY via PyMOL-users < pymol-users@lists.sourceforge.net> wrote: > 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, would I be > able to include PyMOL renders in a hypothetical research paper with the > free, educational-use license? > > Thank you so much in advance, > Alex > > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] File attachments
You can always upload zip to google drive and share link. -- *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] saurabh.gay...@gmail.com / +91 8800412916 <http://example.com/>Bangalore, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> 17/08/23, 09:21:34 am On Tue, Aug 15, 2023 at 11:11 PM Istvan Kolossvary wrote: > Hi, > > I am trying to submit a question with a file attachment for illustration. > However, I always get a "550 Blacklisted file extension detected" message, > and the message is rejected. I tried .zip and then I just attached the .pdb > files directly, but none of them were allowed. What type of file attachment > is not blacklisted? > > Thank you very much, > >Istvan > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] separate two molecule as an object from a complex of four molecules
Have you tried this: https://pymolwiki.org/index.php/Split_object -- *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] saurabh.gay...@gmail.com / +91 8800412916 <http://example.com/>Bangalore, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> 03/08/23, 01:27:34 pm On Thu, Aug 3, 2023 at 8:15 AM Mukhopadhyay, Shreya via PyMOL-users < pymol-users@lists.sourceforge.net> wrote: > Public > > Hello All, > > > > I am trying to separate out two molecules(one copy for each of RSVF F1 and > F2) from one pdb (6OUS). It’s a trimeric protein bound to a Fab. > > > > I want to separate out RSVF1 and F2 proteins as one object from the bound > antibody, ie create one object with only chains A,C,E and B,D,F. If you > could explain the commands to use that will be really helpful to me. > > > > Thanks, > > Shreya > > > > > > Shreya Mukhopadhyay, PhD. (She/Her) > *Post Doc Fellow (Infectious Diseases and Vaccines-Discovery)* > > 770 Sumneytown Pike, West Point B46, 2048-C, PA 19486 > > > > > > This e-mail message, together with any attachments, contains information > of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA > 07065) and/or its affiliates, that may be confidential, proprietary > copyrighted and/or legally privileged. (Direct contact information for > affiliates is available at - Contact us - MSD > <https://www.msd.com/contact-us/>.) It is intended solely for the use of > the individual or entity named on this message. If you are not the intended > recipient, and have received this message in error, please notify us > immediately by reply e-mail and then delete it from your system. > > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] problem with ray of PNG using pymol in non-gui mode
Have you tried setting ray_trace_mode?
Info here: https://pymolwiki.org/index.php/Ray
--
*Saurabh Gayali* / Post Doctoral Fellow
saurabh.gay...@gmail.com / +91 8800412916
*CSIR-IGIB*
<http://example.com/>New Delhi, India
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21/01/22,
10:10:28 am
On Thu, Jan 20, 2022 at 11:02 PM Enrico Martinez
wrote:
> Dear Pymol Users!
> I've faced the problem of saving a PNG image without ray using the png
> command in non-gui mode. First if I do it in pymol gui
> #cmd.png('test.png',width=800,height=800,ray=0)
> .. it produces fine image (without ray)
>
> However if I execute the same command inside of my bash sript:
>
> $pymol -c -d "
> from pymol import cmd
> from pymol import preset
> cmd.load('my_pdb.pdb')
> cmd.show('surface', 'my_pdb and polymer')
> cmd.set('surface_color', 'default', 'my_pdb and polymer')
> cmd.set('transparency', '0.8', 'my_pdb and polymer')
> cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
>
> cmd.png('${vizu}/${output}_${lig_name}_interact_rep${i}.png',width=${image},height=${image},ray=0)
> "
>
> Eventually It produces the correct pymol session but on the PNG image
> I do not see any cartoon representation (only transparent surface) of
> my protein. I did some tests and found that using non-gui mode (like
> in the script shown above) pymol always sets the ray flag to ray=1
> even if it is disabled in my script. Is there any way to disable ray
> (ray=0) in my script besides setting it in the cmd.png?
> Many thanks in advance!
> Enrico
>
>
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Re: [PyMOL] how to create multi-model pdb for protein-ligand complex?
