Re: [PyMOL] what is an object colored ?

You can then color by those indices, eg: > > color 26 > > Cheers, > > -- Jason > > > On Mon, Nov 25, 2013 at 5:42 AM, Jonathan Grimes > wrote: > > dear all, > > i am having implementing these instructions. > > i would like to work out wha

Re: [PyMOL] minimum rotation between views

's angle for the corresponding axis-angle. >> >> Jason, are there standard Python utilities that one can use to get the >> quaternion equivalents of PyMOL matrices? >> >> Bob >> >> >> >> On Mon, Nov 25, 2013 at 9:14 AM, Jonathan Grimes

[PyMOL] minimum rotation between views

is there a script available to calculate the min rotation about a vector that describes the relationship between 2 views…… i am happy to ignore any translational component but i have 2 views of a molecule and want to say that theres a *** deg rotation between the 2 views ? t

Re: [PyMOL] what is an object colored ?

dear all, i am having implementing these instructions. i would like to work out what color an object is…… how is this defined ….. > s["names"][1][5][0][1] > > equals your object name. if I have an object called A1…i am unsure how to make A1 equal to s["names"][1][5][0][1]

[PyMOL] running pse file in batch mode

I've have a pse file with a number of scenes defined. i would like to run the pse file without the gui…..but then select scenes via the external gui window….and render…… can i do this akin to batch mode ??? or can i convert the pse file into a pmol script ?? each scene w

[PyMOL] VRML files

i have been asked to provide vrml files to someone who will use them in a small cartoon film. when you write out a vrml file will you write out the entire contents that have been drawn…..even if i have zoomed in on a small area. i.e. i am displaying the ED for a whole virus

[PyMOL] drawing a bond between the same Calpha atom in different states

Hi All, I have 2 different states of the same molecule..different conformations generated from MD, so the same number of Calpha atoms, with a direct 1:1 mapping between Calphas with the same residue numbering. I would like to draw a "bond" between equivalent C-alpha atoms, a

[PyMOL] what is an object colored ?

ive been given a pse file.and i am trying to work out what color an object is.. i used the command get cartoon_color, pT_A and got back get: cartoon_color = default in object pT_A which could be more helpful. could i get some clues how best to dig this inform

[PyMOL] Help with alignments

I am wanting to align proteins based on superposition of particular chains. Is it possible to do the superposition based on the chains, but to move, in this case the entire complex ??? Thanks Jon Sent from my iPad -

[PyMOL] alignto command

is there a way of getting the alignto command to print out RMS deviations over the aligned regions of the structures. thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetic

[PyMOL] map obj col to ed map

Is there a way of mapping an object color to an ED map mesh. I am drawing a peptide coloured blue to red N-to C termini. I wanted to display the difference map for the peptide with the same colour mapping... Is there a way (trivial or not) that I can do this ?? Many thanks Jo

[PyMOL] sphere_scale

I wanted to changed the size of sphere_scale for all atoms in an object, a selection of Calpha atoms. I thought I could use the command set sphere_scale, 5, object_name this doesnt seem to work and am unclear as to the reason. thanks jon does the command Dr. Jona

[PyMOL] selecting certain residues within X angs of a point/residue

i am wanting to highlight a number of residues on a virus capsid. i have 60 states (objects), and wanted to only select particular residues (say resi 23,45,46 from 3 chains across all 60 objects) that are within say 20A or 40A from a fixed point (or residue). could i get advice on

[PyMOL] Drawing secondary structure for PDB with only Calpha atoms

I have a pdb file, with only Alpha carbon atoms. I want to display the secondary structure. Given that pymol uses the backbone to define SS elements is there a way i can draw the cartoon. i have tried explicitly defining ss using alter command but without success. i want to a

[PyMOL] animating 2 sets of pdbs

apologies for the incoherence of the description but its a reflection of my mind at the moment.. I am trying to model the flexing about the elbow angle of 2 Fabs, that are in close proximity to each other on a viral capsid. i have created the 2 nmr like pdbs (that contain th