[PyMOL] Backbone RMSD

Dear Pymol users, I want to calculate backbone RMSD of proteins having two different conformations (For example 2RH1 and 1F88). With the align command it calculates the executive RMSD, but i need backbone RMSD. Please advise something. Regards *Amita * --

Re: [PyMOL] Residue-residue contacts from PDB

Hi Bhumika - Have a look at the CCP4 program NCONT: http://www.ccp4.ac.uk/html/ncont.html. You can run it within the CCP4 GUI or from the command line. For example, for contacts between helices 1 and 2, type these lines at the prompt (or copy and paste), substituting the correct path to the PD

Re: [PyMOL] Problems visualizing EM structure

Hi Bernhard, this issue came up before and we think PyMOL is doing it right. See this post (workaround included): http://sourceforge.net/p/pymol/mailman/message/32385858/ Cheers, Thomas On 09 Sep 2014, at 13:50, Bernhard Lechtenberg wrote: > Hi all, > > I have problems showing a EM struct

[PyMOL] Problems visualizing EM structure

Hi all, I have problems showing a EM structure in PyMol. When I open the PDB file 3J6J in PyMol, the structure is shown very small in a diameter of about 1Ang. This makes some representations like Cartoon or sticks unusable and comparison with other structures impossible. I checked the file and

Re: [PyMOL] need help

I am very unsure of your question, but I believe you're asking if you have a PDB id, how to load that into pymol. For that, you can use the fetch command ( http://www.pymolwiki.org/index.php/Fetch ) You type: fetch 1acb into the pymol interface and it will download pdb id 1acb and load it into the

Re: [PyMOL] need help

I will try this thank you for your input Sent from my iPhone > On Sep 9, 2014, at 12:00, David Hall wrote: > > I am very unsure of your question, but I believe you're asking if you have a > PDB id, how to load that into pymol. For that, you can use the fetch command > ( http://www.pymolwiki

Re: [PyMOL] symexp eats chain ID

Hi Andreas, good find! The most recent changes in SVN introduce multi-letter chain support. This required a non-trivial refactoring of the internal data structure. You found a reference counting bug, I'll fix that. Cheers, Thomas On 09 Sep 2014, at 06:24, Andreas Förster wrote: > Dear all,

Re: [PyMOL] symexp eats chain ID

Should be a bug of your particular version. I cannot reproduce it following your instructions on MacOSX Good luck! Gian On 9/9/14 12:24 PM, Andreas Förster wrote: > Dear all, > > I've noticed that chain IDs disappear after creating symmetry-related > copies: > > fetch 1ubq > -> You clicked /1ubq/

[PyMOL] need help

Dear all, I need help. I just start using Pymol in Ubuntu, this was advised to me since windows give a lot of trouble. I install pymol already on ubuntu, but I need an manual how to transport the data from the pdb to ubuntu pymol. I can enter pdb nicely but after I dowload the files I cannot tr

[PyMOL] symexp eats chain ID

Dear all, I've noticed that chain IDs disappear after creating symmetry-related copies: fetch 1ubq -> You clicked /1ubq//A/LEU`73/CG symexp symm1, 1ubq, 1ubq and i. 30, 10 -> You clicked /1ubq//(null)/LEU`73/CG -> You clicked /symm100-1//(null)/LEU`73/CG Chain A turns into chain (null). Wh

Re: [PyMOL] Access to pymol commands from the terminal

Thanks Markus, I'll try to examine it! Jed, the main problem with the profit is that I need to superimpose structures in loop which are not always has the same sequence length. Is it possible to superimpose each structure based on some common criterium found for each mobile and reference automati