Have you tried the save command after opening both files? https://pymol.org/dokuwiki/doku.php?id=command:save Though not sure how the different poses will merge. Also looking for a solution for a similar problem. -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> 07/01/22, 05:43:49 pm On Fri, Jan 7, 2022 at 3:43 PM Enrico Martinez wrote: > Dear Autodock Users! > I am dealing with the structural analysis of the protein-ligand > interactions observed in the protein-ligand docking using VINA. > Basically operating with the outputs I have two different pdb files: > 1) for docking receptor (1 protein model) as well as for 2) docking > sollutions (100 solutions). So I use pymol to open the both filles and > visualize them > > pymol sollutions.pdb receptor.pdb > > May you suggest me some pymol command to merge the both in the pymol > to. create multi-model PDB consisted of the both receptor and ligand > poses in order then I could perform some structural analysis of this > combined complex? > Many thanks in advance > Enrico > > > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Distorted 3-10 helix
Have you tried the "DSS" command? https://pymolwiki.org/index.php/Dss ------ *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> 04/01/22, 04:38:43 pm On Thu, Dec 16, 2021 at 11:38 PM Bonsor, Daniel (NIH/NCI) [C] via PyMOL-users wrote: > Dear All, > > > > My latest structure has several 3-10 helices present, however, a few of > them in cartoon form shows the starting residue of the helix to be > distorted/twisted. > > > > The structure is 2.2Ang and I can clearly see the position of the amide > bond and the direction of carbonyl, but I cannot stop the twisting of the > cartoon. > > > > I have tried altering that residue ss to a loop which “works” (as in the > problem goes away) but I really wish to show the full helix. I have also > run DSSPtoPDB and force it not to recognize the 3-10 helices as helices but > in cartoon form you can see they are helices. > > > > Do anyone have suggestions or a way to force it to be a helix? > > [image: A close up of a toy Description automatically generated with low > confidence] > > Thanks, > > > > Daniel > > > > > > [image: Text Frederick National Laboratory on a teal background] > > > > [image: LinkedIn icon] > <https://www.linkedin.com/company/frederick-national-laboratory-for-cancer-research/> > [image: Twitter icon] <https://twitter.com/FredNatLab> [image: Facebook > icon] <https://www.facebook.com/FredNatLab> [image: Instagram icon] > <https://www.instagram.com/frednatlab/> > > *Daniel A Bonsor PhD | Scientist I* > > RAS Structural Biology > > > > > > [image: Phone icon] > > office: 301-846-5134 / cell: 443-983-2930 > > > > [image: Email icon] > > daniel.bon...@nih.gov *[Contractor]* > > > > [image: Location icon] > > Post Office Box B, Frederick, MD 21702 > > > > [image: Link icon] > > frederick.cancer.gov > > > > > > The Frederick National Laboratory for Cancer Research is operated by > Leidos Biomedical Research, Inc. for the National Cancer Institute. > > -- > > > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Ruge problem visualization of PDBQT file on pymol
I hope the "show spheres" command represents the ligands better for you. ------ *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> 04/01/22, 04:31:07 pm On Wed, Dec 15, 2021 at 11:59 PM EDUARDO JOSÉ AZEVEDO CORREA < edua...@epamig.br> wrote: > Dear friends > how are you? I hope you are doing well > I am using autodock vina for virtual screening.. I used the LigPret to > prepare my ligands into mol2 file, however when MGLTools convert the mol2 > to PDBQT and specially the vina output file in PDBQT has become a very > anomalous and strange molecule structure. > This file attached is ZINC100199761 molecule structure in mol2 generated > from SMILE sequence using LigPrep. After LigPrep I pass it > through the Avogadro to obtain the best geometry optimization > Only after that I make the PDBQT conversion using the MGLTools and so the > molecular docking using vina. > > Well did you know what is happening?? Is it a pymol visualization problem > with pdqbt files? > Could Anyone could know what the problem is and how to fix it? > Thanks a lot!! > > have a nice end year > > Kinds Regards > > Eduardo Jose Azevedo Correa > from Brazil > -- > > *Eduardo José Azevedo Corrêa* > > Biólogo| Professor e Pesquisador > > > (37)9997-5771 > > (37)3271-4673 > > *www.epamig.br <http://www.epamig.br/>* > > *EPAMIG Pitangui* > Rodovia BR - MG352 Km35 Zona Rural > > Caixa Postal 43 > > CEP 35650-000 - Pitangui - MG > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Structure alignment -- general question
