Re: [PyMOL] [Help]About indentifying interaction between residues

Hi Nikita - To me this looks like the cartoon representation for missing residues, which is controlled by the cartoon_gap_cutoff setting. If you either `hide cartoon` or `set cartoon_gap_cutoff, 0`, does it go away? Usually the dashed line wou

Re: [PyMOL] [Help]About using PyMOL for Master's thesis

Hello Haruki, My name is Thomas Stewart and I'm one of the PyMOL developers at Schrodinger. You can use an educational license to fulfill course or program requirements such as a Master's thesis or dissertation. We hope to reword the website in the near future to make it more clear when educationa

Re: [PyMOL] help with PyMOL rename command

Thank You a lot indeed explanation ways more clear than the wiki one https://pymolwiki.org/index.php/Rename https://pymolwiki.org/index.php/Rename I know I should have tried more Again Thanks___ PyMOL-users mailing list Archives: http://www.m

Re: [PyMOL] help with PyMOL rename command

Dear wdela, usually each atom in a residue has a different atom name. If this is not the case, the rename command will rename the atoms, that do not have unique names within a residue. It appears as if you cannot specify which atom names the renamed atoms will get. If you want to change to spe

Re: [PyMOL] Help with selecting interface residues between two structures

chain of base. I understand this. However, why “not /base//H+L” returns an empty selection? Thanks! From: Jarrett Johnson Sent: Thursday, June 29, 2023 6:31 AM To: Zhou, Yingyao Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Help with selecting interface residues between two str

Re: [PyMOL] Help with selecting interface residues between two structures

Hi, There might be a cleaner way to do this, but I propose creating a mapping of your chains from base to pred and use the `iterate` command to get the relevant identifiers and map them back to the prediction. Here is a full script that pulls from the PDB that attempts this idea. from pymol impor

Re: [PyMOL] Help - how mutation affects protein structure

Dear Susanna, in addition to MD calculations I suggest you to perform a check on your mutated protein. Circular dichroism is a simple technique that allows to monitor the global fold of your protein. Mutating a residue may affect the folding and this seems an underestimated problem in the li

Re: [PyMOL] Help - how mutation affects protein structure

Hi Susanna, As you can see, pymol allows you to mutate residues. However, in order to assess their influence, you should most likely run MD simulations on both the wild type protein and mutant(s) and compare. Kind regards, Sorin On Tue, Apr 12, 2022, 5:35 PM susanna pagni wrote: > Hello, > >

Re: [PyMOL] help - password cracked

Hello, We're aware of this issue, and I believe all EP license holders may have received this warning from Google. However, this can safely be ignored for now. The password students and other users receive just provides access to the PyMOL Educational Product license and nothing there stores any s

Re: [PyMOL] Help ASPB

 Dear Clarisa, > On Sep 10, 2020, at 2:56 AM, Clarisa Alvarez > wrote: > > Dear David > Thank you very much!you do not know how much you helped me!!Thanks! > I have two questions: > - with you sent I only saw lateral chains, how could I see backbone? You want to click on “H” button and

Re: [PyMOL] Help ASPB

select pos,(resn arg+lys+his) show sticks, (pos and !name c+n+o) color marine,pos disable pos select neg,(resn glu+asp) show sticks, (neg and !name c+n+o) color red,neg disable neg select neutral, (resn gly+ala+val+ile+leu+met+ser+cys+trp+phe+tyr+pro+gln+asn+phe) show sticks, (neutral and !name c

Re: [PyMOL] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

Dear Christoph and David Thanks for the support and solution. The solution given by Christoph solved the issue. Now, the plugin manager is running smoothly. Cheers Vijay On 8/22/17, David Hall wrote: > See https://sourceforge.net/p/pmw/patches/7/ > > >>

Re: [PyMOL] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

See https://sourceforge.net/p/pmw/patches/7/ > On Aug 21, 2017, at 10:32 PM, Vijay Masand wrote: > > Dear Christoph > Thank you for the help. I followed your suggestion, but no success. > However, a new line is appearing now at the bottom of the error

