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From: Jared S. <jar...@co...> - 2024-02-25 06:07:55
|
Hi Shivani - PyMOL's defer_builds_mode <https://pymolwiki.org/index.php/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, Jared On Fri, Feb 23, 2024 at 4:15 PM shivani godbole <shi...@gm...> 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 size, but Pymol keeps crashing every time I > open it. I was hoping you could assist me with the same. My computer > uses 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz 2.42 GHz processor > and has 8 GB RAM and a 64-bit OS. > > Thank you! > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: Jared S. <jar...@co...> - 2024-02-25 04:44:10
|
Hi Nikita - To me this looks like the cartoon representation for missing residues, which is controlled by the cartoon_gap_cutoff <https://pymolwiki.org/index.php/Cartoon_gap_cutoff> setting. If you either `hide cartoon` or `set cartoon_gap_cutoff, 0`, does it go away? Usually the dashed line would be somewhat curved for a normal gap to mimic an unmodeled flexible loop, but I can reproduce something similar to your image by creating a new object containing only with two non-contiguous residues and showing the cartoon for that object: ``` fetch 1shv as cartoon create gap_res, polymer.protein and resi 237+243 show sticks, gap_res ``` Hope that helps. Cheers, Jared On Sat, Feb 17, 2024 at 3:36 AM Maisnam Nikita Chanu <mni...@gm...> wrote: > Dear All, > > My name is Nikita, I am a graduate student at Academia Sinica, Taiwan. > This e-mail aims to ask for help in identifying the bond/interaction > between two residues. > > I am currently learning about PyMol to utilize in my project. I used PyMol > to visualize potential H-bond interactions in specific amino acid residues. > However, I have just discovered that Arg465 and Ser461 show a distinct > interaction, as shown in the file. > Please help identify this interaction. > I would be grateful for any help or suggestions. > > Please don't hesitate to contact me if you have any questions. > I look forward to hearing from you. > > Best regards, > Nikita Chanu > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: Petro <sub...@kh...> - 2024-02-24 11:14:09
|
I would not use pymol for big trajectory analysis. On Fri, 23 Feb 2024 at 22:13, shivani godbole <shi...@gm...> 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 size, but Pymol keeps crashing every time I > open it. I was hoping you could assist me with the same. My computer > uses 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz 2.42 GHz processor > and has 8 GB RAM and a 64-bit OS. > > Thank you! > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: Roy, K. R. <kroy3@CougarNet.UH.EDU> - 2024-02-23 21:58:09
|
Hi Shivani, To avoid PyMOL crashes when handling large movie files, try reducing the file size, increasing virtual memory, minimizing memory usage by adjusting PyMOL settings, loading only specific frames, upgrading RAM or CPU, preprocessing the movie file with external tools, and closing other memory-intensive apps. Regards, [University of Houston logo] Kushal Raj Roy (he/him) MS | BS Research Assistant Department of Biology & Biochemistry University of Houston kr...@uh...<mailto:kr...@uh...> https://uh.edu<https://uh.edu/> CONFIDENTIALITY NOTICE: The information in this email may be confidential and/or privileged. If you are not the intended recipient, then any review, dissemination, or copying of this email and its attachments, if any, or the information contained herein is prohibited. If you have received this email in error, then please immediately notify the sender by return email and delete this email from your devices. ________________________________ From: shivani godbole <shi...@gm...> Sent: Friday, February 23, 2024 3:12:31 PM To: pym...@li... <pym...@li...> Subject: [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 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz 2.42 GHz processor and has 8 GB RAM and a 64-bit OS. Thank you! |
From: shivani g. <shi...@gm...> - 2024-02-23 21:12:58
|
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 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz 2.42 GHz processor and has 8 GB RAM and a 64-bit OS. Thank you! |
From: João C. M. R. <ra...@mb...> - 2024-02-19 07:20:12
|