extra_fit command will work in this scenario. More information in documentation here: https://pymolwiki.org/index.php/Extra_fit -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality11;> 04/01/22, 04:18:41 pm On Tue, Jan 4, 2022 at 3:18 PM George Tzotzos via PyMOL-users < pymol-users@lists.sourceforge.net> wrote: > I’m dealing with 4 heterogeneous structures belonging to the same fold. > I’d like to compare some conserved structural features and for this purpose > it would be useful that the structures are aligned and then visualised in a > grid. > > I understand that the align command works for 2 structures only. Is there > another way achieve what I described above. > > Looking forward to any suggestions > > Many thanks in advance and all the best for 2022 > > > > > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to enable Pymol when give ModuleNotFoundError: No module named '_tkinter' error
Have you tried installing tkinter by following command. sudo python -m pip install tk -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India On Fri, Jun 18, 2021 at 7:23 AM Gundala Viswanath wrote: > Hi, > I am using MacOSX Catalina. > I installed Pymol with this command: > > > brew install brewsci/bio/pymol > > However when I called it > > $ pymol > > It gave me this error: > > > 7, in > import _tkinter # If this fails your Python may not be configured for > Tk > ModuleNotFoundError: No module named '_tkinter' > > > How can I resolve this? > > > My Python version is: > Python 3.8.5 (default, Sep 4 2020, 02:22:02) > [Clang 10.0.0 ] :: Anaconda, Inc. on darwin > Type "help", "copyright", "credits" or "license" for more information. > > G.V. > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Programmatically adding hydrogen and remove water to multiple PDB files
You should use autodocktools [ADT] or openbabel for this purpose. Converting PDB to PDBQT. -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India On Thu, Jun 17, 2021 at 4:01 PM Gundala Viswanath wrote: > Hi > > I'm trying to dock a ligand to several hundred PDB files (receptors). I > thus need to prepare those files like removing water and adding hydrogen. > > I can do that manually using Pymol. But it's too troublesome. Is there a > way to do it programmatically with Pymol command line procedure? > > > Sincerely, > > G.V. > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Farewell
Thank you for the incredible support to the community via this marvelous tool. Hope to see more of your wonderful work in future. Best Regards, -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* <http://example.com/>New Delhi, India On Fri, Apr 30, 2021 at 7:47 PM Thomas Holder wrote: > Dear PyMOL community - > > The time has come for me to hand over my PyMOL development > responsibilities at Schrödinger. It's been an incredible journey for > me to get involved with the PyMOL community, to become a PyMOL fellow > in 2011 and to start working full time for the project in 2012. I'm > extremely grateful to all the people at Schrödinger who made this > possible, and of course to all of you - the user community - who've > shown me every day that my work is meaningful. > > PyMOL has a unique place within Schrödinger, and a highly motivated > and skilled team of developers and scientists stand behind it. They > have some great plans and I'm excited to watch how they will take > PyMOL to the next level. > > I don't think that my PyMOL journey is over yet. But for the next > chapter in my career, I'll "just" be a user and a member of the > community. See you around. > > Cheers, > Thomas > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] [EXTERNAL] png command in Educational Pymol
I think you can superimpose the name externally after the image is produced
using GD libraries of python.
Also I am not sure that Pymol labels could help,
https://pymolwiki.org/index.php/Label
---
I also have a question.
I am also trying to achieve something similar, but with docking output
files where models are saved as frames and I want a particular frame. I
dont know the question should be in the same thread or I should start a new
one.
--
*Saurabh Gayali* / Post Doctoral Fellow
saurabh.gay...@gmail.com / +91 8800412916
*CSIR-IGIB*
<http://example.com/>New Delhi, India
On Tue, Oct 20, 2020 at 9:17 PM Jeff Saxon wrote:
> Right, thank you! just tested it with the recent Pymol version.
> one question - is there any way to plot the name of the loaded pdb on
> the image (produced by PNG command) in some automatic fashion (it
> could be useful when I use it directly from terminal, without GUI)?
>
> вт, 20 окт. 2020 г. в 14:46, Thomas Holder >:
> >
> > See last question here ("Ray tracing does not work"):
> > https://pymol.org/edu/faq.php
> >
> > Cheers,
> > Thomas
> >
> > On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC)
> > wrote:
> > >
> > > Hi Jeff,
> > >
> > > I have the incentive version of PyMOL.
> > > It too is saving draw images with ray tracing when using the batch
> mode and also when using the pymol api in Jupyter.
> > > As you report, saving a draw image from inside PyMOL works.
> > >
> > > This is a very annoying bug.
