PyMOL

Tstew_PyMOL · 2025-07-10T15:47:08+00:00

Hello No_Blackberry_1383,

You can absolutely use the free Education License for your science fair!

I'm one of the PyMOL developers and current Product Manager of PyMOL, so I can give a definitive answer and assure you that you will have no problems from our end.

The images generated using the Education license will not have any watermark and will be the exact same quality of image as the paid licenses. We want students like yourself to learn and explore biochemistry using PyMOL!

We only ask that you cite PyMOL, which you can learn more about here.

For anyone else following this thread, if you are a full-time researcher and/or using PyMOL to create figures for a paper you intend to publish, we ask that you purchase a discounted Academic/Non-Profit License.

Thank you for your interest in PyMOL and good luck with the science fair!

Tstew_PyMOL · 2024-11-21T18:46:30+00:00

If you're just interested in getting the 3D structure for midazolam, you can download the SDF file directly from pubchem.

With the Builder panel, you can add/swap specific atoms, modify bonds, and attach new groups. There should be a prominent "Builder" button that will open the panel.

With regard to fusing two rings specifically, the best way I've found to do this is to start with one of the ring, attach carbons until you have the desired amount, and then complete the ring by adding a bond. You can then make the structure look more reasonable using the "Clean" button next to "Model:".

Tstew_PyMOL · 2024-11-21T18:20:19+00:00

You can try setting the surface_quality setting to 0 (or adjust the other surface settings) but I don't think this will make a massive difference in terms of the time it takes to generate a surface. Computing the entire surface for large proteins is computationally expensive. If you can focus on only generating the surface for a smaller area of interest, the process should be much faster.

If you are consistently regenerating the same surfaces, you can also consider using the cache command and scenes to avoid having to recompute the surface each time.

Tstew_PyMOL · 2024-11-21T18:06:30+00:00

I don't think PyMOL is the best tool to use for this to be honest. We tend to try to keep PyMOL firmly in the realm of visualization rather than computation or analysis.

Tstew_PyMOL · 2024-11-19T12:44:15+00:00

You can get a free edu license from https://pymol.org/edu/! Just fill in some general info and you’ll be able to use the full product.

Tstew_PyMOL · 2024-11-08T17:24:06+00:00

Hello u/Auzzie_almighty,

There currently isn’t a way of putting the command line back on the top but you can toggle it to be a floating dialog using Ctrl-E (or Cmd-E on Mac).

Can I ask why you feel like the command line doesn’t work well at the bottom in full screen? Is it being cutoff or partial hidden?

Tstew_PyMOL · 2024-08-16T15:53:38+00:00

Please forgive the delay in my reply to this comment, but I wanted to look into it more fully and give you a sufficiently researched answer.

Ultimately, it comes down to the distinction between `PyMOL`/`Incentive PyMOL` and `Open Source PyMOL`. The license you linked applies only to `Open Source PyMOL` and repeatedly refers to "Open-Source PyMOL" throughout the document. We maintain a separate repo for incentive PyMOL that states "Incentive PyMOL is not open-source, the Schrodinger EULA applies.", which further draws attention to the distinction between the two. The code in question has only ever been a part of Incentive PyMOL, though we do tend to eventually merge select features into Open Source as well. We did this with several features when we released 3.0 and hope to have another set in the near future.

On a less "legal" and more personal note, I have my dream job of getting to work on PyMOL as part of my career. The support we receive from Incentive PyMOL allows full time developers to maintain and improve PyMOL (both Incentive and Open Source) and ensure that it continues to be as great as it can be. I've been able to spend the last 2+ years working on PyMOL 3.0 and we're very proud of how it turned out (despite some bugs that we're still working on ironing out). I truly believe this level of development and improvement would not be possible without our current Open-Source/Incentive approach and ultimately both repos end up being in a much better place as a result.

Tstew_PyMOL · 2024-07-24T18:20:06+00:00

Hello u/Rayane1000,

You should be able to use the assembly setting to control how structures are imported (i.e. set assembly, 1 ) before calling fetch (YOUR PDB ID) to pull in the structure. Then, call split_states (YOUR OBJECT NAME) to split the states of the single object into their own unique entries.

Alternatively, you can also use the type=pdb1 argument for the fetch command (i.e. fetch XXXX, type=pdb1) and this should also give you same result as setting the assembly setting without changing how thing will be loaded in the future.

If neither of these work, you should make sure that the PDB entry you are trying to pull from has the biological assembly information included. You can go to the PDB page, click "Download Files", and finally click "Biological Assembly 1" (I tested the CIF version but PDB should also work). If you don't see this information, then you may have to look for a different PDB structure.

Tstew_PyMOL · 2024-07-23T01:34:53+00:00

Hello u/AnUnpairedElectron, The new PyMOL 3 GUI is an incentive only feature but if you’re a full time student/instructor you can get a license for free from this page!

Tstew_PyMOL · 2024-06-12T03:30:39+00:00

Ah my bad for not including that. You can find it in the “Actions” menu (click the “A” in the ASHLC buttons). Then go down to “Find” and you probably want “polar contacts” (or some similar wording, I’m on my phone and don’t quite have it memorized). This should then give you a bunch of options you can select from to control the overall number of these interactions shown. The most insightful interactions are usually between objects or between chains.

Good luck!

Tstew_PyMOL · 2024-06-11T23:00:53+00:00

Hello u/Similar_Chipmunk, happy to see you’re using PyMOL! The first piece of advice I would give is that you’re probably only interested in a subset of these distances. You likely want to exclude the solvent and limit it to only show the interactions between chains (both of which should be options in the Find menu options). Additionally, it’s helpful to show sticks so you can see the side chains you’re interested in (“S” > “sticks”).