Re: [PyMOL] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

Dear Christoph Thank you for the help. I followed your suggestion, but no success. However, a new line is appearing now at the bottom of the error message, here is the complete error message: Error: 1 TypeError Exception in Tk callback Function: .plugin_manager at 0x01B40CB228C8> (type: )

Re: [PyMOL] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

Hello, try to uninstall Pmw and reinstall it using Pmw-2.0.1-py3-none-any.whl from . C:\Python36\python.exe -m pip uninstall Pmw C:\Python36\python.exe -m pip install Pmw-2.0.1-py3-none-any.whl Christoph On 8/21/2017 8:27 AM, Vijay Masand wr

Re: [PyMOL] Help Download structural alignment

Hi Clarisa, you can save an alignment using the create and save commands, e.g.: fetch 1oky 1t46, async=0 as ribbon align 1oky, 1t46 create aligned, all save aligned.pdb, aligned You can also save the alignment in clustalw format, see http://pymolwiki.org/index.php/Align. I hope this is what you

Re: [PyMOL] Help for saving movie in png

Hi Pranab, Am 13.11.2015 um 17:00 schrieb Pranab Jyoti Bhuyan: > Can you please tell me how to save a movie as a series of *.png files > from terminal in linux? This can be done with the mpng command. See http://pymolwiki.org/index.php/Mpng Cheers, Christian ---

Re: [PyMOL] help

Clarisa, Depending on what you want to do with the file, you may not need to save a new PDB at all. You could for example, * Issue the command symexp ,,(all),4.0 to generate nearby symmetry mates, then remove the objects you don't need to form the proper dimer. ( is your PD

Re: [PyMOL] help

Hi Clarisa, If I understand correctly you generate the dimer, but you are not able to save it. Wich error did you get? Did you select all the object when saving the file? By the way, may be you will find this wiki page useful. Cheers, Osvaldo. On Wed, Oct

Re: [PyMOL] Help with rms_cur command

Doh! Thanks. From: David Hall [mailto:li...@cowsandmilk.net] Sent: Monday, October 06, 2014 1:00 PM To: Soisson, Stephen M Cc: Subject: Re: [PyMOL] Help with rms_cur command almost definitely is http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg1.html -David On Mon, Oct

Re: [PyMOL] Help with rms_cur command

almost definitely is http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg1.html -David On Mon, Oct 6, 2014 at 12:17 PM, Soisson, Stephen M < stephen_sois...@merck.com> wrote: > Hi everyone- > > > > I’m having a few issues with the rms_cur command that I am hoping someone > can h

Re: [PyMOL] Help to compile u3d converter - IDTF to U3D on linux 64

On 04/03/13 12:21, Troels Emtekær Linnet wrote: > Dear Pymolers. > > I am playing around with creating a pdf file with 3 D graphics. > I am saving in *idtf* format, which I convert to *u3d, *and then include > in pdf through latex. > > I can do this on windows, but I can't compile IDTFConverter *

Re: [PyMOL] Help with alignments/ more general create and align question

with existing tools. Thanks. > From: jason.vertr...@schrodinger.com > Date: Tue, 11 Dec 2012 07:38:32 -0600 > To: jonat...@strubi.ox.ac.uk > CC: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Help with alignments > > Hi Jo

Re: [PyMOL] Help with alignments

Hi Jon, align prot1 and chain A, prot2 and chain X 'super' and 'cealign' should work similarly. Cheers, -- Jason On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes wrote: > > I am wanting to align proteins based on superposition of > particular chains. Is it possible to do the superposition

Re: [PyMOL] Help with autodock plugin for PyMOL

What is the atom name of EFP.ligand:A:EFP999? Can you check your pdb file? Do you rename them before running the plugin? Den 26/10/2012 23.26 skrev "Ragnar Thomsen" : > I have a problem when running the autodock plugin for PyMOL. I followed the > tutorial at http://www.pymolwiki.org/index.php/Auto

