Hello everyone, Not sure if this fits your interest, but this Dear manaswwm. You are closer with Protter. I write them. VMD is packed with features, but its interface and ease of use need to be improved.PyMOL is open source and the sourcecode is freely available (you only have to paid for precompiled binaries)I was using PyMol and VMD for a long time, but since I’ve introduced myself to BallView – like it most.Chem3D (Perkin-Elmer/CambridgeSoft) is an excellent viewer and molecular modeling platform that provides a GUI for Conflex, Gamess, Gaussian, MOPAC, and Autodock.
The open source project is maintained by Schrödinger and ultimately funded by everyone who purchases a PyMOL license. A subreddit dedicated to bioinformatics, computational genomics and systems biology.Press J to jump to the feed. For any given structural prediction/ homology model I probably use about 4-5 different softwares as well as 10-20 online resources. modified 5 months ago As I saw one day, a chemist studying protein-ligand docking / steric restrictions was delighted by the not too well known PV protein modeler. Visualizing a bundle of NMR structures, MOLMOL is easier. I am trying to align a ligand to a protein fragment using their pdb files. Press question mark to learn the rest of the keyboard shortcutsCookies help us deliver our Services. • I'm sure the other programs can do great visualizations as well, but require a lot more tinkering. Protter doesn't do structural modelling, it appears only to use Uniprot IDs as far as I can tell.You can use Phyre, SWISS-MODEL, ITASSER for instance, to generate a PDB file.But I don't know/think any of these do TM proteins specifically, they're generally for secondary structure tracing.have you tried vmd? PyMOL vs BioLuminate vs Chimera vs Rosetta vs VMD?

By using our Services or clicking I agree, you agree to our use of cookies. I found this script online: Which programs would you recommended first learning, and which of them should I prioritize learning? Press question mark to learn the rest of the keyboard shortcutsCookies help us deliver our Services. There are various viewers available, but usually each of us, at a certain point at his career, chooses a specific one and specializes in it. I'm sorry if this post is a little out of place here, as it is a relatively simple question, but what are the differences between these programs?

Sometimes I’ll make the same homology model (as in primary sequence is same) on a few different programs and then run an alignment on them just to see the differences. My protein candidates...Hi,

technical question.

I have a transmembrane protein with unknown 3D structure.I did membrane domain prediction on Protter and Phyre, but the pictures that the program generate are simple, and I need to create better pictures.In that way I am trying to open the "flat structure" on PyMol or Chimera, but unsucessfull.More specifically, I wanna create or reproduce a picture like the one figure 2A from the work DOI: 10.1126/science.aav0778.Chimera and Pymol don't produce those types of images as far as I know (with the possible exception of some plugins), they're mainly for viewing full 3D crystal structures.I have seen those diagrams before, but I'm not sure exactly what program makes them. I know chimera can produce it, by use "pipes and planks" toll. I am writing a python scrip...Hello everyone, It has a powerfull scripting language, similar to that of Jmol but much more easy to use in my opinion.I used PyMol, VMD, RasMol and YASARA, and stayed with YASARA for years now.I used PyMol and ICM for research and used to teach using PyMol. I have a peptide sequence and I woul...Hi. technical question. VMD has great rendering capabilities, while pymol is a bit more user friendly.Note that OpenAstex is a very nice alternative, especially for web pages (as an applet). IB Chemistry on ICT, Protein Sequencing , Chimera, Jmol, Pymol for Internal Assessment on Hemoglobin, Myoglobin and Cytochrome I will change for another program since Pymol is not free and opensource anymore since schrodinger took over the licensing.

I did not tried vmd yet, but I believe the problem would be the same.

G proteins(guanin… A subreddit dedicated to bioinformatics, computational genomics and systems biology.Press J to jump to the feed.
If their methods/captions don't say exactly the tool that was used I'd advise getting in touch with the authors or the journal. They say that all images of the article were made on Chimera or PyMol. I’d start with learning one, see what you like about if, see what you don’t, and take it from there. I am a beginner in bioinformatics and I am using homology modelling to predict the tertiary s...


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