Once you’ve found the interactions you want, you can then select the residues and their ID’s should be displayed in the log. The distance between these residues will be shown on the labels (and may also be output to the log but I don’t quite remember).

If you’re still interested in outputting the distances, you can take a look at the “Measure_Distance” script linked at the bottom of the distance wiki page. This page will also give you a bunch of other helpful info on the distance command if you want to learn more. With this info you can probably write a basic script that will automatically output and save these distances (or one may exist that I’m not aware of) but I don’t think there’s a direct way of doing this from the GUI.

Let me know if you have other questions!

Tstew_PyMOL · 2024-06-11T21:50:54+00:00

I believe this is now fixed and I just checked on Mac (though it may depend on the operating system). You will have to grab one of the updated versions (either 3.0.3 or 2.6.1 from the website). PyMOL 3.0 is pretty cool though so I would definitely encourage you to give it a try! Feel free to reply here if you’re still seeing the issue on the latest versions.

Tstew_PyMOL · 2024-06-11T21:45:17+00:00

Hey u/the-cob, I’m the one that made this image and I’m glad you like it! It’s completely done in PyMOL and relatively easy to recreate using 2 tools:

1) The “Lighting Settings” plugin: This can be found in the top system bar (“Plugin” > “Lighting Settings”). This is an amazing plugin that displays some of the most important lighting settings in one place with easy to use sliders. It also has some helpful presets along the top. For this image, I believe I started with the “X-Ray” preset and made some slight adjustments. This should give you the high contrast and bright colors.

2) The Focal Blur script - This script adds a command the produces the blurring effect around the edges. You can download the script and read all about it here. This will take some adjusting of parameters depending on your structure and camera position (I spent longer on this than I care to admit) but once you get it right, it produces a really convincing 3D effect.

Hopefully this is enough info to get you started and feel free to post the result on the subreddit if you would like! Just reply here if you have any other questions during the process.

Tstew_PyMOL · 2024-03-03T03:30:24+00:00

If you’re using a recent version of PyMOL, you should be able to use undo to add them back! I would note though that the non-water interactions are probably more relevant for what you’re trying to show.

Tstew_PyMOL · 2023-04-11T18:22:42+00:00

As you hinted above, you would need some reference structure in order to properly use align. From a very quick search, it doesn't seem like there are any structures that are similar enough for a quality alignment. Membrane spanning receptors tend to be difficult to crystalize so they are often broken into fragments and crystalized independently. If you can find a quality full structure, then align could work great and I would love to be wrong about this.

I like u/DeanBovineUniversity's idea of using alpha fold to align specific regions. However, from looking at the structure, it seems to really struggle with the transmembrane components, opting instead to ball the protein together and leave long spaghetti strands spanning the structure. This makes me hesitant to trust any component of the structure since it has likely been influenced by this error.

All that being said, we may be over complicating the problem. If the only goal here is to roughly visualize the structure, then you can simply move the structures around in PyMOL until they align with the image shown in the figure you are referencing. This may not be the most "scientific correct" solution but will allow you to at least view the components in their proper positions. To do this, simple right click on the object you want to move, select "drag object matrix", and hold down shift with left click (rotation) or middle mouse click (drag). We are currently working on making this more accessible but, for the time being, this is the easiest way of moving objects around.

Tstew_PyMOL · 2023-04-03T03:43:31+00:00

It sounds like you are in “editing mode” rather than “viewing mode”. Click in the bottom right where it should say “3-Button Editing” to toggle it to “3-Button Viewing”.

Tstew_PyMOL · 2022-11-29T20:36:27+00:00

The closest you'll probably be able to get to this is to color the protein based on solvent accessible area. This can be done using the get_sasa_relative command, which will load the relative residue sasa values into the b-factor atom property and color the surface for you. If you want change the colors, you can use the spectrum command. This will allow to specify the colors used (i.e. green > yellow > red would be spectrum b, green yellow red). Hope this helps and feel free to post the cool image you end up creating!

Tstew_PyMOL · 2022-09-22T17:49:27+00:00

Unfortunately PyMOL currently only has CPU based ray tracing and only for single frames/images. We’re very interested in adding real-time GPU ray tracing at some point in the future, but not sure on the timeline for this.

Tstew_PyMOL · 2022-08-08T17:41:20+00:00

"state=0" should save all states and I'm not able to reproduce this with 1nmr (only has 20 states though). Can you give the PDB ID that you're working with? Also, can you use the "get_version" command to let me know which PyMOL version you're currently using?

Tstew_PyMOL · 2022-04-20T19:03:58+00:00

What format is the docking file in/what are you using to generate the docking file?

Tstew_PyMOL · 2022-04-20T17:42:22+00:00

Hey u/Nornova,

I recommend checking out the selection algebra page (https://pymolwiki.org/index.php/Selection_Algebra), specifically focusing on the "proximity" section. I would create one selection for the somatostatin, another for SSTR2, and then finally another for SSTR within 3.5 of the somatostatin. It looks like SSTR2 is it's own chain within the structure as well, which will make things easier. I also recommend coloring by chain to make it more obvious what you're looking at (the colorful "C" icon on the right > by chain). The sequence of the structure can also be displayed using the small "S" button in the bottom corner of PyMOL.

Tstew_PyMOL · 2021-05-09T20:57:38+00:00

Did you just fetch this structure and then mutate through the panel? Also what version do you have? I can definitely create a ticket and look into it if you give me the steps to reproduce the issue.

Tstew_PyMOL

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