Re: [PyMOL] Help auto interpolate

Hi Anke, > we are currently trying to do movies and are running into some problems > concerning the “auto interpolate” function of pymol. We realized that camera > and molecule positions are always interpolated back to the position of frame > 1 at the end of the movie. Autointerpolate is not the

Re: [PyMOL] Help converting shell script to python

Case closed. Thanks to Hongbo Zhu for a solution. Best Troels 2011/12/12 Troels Emtekær Linnet > Hi guys. > > I am trying to use the plugin: MSMS > on > a win machine. > The plugin is dependent on a shell script: pdb_to_xyzrn > But I cant execute it o

Re: [PyMOL] help needed

Hi Anasuya, > I have around 19,200 unique PDB files. Each of them have one or more > ligands in it. For each ligand, I have to extract a zone which > contains complete residues within 4.5Angstroms of the ligand [ i.e. > ZONE1] and then extract another zone, which has complete residues > within 4.5

Re: [PyMOL] Help

Hi Babban, For modeling the polymers you probably want to try a docking program. Maybe HADDOCK suits your needs... Hope it helps, Tsjerk On Sun, Jul 31, 2011 at 1:42 AM, Babban Mia wrote: > Dear users, > > Is there some program to calculate the zeta potential or streaming > potential > of prot

Re: [PyMOL] Help

Hi Babban, regarding your questions on peptide building: > My last doubt is about creating polymers out a given PDB ? > I am studying the fibrils of some proteins and although the structure of > fibril is not know but through some analysis I have come to understand > the region in peptide which

Re: [PyMOL] Help for surface coloring

I have a slightly different answer using (almost:) only PyMOL commands: # take 1acb as example fetch 1acb, async=0 import numpy # center is [x0,y0,z0] x0,y0,z0=[1,2,3] alldist = [] iterate_state 1, 1acb, alldist.append(numpy.sqrt(numpy.sum([(x-x0)**2,(y-y0)**2,(z-z0)**2]))) # assign dist to b-

Re: [PyMOL] Help for surface coloring

Hi Robert, I did something like this in the past. Check out the ramp_new command page on the PyMOLWiki for an example (http://pymolwiki.org/index.php/Ramp_new#Elaborate_examples) for arbitrary functions. Here's a very quick way to color a surface by distance from a given point--here I chose the o

Re: [PyMOL] Help for surface coloring

Hi Robert, you can set the distance between each atom and the center as b-factor, and then use spectrum (or spectrumany [1]) for coloring. I wrote a small python script that will do that, see attachment. Example (in PyMOL command line): run distancecoloring.py centerdistance2b (all) spectrum

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Hi Hari, I'm glad that worked for you. I contacted Planar and they also had a few hints for us: > I have heard of synch issues with the Quadro FX3700 in Windows XP, so there > could be an issue in Linux as well.  Here are a few ideas to try out: > 1. We found that connecting the 3-pin mini-din s

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Thanks a tonne Marc . Turning OFF "Force Full GPU scaling" in the DFP-0 and DFP-1 settings of the n-vidia-settings panel made all the difference. Once I unchecked that box it made the stereo stop flickering and switching from coming at you to going away from you ( i.e flipping). Stereo with the nv

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Hello Hari, I had some flickering problems when I first tried the stereo mode on an Alienware LCD display. There is one option in the Nvidia driver that seems to keep the display at 60Hz, it is called "Force Full GPU Scaling". Make sure that the option is turned off, otherwise you won't be able

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Thanks Rafael and Jason, I upgraded to the latest driver version for Linux i.e 275.19 and now have stereo working with some caveats. I am running the PLANAR SA2311 at 120 Hz and 1920x1080 resolution and the stereo is rather finicky with the nvidia 3dvision setup. I see a lot of random stereo im

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Hi Hari, Please update your driver and ensure that your monitor's refresh rate is 120 Hz. Cheers, -- Jason On Wed, Jul 20, 2011 at 12:41 PM, hari jayaram wrote: > Hi, > I am using the nvidia driver : 195.36.24 > OS: Ubuntu Lucid lynx 10.04 , 64 bit > I have a "working" xinerama config with two