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. However, I would like to understand how Align calculates the rmsd, specifically how does it handle alternate residue conformations. Does it pair side-chain conformations based on their name (e.g. A, B, C..) or on their spatial proximity (i.e., conformations are paired regarding their position). I can imagine 2 scenarios that might be problematic: 1) where the side-chain conformations closer in space have different names; 2) where one structure has a double side-chain conformation, and the other has a single conformation. Best regards, Joao Ramos |
From: Maisnam N. C. <mni...@gm...> - 2024-02-17 08:33:55
|
Dear All, My name is Nikita, I am a graduate student at Academia Sinica, Taiwan. This e-mail aims to ask for help in identifying the bond/interaction between two residues. I am currently learning about PyMol to utilize in my project. I used PyMol to visualize potential H-bond interactions in specific amino acid residues. However, I have just discovered that Arg465 and Ser461 show a distinct interaction, as shown in the file. Please help identify this interaction. I would be grateful for any help or suggestions. Please don't hesitate to contact me if you have any questions. I look forward to hearing from you. Best regards, Nikita Chanu |
From: Thomas S. <tho...@sc...> - 2024-02-16 16:56:23
|
Hello Haruki, My name is Thomas Stewart and I'm one of the PyMOL developers at Schrodinger. You can use an educational license to fulfill course or program requirements such as a Master's thesis or dissertation. We hope to reword the website in the near future to make it more clear when educational and academic licenses should each be used. Thanks, Thomas Stewart On Thu, Feb 15, 2024 at 4:08 AM MF SOEJIMA Haruki < soe...@st...> wrote: > To whom it may concern, > > My name is Haruki Soejima and I am studying at the Graduate School of > Marine Biosciences, Kitasato University, Japan. > The purpose of this e-mail is to ask you a question about the license of > PyMOL. > > I used the “Educational-Use-Only PyMOL” in my study for my Master's > thesis. However, I have just discovered that I must purchase a license for > “PyMOL” for academic purposes. > Is my Master's thesis educational or academic? > I will pay the cost as soon as possible if it is academic. > > Please don't hesitate to contact us with any further queries. > I look forward to hearing from you. > > Best regards, > Haruki Soejima > > ーーーーーーーーーーーーーーーーー > 北里大学 大学院 > 海洋生命科学研究科 > 水族病理学研究室 > MF22013 > 副島 晴希(ソエジマ ハルキ) > 電話:080‐5698‐3992 > メール:soe...@st... > ーーーーーーーーーーーーーーーーー > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: MF S. H. <soe...@st...> - 2024-02-15 09:06:59
|
To whom it may concern, My name is Haruki Soejima and I am studying at the Graduate School of Marine Biosciences, Kitasato University, Japan. The purpose of this e-mail is to ask you a question about the license of PyMOL. I used the “Educational-Use-Only PyMOL” in my study for my Master's thesis. However, I have just discovered that I must purchase a license for “PyMOL” for academic purposes. Is my Master's thesis educational or academic? I will pay the cost as soon as possible if it is academic. Please don't hesitate to contact us with any further queries. I look forward to hearing from you. Best regards, Haruki Soejima ーーーーーーーーーーーーーーーーー 北里大学 大学院 海洋生命科学研究科 水族病理学研究室 MF22013 副島 晴希(ソエジマ ハルキ) 電話:080‐5698‐3992 メール:soe...@st... ーーーーーーーーーーーーーーーーー |
From: Takanori N. <tna...@os...> - 2024-02-07 11:09:39
|
Hi, Probably you need to explicitly define bonds. Relevant pages are: https://pymolwiki.org/index.php/Bond https://pymolwiki.org/index.php/Unbond https://pymolwiki.org/index.php/Sticks If these points are not atoms, you can use CGOs instead: https://pymolwiki.org/index.php/CGO_Shapes Best regards, Takanori Nakane On 2/7/24 19:25, Daniele Notarmuzi wrote: > Hello! > > I am trying to draw sticks given a set of coordinates and sometimes I > succeed, sometimes I do not. In my silly mind, what I would like to do > is to give two set of 3D coordinates and have a stick drawn between > them. For example, given the set of coordinates > > 0.0 0.0 0.0 # coord 1 start > 1.0 0.0 0.0 # coord 1 end > 0.0 0.0 0.0 # coord 2 start > 0.0 1.0 0.0 # coord 2 end > 1.0 0.0 0.0 # coord 3 start > 0.0 1.0 0.0 # coord 3 end > > I would like to obtain a triangle. This actually happens. However, if I > replace all the 1.0 with 2.0, I only get the two short sides of the > triangle and if I replace the 1.0 with 3.0 I get nothing. > > I deduce that there is a certain distance below which a stick is drawn > (?). I do not see how to make this criterion work for my problem, given > that there could be coordinates that are very close but do not need to > be connected and coordinates that are very far and that do need to be > connected. > > So my question is: how to draw sticks between points, given the "head" > and the "tail" coordinates of each stick I want to draw? > > Thank you in advance. > > PS: sorry if the question is silly, I have looked around and found > nothing... > > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: Daniele N. <dan...@gm...> - 2024-02-07 10:26:17
