Re: [ccp4bb] PyMol question

you can try the 'hide cell' command. This should hide the unit cell box, however, I don't know why it is not displayed in your 'unrendered' gui... Cheers, Johannes 2017-12-11 23:47 GMT+01:00 Cygler, Miroslaw : > Hi, > When I loaded the ed map into PyMol v1.8.4.1 and

[ccp4bb] PyMol question

Hi, When I loaded the ed map into PyMol v1.8.4.1 and used iso mesh around part of the protein all is well until I use the RAY command. In the ray traced image I see the unit cell box that does not show on the image in the normal view. How can I remove the box from the ray traced image? Thanks

Re: [ccp4bb] PyMOL question

Hi Lindsey, The following should work: select sele, obj1 and not (obj1 like obj2) or to match all identifiers, not only resi/name: select sele, obj1 and not (obj1 in obj2) There are also actual "diff" and "symdiff" commands available from PSICO (https://pymolwiki.org/index.php/Psico).

[ccp4bb] PyMOL question

Hello! Does anyone know how to select residues in object 1 that are different from object 2? I know how to select residues that are similar ("select name, obj1 like obj2") but can't figure out how to do the opposite. I am running PyMOL on a Mac. Thank you, Lindsey

Re: [ccp4bb] pymol question

Hi Sebastiano 2012/5/18 Sebastiano Pasqualato sebastiano.pasqual...@gmail.com Hi all, is there a way in Pymol to have a loop/tube representation of the protein backbone that would pass through the N-CA-C-N(+1)-CA(+1)-C(+1) atoms rather than CA-CA(+1) atoms? I know this is possibly not

[ccp4bb] Pymol question

Hi, I'm a little stuck with a Pymol script. I'd like to represent my protein with fancy helices and B-sheets, and in a looped domain I want to show a few residues, but only the side chains. In my script I tried using set cartoon_side_chain_helper, on, HISA on the selection of residues I want to

Re: [ccp4bb] Pymol question

Hi Christopher, I saw your script and there's many ways to the same destination. Here's how my brain thinks: load A.pdb hide everything, A show cartoon, A [cmds for whatever else I like: fancy helices etc. etc.] Option 1: show sticks, A and resi 197-199 Option 2: And if you hate that the

Re: [ccp4bb] Pymol question

Hi Chris, set cartoon_side_chain_helper=1, HISA should be set cartoon_side_chain_helper=1 That setting cannot yet be applied just to a specific set of atoms: it's a global setting. This is something we should add to our to-do list. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product

Re: [ccp4bb] Pymol question

Dear Maher, as far as I know pymol uses the APBS (http://www.poissonboltzmann.org) for the calculations and your question is answered in the FAQ: http://www.poissonboltzmann.org/apbs/frequently-asked-questions/what-are-the-units-of-electrostatic-potential (kT/e) I don't know if this also answers

Re: [ccp4bb] Pymol question

Firstly, I think in Pymol there is no true electrostatic potential calculator, but only a charge-smoothed surface presentation ( http://www.pymolwiki.org/index.php/Protein_contact_potential). So, If you want to calculate the real electrostatic potential in Pymol (by Possion-Boltzman method), you

[ccp4bb] Pymol question

Hi everyone, I have two questions: 1- Does anybody know what are the units on the display ruler after you calculate the vaccum electrostatics using pymol? 2- What are the default kT/e values used by pymol? Thank you, Maher