> > > You should report it as an issue on the PyMOL github site.
> > >
> > > Perhaps this is not an issue with an order version of PyMOL.
> > > Try one from before the switch from lines to cartoon as the default
> molecular representation (say version 2.1).
> > >
> > > Best regards,
> > >
> > > Blaine
> > >
> > > 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
> > >
> > >
> > > From: Jeff Saxon [jmsstarli...@gmail.com]
> > > Sent: Tuesday, October 20, 2020 5:48 AM
> > > To: Mooers, Blaine H.M. (HSC); pymol-users
> > > Subject: Re: [EXTERNAL] [PyMOL] png command in Educational Pymol
> > >
> > > Hi Blaine,
> > > I've just checked on trial 26 day version of Pymol it use always RAY=1
> > > while I run pymol from script regardless of ray flag (tested with
> > > ray=1, ray=0, without ray as in you case etc :-)
> > > I am going to try open source pymol!
> > > Cheers,
> > > J
> > >
> > > вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
> > > :
> > > >
> > > > Hi Jeff,
> > > >
> > > > I do not know the answer to your question. This is a work around.
> > > > Try dropping ray=0 and adding the draw command with the dimensions
> in pixels (width, height).
> > > >
> > > > cmd.draw(1600,1600);cmd.png('test1600.png')
> > > >
> > > > I would not use the Educational PyMOL for the kind of serious work
> that you are trying to do.
> > > > The PyMOL Wiki has several pages about open source versions of PyMOL.
> > > > Use one of those instead.
> > > >
> > > > Best regards,
> > > >
> > > > Blaine
> > > >
> > > > 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
> > > >
> > > >
> > > > From: Jeff Saxon [jmsstarli...@gmail.com]
> > > > Sent: Tuesday, October 20, 2020 5:24 AM
> > > > To: pymol-users
> > > > Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
> > > >
> > > > hello,
> > > > I am using educational version of Pymol to generate png image of
> > > > protein-ligand complex
> > > >
> > > > First, there are no problems in the case
Re: [PyMOL] Skip Activation Window Remove
You can always use the Educational version of Pymol. Regards, *Saurabh Gayali* - <https://www.avast.com/en-in/recommend?utm_medium=email_source=link_campaign=sig-email_content=webmail_term=default3=679038cc-2984-4da3-8f35-9d7818611687> I’m protected online with Avast Free Antivirus. Get it here — it’s free forever. <https://www.avast.com/en-in/recommend?utm_medium=email_source=link_campaign=sig-email_content=webmail_term=default3=679038cc-2984-4da3-8f35-9d7818611687> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Thu, Jul 18, 2019 at 5:46 AM Neena Susan Eappen wrote: > Hello PyMOL users, > > I have been using official PyMOL build which requires a license. I do not > need any special features of pymol, is there a way to remove this 'No > License File' window? > > Many thanks, > Neena > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Align more than two structures
extra_fit aligns multiple objects to a reference object. https://pymolwiki.org/index.php/Extra_fit Regards, *Saurabh Gayali* - On Wed, Jul 10, 2019 at 9:25 AM Neena Susan Eappen wrote: > Hello PyMOL users, > > How to align more than two structures in pymol? > > Thank you, > Neena > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] How to color stick and surface representation separately
there are two ways to achieve this (might not be correct ways, but it will give you results) 1. Open the molucule and choose show as Surface [image: image.png] This will show complete molecule as a surface. Remember choosing show as surface after choosing line or cartoon will remove former from viewport. - Now choose parts you want to keep and color them before moving on to next part Next select the same molecule and enable line [image: image.png] remember to not choose line in show as menu but directly from show menu This will keep the old object and add the new line visualization. This way you can show both custom color surface and default color of line/cartoon this way has limitation that you cannot color the second scheme but have to use the default coloring way. 2. Copy the molecule you want to load and create a copy in the folder Load both moleculaes [You won't even need to align them] now You can choose any visualization for both moleculaes as they are separate files. Regards, *Saurabh Gayali* - <https://www.avast.com/en-in/recommend?utm_medium=email_source=link_campaign=sig-email_content=webmail_term=default3=679038cc-2984-4da3-8f35-9d7818611687> I’m protected online with Avast Free Antivirus. Get it here — it’s free forever. <https://www.avast.com/en-in/recommend?utm_medium=email_source=link_campaign=sig-email_content=webmail_term=default3=679038cc-2984-4da3-8f35-9d7818611687> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Sat, Jul 6, 2019 at 2:29 PM sunyeping via PyMOL-users < pymol-users@lists.sourceforge.net> wrote: > 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 blue. However, I don't know how to do this. I can color > the residue (please see the Gln in the yellow circle at > https://drive.google.com/open?id=1bviFQGUKgqLdbE-cUNDtzDZSdabc0N4Z), but > both the stick and the surface representations are colored by element. > Could anyone tell me how to color stick representation of this Gln by > element but keep its surface representation as blue? > > Thank you in advance > Yeping > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] .