|
Hello! I am trying to draw sticks given a set of coordinates and sometimes I succeed, sometimes I do not. In my silly mind, what I would like to do is to give two set of 3D coordinates and have a stick drawn between them. For example, given the set of coordinates 0.0 0.0 0.0 # coord 1 start 1.0 0.0 0.0 # coord 1 end 0.0 0.0 0.0 # coord 2 start 0.0 1.0 0.0 # coord 2 end 1.0 0.0 0.0 # coord 3 start 0.0 1.0 0.0 # coord 3 end I would like to obtain a triangle. This actually happens. However, if I replace all the 1.0 with 2.0, I only get the two short sides of the triangle and if I replace the 1.0 with 3.0 I get nothing. I deduce that there is a certain distance below which a stick is drawn (?). I do not see how to make this criterion work for my problem, given that there could be coordinates that are very close but do not need to be connected and coordinates that are very far and that do need to be connected. So my question is: how to draw sticks between points, given the "head" and the "tail" coordinates of each stick I want to draw? Thank you in advance. PS: sorry if the question is silly, I have looked around and found nothing... |
From: Saurabh G. <sau...@gm...> - 2024-01-13 19:49:35
|
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] sau...@gm... / +91 8800412916 <http://example.com/>Bangalore, India [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 14/01/24, 01:19:07 am On Sun, Jan 14, 2024 at 12:56 AM ALEX ZATUCHNEY via PyMOL-users < pym...@li...> 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/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: ALEX Z. <aza...@hc...> - 2024-01-13 19:24:31
|
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 |
From: Naveen R. <nav...@gm...> - 2024-01-05 12:48:00
|
Hello all, I recently brought a new laptop (Windows 11) and had installed Anaconda along with their python interpreter. When it came time to install PyMOL, I saw on the website that it was possible to install PyMOL through Anaconda. This was very convenient for me, as with my previous laptop (Windows 10), I ran into issues having two python installs on the same device. Installing PyMOL through Anaconda in the base (root) environment would save me from a potential hassle. I ran the command on the PyMOL website (conda install -c conda-forge -c schrodinger pymol-bundle) in the Anaconda prompt, installing PyMOL in the default environment. When I tried to open PyMOL through the desktop, nothing happens. However, when I try to open PyMOL through the Anaconda Navigator, I get the following error message: Traceback (most recent call last): File "C:\ProgramData\anaconda3\Scripts\pymol-script.py", line 6, in from pymol import launch File "C:\ProgramData\anaconda3\Lib\site-packages\pymol\__init__.py", line 620, in import pymol._cmd ImportError: DLL load failed while importing _cmd: The specified module could not be found. After this error, I installed PyMOL through the installer (to check if it was an issue with the PyMOL version) and it worked. With this in mind I carried out the following troubleshooting steps: * Install PyMOL through Anaconda (with the command from the website) on another PC that has not PyMOL installed before. * Compare the installed packages in the install from Anaconda and from the installer. Resolve the differences in the Anaconda install. * Install PyMOL through Anaconda using other commands I found on the internet, including the one used to install a previous versions of PyMOL. All of the afformentioned steps were unsucessful in getting the Anaconda install to open. I have also compared the "__init__.py" from the Anaconda and installer installs and they are the same. I have also attempted to find the "__cmd" file in the installer install but was unsucessful. I am at a loss as to what is causing the installer install to go through but the Anaconda install to fail. I was hoping if others have a fix for this so that the Anaconda installation opens as I have tried looking for a solution online but failed to find anything useful. Hope you have a nice day. Best Wishes, Naveen Ravichandran |
