[PyMOL] floating external gui

Hi, I am using a compiled version of pymol. I like the floating window. The CNTR-E does not work to toggle floating, I have to use the mouse (display, external gui, toggle floating). Is it possible to start pymol with floating external gui? Thanks, Tamas

Re: [PyMOL] click and select bug in 2.2

it with decoupled windows, but somehow the two windows are pretty inconvenient in this version.) Cheers, Thomas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47| mailto:ta

[PyMOL] click and select bug in 2.2

Hi, I use pymol 2.2 (debian stable release). Sometimes pymol starts to behave in a strange way. Clicking to an amino acid select a residue somewhere else in the protein. (This is not caused by me missing the click in the 3D) I would be happy not to downgrade pymol if you have a solution to

Re: [PyMOL] Grid mode problem

Use a selection in your commands in your scripts. Set the selection to one of your proteins in one of your script and the selection to the other one in the other script. On 4/24/20 3:02 PM, George Tzotzos via PyMOL-users wrote: Below is a summary of a task I’m trying to implement in pymol

Re: [PyMOL] Grid mode problem

script). Is this line correct because it didn’t get rid of the problem? On 24 Apr 2020, at 14:39, Tamas Hegedus wrote: Use a selection in your commands in your scripts. Set the selection to one of your proteins in one of your script and the selection to the other one in the other script. On 4

Re: [PyMOL] Script for drawing docked ligand-active site pics

Hi, I do not provide a full solution... I suggest * try every particular step in pymol, in the command window * if one step is successful, then put it (finally everything) into a file * use python commands (not pymol; e.g. cmd.color("blue", "lig_01")) * run the file either using "run

Re: [PyMOL] Wait for processing to complete before invoking new commands

Something is fishy... as I do not expect this to happen. I have never experienced this problem. I made different types of mistakes resulting in such a phenomenon. * using a for loop and in the command, loading the ligand, I did not inserted the loop variable into the file name (e.g. I used

Re: [PyMOL] Number of parameters is off for cmd.set_view?

please see https://pymolwiki.org/index.php/Set_View set_view (...)  where ... is 18 floating point numbers cmd.set_view(string-or-sequence view) !!! you provided 18 floating point numbers here and not a string or sequence. On 4/29/20 8:40 PM,

Re: [PyMOL] Extract all phi and psi angles

Hi, For this type of analysis I would use MDAnalysis (Python): https://www.mdanalysis.org/ https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html Tamas On 5/9/20 5:08 PM, Neena Susan Eappen wrote: Hi Jarrett, Thank you for your reply. However, that command gives

Re: [PyMOL] tertiary structure/protein folding

Hi, Predicting tertiary structure with high accuracy is the holy grail... I can suggest to perform homology modeling. See Modeller. If your target is small, you can use molecular dynamics (w replica exchange). Tamas On 2020. 05. 21. 18:49, Grace Ciabattoni wrote: Hello, I am trying to model

Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?

You may write and use a script after splitting the object. a pseudo code: for i in range(1, 1001):     spectrum b, rainbow, frame_i     enable frame_i     sleep sometime     disable frame_i On 8/31/20 12:56 PM, ZHANG Cheng wrote: Hi Blaine, Thank you for your suggestion. "set all_states, on"

Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?

would still like not splitting the object if possible. On 8/31/20 1:54 PM, Tamas Hegedus wrote: You may write and use a script after splitting the object. a pseudo code: for i in range(1, 1001):     spectrum b, rainbow, frame_i     enable frame_i     sleep sometime     disable frame_i On 8/31

Re: [PyMOL] MD analysis (distance, dihedral etc)

It is. -- Pseudo code: sel1 = u.select_atoms... sel2 = u.select_atoms... # it is important to make the selection out of the loop for t in u.trajectory:     d = numpy.norm(sel1.center_of_geometry - sel2...) -- dihedral is somwhat more complex: SEL = "resid %i and name %s"

Re: [PyMOL] How to hold/wait for some time?

This one? https://www.tutorialspoint.com/python/time_sleep.htm On 8/31/20 7:51 PM, ZHANG Cheng wrote: I use the command below, trying to display the object one by one, with 2 seconds in between. So how to "wait for 2 seconds"? from pymol import cmd cmd.enable('protein_1') # how to hold for 2

Re: [PyMOL] How to hold/wait for some time?

for a few seconds. However, nothing come out on the Pymol interface. -- Original -- *From:* "Tamas Hegedus" ; *Date:* Tue, Sep 1, 2020 02:21 AM *To:* "pymol-users"; *Subject:* Re: [PyMOL] How to hold/wait for some time? This one? https://www.tutor

Re: [PyMOL] extract monomer from trimer structure

Hi, I think that: * You have a couple chains in a monomer. * You have to know which chains build a monomer. * Then you create a new object from these chains. E.g. create monomer, chain A1 or chain B1 or chain C1 or etc... (here the "or" is an operator and it does not indicate that I do not

Re: [PyMOL] Selecting the water within a protein channel

Hi, I would run HOLE, which detects the tunnel/channel and generates a file for you (SPH?) which is a pdb file with SPH (sphere) atoms corresponding to the tunnel/channel volume. You can select water molecules (or anything else) around these SPH atoms. Suggestion: the ends of the tunnel are

Re: [PyMOL] CCP4 maps not aligning to my PDB file

12, 2021 at 12:42 PM Tamas Hegedus <mailto:biohege...@gmail.com>> wrote: Hi, PyMOL seems not to primarily target working with densities. I suggest to use Chimera if you work with cryo EM maps. E.g. you can use it to fit your struct into the density map. If you deci

Re: [PyMOL] CCP4 maps not aligning to my PDB file

Hi, PyMOL seems not to primarily target working with densities. I suggest to use Chimera if you work with cryo EM maps. E.g. you can use it to fit your struct into the density map. If you decide to use Chimera, be careful, a first step of frustration could be caused by the extension of the

Re: [PyMOL] Align in PyMOL via Python script

Hi, You probably use the script version. In this case you have to use "print" cmd: align x, y output: ... Executive: RMSD =4.030 (10847 to 10847 atoms) cmd: print(cmd.align("x", "y")) output: (4.0296430587768555, 10847, 5, 24.87837028503418, 13476, 1234.0, 1192) Bests, Tamas On

Re: [PyMOL] where can I ask questions? Is there any forum?

Hi, I think that you have two issues: #1 pymol autodock/vina plugin; it should work on windows, since it is written in python. The issue u might encounter: it may have written in an older python version than the pymol install #2 you have to perform the docking with autodock or autodock vina.