We’re rewarding the question askers & reputations are being recalculated! Read more.

Questions tagged [pymol]

a molecular visualization system created by Warren Lyford DeLano. This tag can be used in questions related to the use and the visualizations produced using this software.

Filter by
Sorted by
Tagged with
3
votes
1answer
2k views

Generate full dimer from monomer with C2 symmetry?

I downloaded a PDB file of a dimer, but it only contains the monomer, and it says that the dimer can be obtained from C2 symmetry. For an example see here: http://www.rcsb.org/pdb/explore/explore.do?...
3
votes
0answers
89 views

Automating figure-making with PyMOL

What I want to do I have a list of almost 200 PDB entries that I need to visually inspect. Luckily, the thumbnail image displayed on the PDB website (examples with RCSB or PDBe for a well-known ...
1
vote
1answer
345 views

Can pymol show cartoon (secondary structure) for a pdb of multiple frames?

I am using pymol to visualise the secondary structure of protein using its cartoon representation. The ...
3
votes
1answer
1k views

How to perform a DNA structural alignment in pymol

How can I "fit" two DNA structures having different nucleotide sequences in PyMol? I would like to use the structure of a DNA-binding protein in PDB (1h9t), which is bound to DNA in the PDB file, ...
1
vote
1answer
86 views

Is there a way to see what representations are currently displayed in PyMOL?

I am using PyMol to visualize .pdb protein structures. I show/hide representation a lot, and sometimes I get confused with what representations are currently displayed. So I end up with doing a lot ...
2
votes
0answers
544 views

Turn off multithreading in pymol [closed]

By default, pymol seems to grab the number of cores on the system for rendering. How can I force it to only use one core? Motivation: I have a large collection ...
14
votes
1answer
1k views

How do I get the current “camera position” in PyMol so I can reuse it in scripts?

I have a few protein models I want to take pictures of with various ligands bound. It would be nice if I could do it from the same "position", but the only way I can figure out to repeat the same ...