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

Hi Hari, According to the NVidia's website, the Planar SA2311W is compatible with 3DVision since the version 260.19.36 of the Nvidia's video driver. Apparently the driver you're using is a way too old . Rafael. On 7/20/11 6:41 PM, hari jayaram wrote: Hi, I am using the nvidia driver : 195.36

Re: [PyMOL] help with moving objects separately

Mary, The duplication idea was correct, but most likely needed to be done via the command line for flexibility: duplicating a single object of two+ chains results in an object of two+ chains. Thus, calling rotate on the new object will rotate both chains in the new object. If you want to just ro

Re: [PyMOL] Help Needed

>From a purely structural perspective you can look at the interface residues script on the PyMOLWiki: http://pymolwiki.org/index.php/InterfaceResidues The interface could be detected by run /path/to/interfaceResidues.py fetch 1bm2 interfaceResidues 1bm2, c. A, c. L But, you ma

Re: [PyMOL] Help Needed

Dear Kousik, Sue Jones PROTORP server should do the trick: http://bioinformatics.sussex.ac.uk/protorp Cheers, Thomas On Wed, Dec 9, 2009 at 14:57, Kousik Kundu wrote: > > Dear Sir, >         I, Kousik Kundu, am a Ph.D student at university of Freiburg, > Germany. I am using Pymol for my rece

Re: [PyMOL] help about mutation

Chandan, PyMOL's mutagenesis wizard is purely geometric, and is intended to offer up Dunbrack rotamers as per: http://dunbrack.fccc.edu/bbdep/bbdepdownload.php Cheers, Warren From: Chandan Choudhury [mailto:iitd...@gmail.com] Sent: Wednesday

Re: [PyMOL] help with removing script (using Vista 64-bit)

Noah, Navigate to: C:\program files\delano scientific\pymol\modules\pmg_tk\startup And remove the files: color_by_restype.py and color_by_restype.pyc Cheers, Warren From: F. Noah Biro [mailto:fnoahb...@gmail.com] Sent: Thursday, March 19, 200

Re: [PyMOL] help with batch mode

n...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Andreas Förster > Sent: Wednesday, February 13, 2008 11:20 AM > To: Michael Summers > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] help with batch mode > > Hey Michael,

Re: [PyMOL] help with batch mode

Mike, As for NMR ensembles, so long as all of the structures loaded as multiple states in a single object (the default behavior for NMR ensembles in multi-model PDB format): print cmd.intra_fit(selection, state) will fit all of the other states to the indicated states and return the RMS values a

Re: [PyMOL] help with batch mode

Hey Michael, with some commands, you can use the (somewhat poorly documented) option 'quiet=0' to get results sent to standard output, like so: load ./final/final.001.pdb load ./final/final.002.pdb fit (final.002///13-30/c,ca,n), (final.001///13-30/c,ca,n), quiet=0 Andreas Michael Summers

Re: [PyMOL] Help for X.org-based Stereo 3D on Linux?

DeLano Scientific wrote: > PyMOL Users, > > We have gotten a couple of questions recently regarding running nVidia-based > Stereo 3D under the "X.org" X-server instead of using XFree86. > > We don't have X.org set up in house yet, so I was hoping someone else might > be able to provide a defini

Re: [PyMOL] Help with labels?

Hi labelers, I almost don't dare say this here, but for depth cued labels the best program/interface that I would know of is Lothar Esser's GL_RENDER. As far as I understand it is a graphical front end to bobscript/molscript that allows you to attach labels to atoms by clicking on them. The p

Re: [PyMOL] Help with labels?

A little side note: Ray tracing in stereo should be done with: ray width, height, angle=-3 png image_right ray width, height, angle=3 png image_left instead of with > > turn y, -3 to the first script > > > > turn y, 3 to the second one > > in order to get the shadows right Andr

Re: [PyMOL] Help with labels?