IPyMOL allows you to control PyMOL <https://www.pymol.org/> sessions via IPython. This tool is ideal for situations where you’d like to present your work neatly in a Jupyter Notebook <https://jupyter.org/> or conveniently prototype PyMOL scripts. https://pypi.org/project/ipymol/ Regards, *Saurabh Gayali* - On Wed, Jul 3, 2019 at 5:50 PM O.L. Simpson wrote: > Dear Pymol Users, > > How can I integrate PyMOL into Jupiter notebooks to visualise structures? > > Best > > m.o.l.s > > > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Export molecule does not keep COLOUR* changes - RESOLVED
A similar thing happen in 3d software where generic .Obj files do not have any information of material analogous to colors in this case. They bypass this limitation by having a software specific saving file format containing all information or a separate file for material. In pymol phool scripting file can help stor coloring informatiomation for the molecules as it is highly unlikely to store color information in its generic pdb/cif format. In another approach such information can be hidden in comments in specific format that pymol would develop to parse on load event. On Thu, 27 Jun 2019, 20:09 Sarameri, Jesse, wrote: > Hello, > > > That might also explain why the same molecule loaded in LiteMol gives > different colouring. > > So the conclusion is that the colors are not defined in molecules but > instead in programs > > that displays them. > > > Thank you! > > > Regards, > > Jesse Sarameri > > > -- > *Lähettäjä:* Ali Kusay > *Lähetetty:* tiistai 25. kesäkuuta 2019 20.52.33 > *Vastaanottaja:* Sarameri, Jesse > *Kopio:* pymol-users@lists.sourceforge.net > *Aihe:* Re: [PyMOL] Export molecule does not keep changes > > > Hi Jesse, > > > > I am not aware of a structure file (i.e. PDB) which can store information > such as color and thus when you load a PDB file pymol applies the default > colors to it. > > > > You can however make it so that all proteins loaded into pymol are > automatically assigned the grey colour, this is done by editing the pymolrc. > > > > In the menu go: > > File -> Edit -> pymolrc (will create file) -> type “set cartoon_color, > grey80” > > > > When you close and reopen pymol, this will ensure that all proteins loaded > into pymol are given the grey80 colour, you can make any additional edits > to the pymolrc file as you please i.e stick color is still default > > > > Cheers, > > > > Ali > > > > *Ali Kusay *| BPharm (Hons) | PhD Candidate & Pharmacist > > *Supervised by *A/Prof Thomas Balle > > The University of Sydney School of Pharmacy | Faculty of Medicine and > Health > > 424, Brain and Mind Centre | The University of Sydney | NSW 2050 > > > > *From: *"Sarameri, Jesse" > *Date: *Wednesday, 26 June 2019 at 6:34 pm > *To: *"pymol-users@lists.sourceforge.net" < > pymol-users@lists.sourceforge.net> > *Subject: *[PyMOL] Export molecule does not keep changes > > > > Hello! > > (English is not my native language; please excuse typing errors.) > > Goal is to recolor molecule so it stays that way after the edit. > > > > This is how I thought it would work: > > Lets start by opening any molecule (like downloading 5jh0.cif from > https://www.rcsb.org/structure/5jh0) > > Changed the color of the molecule to grey, save as session (.pse file), > open it and still grey, great! > > But if I want to export to molecule (.pdb for example), open the molecule, > no changes applied. > > Tried to change Saved state settings and different formats but no effect. > > No error messages either. > > > > I did RTFM and STFW not able to find answer. > > (If I missed it, feel free to send pics with red circles and arrows to > highlight it.) > > > > Software and hardware used: > > Open source PyMOL version 2.1.0. > > Windows 10 > > Lenovo X280 Laptop > > > > Many thanks for help incase someone else might encounter this problem. > > > > Regards, > > Jesse Sarameri > > > ___ > 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 list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