From: Tomas M. <tom...@gm...> - 2023-12-26 12:40:57
|
Dear All, I have multiple aligned PDB files loaded in PyMOL, each representing different conformations of the same protein. I'm interested in creating a graph displaying RMSD per residue, similar to those shown at https://www.ks.uiuc.edu/Training/Tutorials/science/aars/aars_html.bak/node22.html or https://www.compchems.com/how-to-compute-the-rmsf-using-gromacs/#the-gmx-rmsf-command. I'm wondering if anyone has a script available that can calculate RMSD per residue and write the data to a text file for graph generation. If so, would they be able to share it with everyone? Thank you for your help. Best wishes, Tomas |
From: Shekhar J. <she...@st...> - 2023-12-06 19:41:50
|
Dear All, I want to measure the angle between two RNA helices. I tried using script "angle_between_helices.py" but it does not work for RNA structure. Does anybody in the community have an idea or know a method to calculate angle between two helices in pymol, please? Regards, Shekhar |
From: Priyasha M. <maj...@gm...> - 2023-12-06 11:49:52
|
Dear All, I am working with a genomic sequence. There is a modification in one of the nucleic acid of this DNA sequence. When I am viewing this in pymol, I can see it in sticks and it looks disconnected from the rest of DNA backbone. I am not able to see it in cartoon format. Can someone tell me how to show this Non-Standard nucleic acid in cartoon representation connected to the backbone,as it is a part of it? Thank you Regards, Priyasha Majee |
From: Thomas H. <th...@th...> - 2023-12-05 04:49:00
|
Hi Istvan, The psico extension provides a "save_traj" command. https://pymolwiki.org/index.php/save_traj https://pymolwiki.org/index.php/psico Cheers, Thomas On Mon, Dec 4, 2023 at 5:11 PM Istvan Kolossvary <iko...@gm...> wrote: > > Hi, I was wondering, does Pymol have a way to save a trajectory directly in .dcd, .xtc, .gro, or some other popular file format? > > Thanks for any suggestions, > > Istvan > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: Istvan K. <iko...@gm...> - 2023-12-04 22:40:15
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Thank you, Thomas! I was so hoping something like that exists. :) It is about saving a movie and the associated coordinates with it for further analysis. Thanks again. Best, Istvan On Mon, Dec 4, 2023 at 2:28 PM Thomas Holder <th...@th...> wrote: > Hi Istvan, > > The psico extension provides a "save_traj" command. > > https://pymolwiki.org/index.php/save_traj > https://pymolwiki.org/index.php/psico > > Cheers, > Thomas > > On Mon, Dec 4, 2023 at 5:11 PM Istvan Kolossvary <iko...@gm...> > wrote: > > > > Hi, I was wondering, does Pymol have a way to save a trajectory directly > in .dcd, .xtc, .gro, or some other popular file format? > > > > Thanks for any suggestions, > > > > Istvan > > _______________________________________________ > > PyMOL-users mailing list > > Archives: http://www.mail-archive.com/pym...@li... > > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > |
From: Petro <sub...@kh...> - 2023-12-04 17:59:32
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Hi. I doubt it. I also would say that mdanalysys or pytraj will be better for big trajectories. If trajectory is big, Pymol will struggle. Petro. On Mon, 4 Dec 2023, 17:06 Istvan Kolossvary, <iko...@gm...> wrote: > Hi, I was wondering, does Pymol have a way to save a trajectory directly > in .dcd, .xtc, .gro, or some other popular file format? > > Thanks for any suggestions, > > Istvan > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe |
From: Istvan K. <iko...@gm...> - 2023-12-04 16:06:24
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Hi, I was wondering, does Pymol have a way to save a trajectory directly in .dcd, .xtc, .gro, or some other popular file format? Thanks for any suggestions, Istvan |
From: Jarrett J. <jar...@sc...> - 2023-11-29 14:27:32