For publication, I generally do the labels manually in an external program such as Photoshop. Stereo is a little tricky, but it can be done. Jim N. On Oct 18, 2004, at 11:07 AM, jwal...@csb.wfu.edu wrote: Hi, I am trying to add labels to my figures to get them ready for publication. I hav

Re: [PyMOL] Help/suggestions for illustrating lattice arrangement

Hi Roger, the easiest solution is probably to create a fake pdb file with dummy atoms (located roughly in the center of mass) to represent each molecule in your ASU. make sure the pdb file contains the same CRYST entry as your original file. you can load it into pymol and then scale up the ato

Re: [PyMOL] Help/suggestions for illustrating lattice arrangement

Hi Roger, Unfortunately, there is no CGO ellipsoid. What you might try is represent the units in the lattice as arrows as to indicate their orientation (determined as the principal or principle ;) axis), and have one unit in (cartoon) detail, with a more slender arrow inside. I think it would

Re: [PyMOL] Help/suggestions for illustrating lattice arrangement

Hi Roger, * Roger Dodd [2004-10-07 16:33] wrote: > > I am trying to prepare a figure illustrating a fairly complex packing > arrangement in a large H32 (R32) unit cell, where the packing may > actually have some biological relevance. To try and show the packing > I've been generating symmetry

Re: [PyMOL] help compiling/ running APBS plugin on macG5

> I also notice that the same place that has APBS has this site that > computes electrostatics from a PDB file and returns a PQR file. This > would be lovely for people like me to use for the calculations. Now > how can I use the PQR file to create an electrostatic surface with > pymol? A PQR fi

RE: [PyMOL] Help for user-defined functions

PM > To: Gareth Stockwell > Cc: pymol-users > Subject: Re: [PyMOL] Help for user-defined functions > > > Hi, > > I haven't seen this documented anywhere, so I have no idea if it's the > Right Way to do things, but I think all you need to do is add > >

Re: [PyMOL] Help for user-defined functions

Hi, I haven't seen this documented anywhere, so I have no idea if it's the Right Way to do things, but I think all you need to do is add cmd.help_sc.append('some_func') after the cmd.extend('some_func',some_func) call. should this be built in to cmd.extend()? -michael -- This isn't a democrac

Re: [PyMOL] HELP Load biological unit

Dear All, Help, I don't know what I am doing wrong. I want to load a dimer into pymol, 3GRS, the standard PDF file from the PDB bank only gives co-ordinates for a monomer but if I download the PDB file for the biological unit http://www.rcsb.org/pdb/cgi/explore.cgi?job=download&pdbId=3GRS&pag

Re: [PyMOL] help compiling pymol on OSX

Craig, You'll have to install not only X11, but also its SDK. Go to: http://www.apple.com/macosx/x11 then scroll to the bottom of the page, and on the right hand side you'll see a small box with the title "Developer’s Kit"; inside this box are links to both of the installers you need.

RE: [PyMOL] help with surface parameters

Scott, > From: Scott Classen [mailto:clas...@uclink.berkeley.edu] > > Hello fellow PyMOLers, > Is the surface in PyMOL a solvent accessible surface or > a molecular > surface? It looks like a solvent accessible surface to me. Is > there any > way to change the radius of the water probe

[PyMOL] RE: pyMol help (Ball & Sticks)

From: George Nicola >I've tried several settings and commands but cannot figure out how to make >a simple ball-and-stick representation of a molecule. Can it be done in >Pymol? George, Yes, but it is non-obvious: hide lines show sticks show spheres set stick_radius=0.1 set sphere_scale=0.25

Re: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX

> Luca Jovine wrote: >> 3) And finally, how do people who use PyMol on Mac OSX cope with the mouse >> issue? Is any of you using a 3-button mouse, and, if so, which one? Hi Luca, A simple logitech wheel optical mouse works wonderfully with PyMol on MacOS X. MacOS X has basic built-in drivers for

Re: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX

Luca Jovine wrote: > 1) Is there any typed command one can use to color a selection by atom > type (rather than manually doing so by using the internal GUI pop-up menus)? The "util" module contains a number of functions that color the atoms according to type, with different colors for the C atoms.