Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

ng in gui)? Cheers, J. пт, 26 февр. 2021 г. в 12:29, Ali Saad Kusay : > > Hi Jeff, > > The sphere size is controlled by the vdw property, to change it: > alter *, vdw=1.0 # this will set the sphere size to be equal for all atom i.e. hydrogens atom woul

[PyMOL] FW: Names of objects in GUI in pymol

Resending since I forgot to copy the PyMOL mailing list On 23/2/21, 7:17 am, "Ali Saad Kusay" wrote: Hi Jeff, There is several ways you can do this with string function in python https://www.w3schools.com/python/python_ref_string.asp. This is an easy one liner whi

Re: [PyMOL] Question about visualisation of the spheres objects on PNG image

Hi Jeff, The sphere size is controlled by the vdw property, to change it: alter *, vdw=1.0 # this will set the sphere size to be equal for all atom i.e. hydrogens atom would be same size as carbon you also need to use the "rebuild" command to implement the changes At this point, you can

Re: [PyMOL] Calculating r.m.s.d values for ligands once proteins have been aligned

Hi Sacha, You should be able to do this using the rms_curr command (https://pymolwiki.org/index.php/Rms_cur) This will compute the rmsd without performing a superimposition Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy |

Re: [PyMOL] equals operator for q and b

Hi Benedikt, You can do a work around with '<' or '>': Sele qm, q>0.999 and q<1.001 I checked that this works like this for my "obj" in PyMOL: stored.q = [] iterate obj, stored.q.append(q) q_arr = np.array(stored.q) q_1 = q_arr[q_arr == 1] # only keep values of q that equal 1

Re: [PyMOL] Names of objects in GUI in pymol

, while I need to move it a litle bit in one of the directions ... Cheers, пн, 22 февр. 2021 г. в 14:14, Ali Saad Kusay : Hi Jeff, The name of an object is stored in the model attribute. Select an atom in the object and use this command: label sele, model If you want to automate this over all your

Re: [PyMOL] Names of objects in GUI in pymol

Hi Jeff, The name of an object is stored in the model attribute. Select an atom in the object and use this command: label sele, model If you want to automate this over all your PyMOL objects, you can use this script, this will put a label at the centre of each object but it has to create a

Re: [PyMOL] Structure alignment -- general question

Hi George, You can do pairwise alignments, i.e. align 3 of the structures to one structure. You can also use the "extra_fit" method (https://pymolwiki.org/index.php/Extra_fit), i.e: extra_fit name CA, "object", super Replace object with the structure you want the other 3 to align to, this

Re: [PyMOL] Complement or Inverse Selection in Pymol

: Gert Kruger Date: Saturday, 27 November 2021 at 5:05 pm To: Ali Saad Kusay Cc: "pymol-users@lists.sourceforge.net" Subject: Re: [PyMOL] Complement or Inverse Selection in Pymol Dear Ali, Many thanks for your kind and very helpfull reply! One question: You wrote: "Doing somethi

Re: [PyMOL] Complement or Inverse Selection in Pymol

Hi Gert, These selection commands will generate a selection object called "other_waters " See https://pymolwiki.org/index.php/Selection_Algebra You can do: select other_waters, br. (resn WAT and not sele) # after you make the selection in your email or select other_waters, br. (resn WAT

Re: [PyMOL] surface representation of the protein-ligand interactions

Hi Enrico, You can carve the protein surface around the ligand, i.e. show only the surface behind the ligand, see this guide: https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces You can also try and made the surface more transparent, but this doesn't always give the best results,

Re: [PyMOL] Set label for visible amino acids

Hi Enrico, This is actually quite simple, see the PyMOL wiki: https://pymolwiki.org/index.php/Aa_codes Paste this python dictionary into PyMOL: one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \ 'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',\

Re: [PyMOL] surface representation of the protein-ligand interactions

well captured on the png as well. What should I include in my script ? пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay : > > Hi Enrico, > > You can carve the protein surface around the ligand, i.e. show only the surface behind the ligand, see this guide

Re: [PyMOL] distance-based selection of the side-chains

resentation, notably for hydrophobic (Gly, Ala) residues. How could it be fixed ? чт, 27 янв. 2022 г. в 12:38, Enrico Martinez : > > Thank you very much, Ali!! > Cheers, > Enrico > > чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay : > > &g

Re: [PyMOL] distance-based selection of the side-chains

Hi Enrico, You need to use the byres or br. Selection (https://pymolwiki.org/index.php/Selection_Algebra) I.e: cmd.select('br. (rep sticks & visible beyond 4 of not polymer)') Also, consider hiding all protein residues and showing only the ones near the protein, i.e.: cmd.show('sticks','br.