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No worries. Glad it worked. Jarrett J. On Wed, Nov 29, 2023 at 12:09 AM Anna Elmanova <ann...@un...> wrote: > Dear Jarrett, > > Thanks a lot, that is exactly what I was looking for. > > I thought I used the option, but probably have used something else > instead. I tried it on my commands and it worked. Many thanks! > Best regards, > > Anna > On 29.11.2023 04:47, Jarrett Johnson wrote: > > Hi Anna, > > Toggling an object's activity by clicking on the GUI uses the underlying *disable > *command. If you already know the name of the color ramp, you can simply > type > > *disable my_ramp* > > otherwise, if you want to hide any and all color ramps, you can use an > API-only command (which is also submittable via PyMOL's command-line): > > *for ramp in cmd.get_names_of_type("object:ramp"): cmd.disable(ramp)* > > Hope this helps, > Jarrett J. > > On Tue, Nov 28, 2023 at 10:39 AM Anna Elmanova <ann...@un...> > wrote: > >> 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 try to do >> so, I lose the potentials on the surface also. Can this be resolved? I >> would be grateful for help. In the GUI I can just turn off the bar, but >> there is no log message for the command. I need to hide it from the >> command line, therefore I am asking.. >> >> Thank you for suggestions. >> >> -- >> Best regards, >> Anna Elmanova >> >> >> PhD student at Leibniz-Institut für Photonische Technologien e.V. >> (Leibniz-IPHT) and Friedrich Schiller Universität Jena >> >> >> +49 3641 948359 >> Technische Optik Gebäude (Lessingstraße 8) >> Raum 229 >> >> >> >> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pym...@li... >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > > > -- > > *Jarrett Johnson* | Senior Developer, PyMOL > > -- > Best regards, > Anna Elmanova > > > PhD student at Leibniz-Institut für Photonische Technologien e.V. (Leibniz-IPHT) and Friedrich Schiller Universität Jena > > > +49 3641 948359 > Technische Optik Gebäude (Lessingstraße 8) > Raum 229 > > -- *Jarrett Johnson* | Senior Developer, PyMOL |
From: Jarrett J. <jar...@sc...> - 2023-11-29 04:14:15
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Hi Anna, Toggling an object's activity by clicking on the GUI uses the underlying *disable *command. If you already know the name of the color ramp, you can simply type *disable my_ramp* otherwise, if you want to hide any and all color ramps, you can use an API-only command (which is also submittable via PyMOL's command-line): *for ramp in cmd.get_names_of_type("object:ramp"): cmd.disable(ramp)* Hope this helps, Jarrett J. On Tue, Nov 28, 2023 at 10:39 AM Anna Elmanova <ann...@un...> wrote: > 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 try to do > so, I lose the potentials on the surface also. Can this be resolved? I > would be grateful for help. In the GUI I can just turn off the bar, but > there is no log message for the command. I need to hide it from the > command line, therefore I am asking.. > > Thank you for suggestions. > > -- > Best regards, > Anna Elmanova > > > PhD student at Leibniz-Institut für Photonische Technologien e.V. > (Leibniz-IPHT) and Friedrich Schiller Universität Jena > > > +49 3641 948359 > Technische Optik Gebäude (Lessingstraße 8) > Raum 229 > > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL |
From: Jarrett J. <jar...@sc...> - 2023-11-29 04:03:14
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Hi Joel, This is unfortunately an oversight on my part. This fix unfortunately never made its way to a patched version. I will make sure it does for the next patch. In the meantime, if you ever do come across this issue, the workaround is to disable undo from the Edit menu. Best, Jarrett J On Tue, Nov 28, 2023 at 3:50 PM Joel Tyndall <joe...@ot...> wrote: > Hi all, > > > > I tried to help Anna with her issue around the colour bar (which seemed > unusual) only to find that I cannot generate the electrostatic maps at all > on 2 different PCs running windows (10 I believe). > > > > The error is Pop-error: invalid source selection name ‘assign_tmp1’ > > > > Running 2.5.1 > > > > Joel > > > > > > Joel Tyndall | BSc(Hons) PhD > > Professor in Medicinal Chemistry > School of Pharmacy | He Rau Kawakawa > University of Otago | Te Whare Wānanga o Otāgo > > PO Box 56 9054 > > Dunedin | Ōtepoti > > New Zealand | Aotearoa > > Website | pharmacy.otago.ac.nz > > > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pym...@li... > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > -- *Jarrett Johnson* | Senior Developer, PyMOL |
From: Joel T. <joe...@ot...> - 2023-11-28 20:49:15
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Hi all, I tried to help Anna with her issue around the colour bar (which seemed unusual) only to find that I cannot generate the electrostatic maps at all on 2 different PCs running windows (10 I believe). The error is Pop-error: invalid source selection name ‘assign_tmp1’ Running 2.5.1 Joel Joel Tyndall | BSc(Hons) PhD Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Website | pharmacy.otago.ac.nz |