Re: [PyMOL] Distance measure between pseudo atoms does not update over states

Hi Jarrett, Thank you very much for the fix, it works perfectly. Best regards, Istvan On Wed, Jul 19, 2023 at 9:02 PM Jarrett Johnson < jarrett.john...@schrodinger.com> wrote: > Hi Istvan, > > I can reproduce the same issue. Seems to be some unintended behavior with > how this multistate

Re: [PyMOL] Distance measure between pseudo atoms does not update over states

Hi Istvan, I can reproduce the same issue. Seems to be some unintended behavior with how this multistate pseudoatom object is created. I've attached a modified center_of_mass.py script so that it should behave the way you expect. Let me know if this works for you. Example that I tried with this:

[PyMOL] Distance measure between pseudo atoms does not update over states

Hi, I have a simulation trajectory loaded in Pymol and I want to display certain interatomic distances interactively. This works perfectly fine with normal atoms, I can see how these selected distances change over the course of the simulation using the wizard and playing the movie. However, it

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

You are right, thank you! Cheers, Enrico чт, 27 янв. 2022 г. в 13:32, Ali Saad Kusay : > > Hi Enrico, > > I think it's because you are selecting side chains, glycine has no sidechain > and alanine has single carbon atom side chain so this representation won't > work for it. You would need to

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

Hi Enrico, I think it's because you are selecting side chains, glycine has no sidechain and alanine has single carbon atom side chain so this representation won't work for it. You would need to remove the sidechains from the selection to make it apply to the backbone atoms, i.e.

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

additional question in the same field: as I've mentioned before, before applying distance-based filtering, I would like to change the representation of the lines to ball-and-stick for the residues involved in the interactions: cmd.select('rep lines and sidechain') cmd.show_as('sticks', 'sele')

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

Thank you very much, Ali!! Cheers, Enrico чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay : > > 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,

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.

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

Dear Pymol Users! I am working on the visualization of the protein-ligand contacts identified using preset.ligand_cartoon('pdb',_self=cmd) Since the command also displays some residues, which are not involved in the interactions (with the radicals located too far away) with the ligand, I need to

Re: [PyMOL] distance

gt; Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > From: Joseph Brock > Sent: Friday, 26 October 2018 8:57:44 AM > To: Jarrett Johnson > Cc: Pymol User list > Subject: Re: [PyMOL] distance > > Thanks Jarrett! I will try that! >

Re: [PyMOL] distance

8:57:44 AM To: Jarrett Johnson Cc: Pymol User list Subject: Re: [PyMOL] distance Thanks Jarrett! I will try that! Cheers, Joseph. Joseph S. Brock | PhD Researcher Drew Lab Department of Biochemistry and Biophysics Stockholm University From: Jarrett Johnson

Re: [PyMOL] distance

Subject: Re: [PyMOL] distance Built from source (github repo). On Thu, Oct 25, 2018 at 5:56 PM Joseph Brock mailto:joseph.br...@dbb.su.se>> wrote: Hi Jarret, Thanks for the reply! Unfortunately so ;( Did you build from source or install via apt-get? https://pymolwiki.org/ind

Re: [PyMOL] distance

nux_Install > > > Cheers, > > Joseph. > > > > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > -- > *From:* Jarrett Johnson > *Sent:* Thursday, 25 October 2018 11:34:

Re: [PyMOL] distance

From: Jarrett Johnson Sent: Thursday, 25 October 2018 11:34:28 PM To: Joseph Brock Cc: Pymol User list Subject: Re: [PyMOL] distance Hi Joseph, I'm not able to replicate that on my end using open-source PyMOL 2.2 on Ubuntu 16.04. Does this behavior also occur for molecules

Re: [PyMOL] distance

Hi Joseph, I'm not able to replicate that on my end using open-source PyMOL 2.2 on Ubuntu 16.04. Does this behavior also occur for molecules fetched straight from the PDB? Jarrett J. On Thu, Oct 25, 2018 at 4:44 PM Joseph Brock wrote: > Hi pymol users, > > > I've observed a weird behaviour

[PyMOL] distance

Hi pymol users, I've observed a weird behaviour with the open source pymol (v 1.7.2.1-2.2 running on ubuntu 16.04). When I try to create some distance objects either via the command line of the actions menu, an object is created but no dashed lines appear. When I "zoom" this object it is

Re: [PyMOL] distance wizard

nevermind, I was entering @distance.py instead of run distance.py On Fri, Oct 13, 2017 at 2:05 PM, Leigh M wrote: > Hi Jared- > > I just use the C-alpha xyz coordinates and use d = math.sqrt(dx**2 + > dy**2 + dz**2). > I've been using python alone without pymol...using

Re: [PyMOL] distance wizard

Hi Jared- I just use the C-alpha xyz coordinates and use d = math.sqrt(dx**2 + dy**2 + dz**2). I've been using python alone without pymol...using your code with the pymol api works for individual distances but I'm calculating hundreds of distances and need to write to a csv which does not seem to

Re: [PyMOL] distance wizard

Hi Leigh -  How are you getting the coordinates?  This works for me: ``` import math # Show more digits for the distance label set label_distance_digits, 10 # Make an alanine residue fab A, ala # Get coordinates from 2 atoms o = cmd.get_coords("/ala///1/O")[0] h =

Re: [PyMOL] distance wizard

yep! On Thu, Oct 12, 2017 at 2:07 PM, Roger Rowlett wrote: > You are using d = sqrt(dx^2 + dy^2 + dz^2), right? (Where dx = x2 - x1, > etc.) > > ___ > Roger S. Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry >

Re: [PyMOL] distance wizard

You are using d = sqrt(dx^2 + dy^2 + dz^2), right? (Where dx = x2 - x1, etc.) ___ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax:

[PyMOL] distance wizard

Anyone know how pymol calculates distance between two atoms? I wrote a python script that calculates distance using the distance formula and the xyz coordinates in the pdb, and it differs from the wizard by ~40%. Any ideas on what might be going on would be helpdul Thanks! Leigh

Re: [PyMOL] Distance or measurement labels Version 1.6 and 1.7 does not show

Hi Thomas, now I have the label visible immediately (w/o using ray)! Thank you very much! Burkhard. On 02/28/2014 04:54 AM, Thomas Holder wrote: Hi Burkhard, bug fixed in SVN rev 4067. Let me know if it works for you. Cheers, Thomas On 27 Feb 2014, at 10:07, Thomas Holder

Re: [PyMOL] Distance or measurement labels Version 1.6 and 1.7 does not show

Hi Burkhard, this was a very strange ATI only bug which we already could fix in our Incentive PyMOL release. The fix should soon make it into the open-source version as well. Thomas On 26 Feb 2014, at 02:30, endew...@prisner.de wrote: Dear PyMOL Experts, I did check on the mailing list and

Re: [PyMOL] Distance or measurement labels Version 1.6 and 1.7 does not show

Hi Burkhard, bug fixed in SVN rev 4067. Let me know if it works for you. Cheers, Thomas On 27 Feb 2014, at 10:07, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Burkhard, this was a very strange ATI only bug which we already could fix in our Incentive PyMOL release. The fix

[PyMOL] Distance or measurement labels Version 1.6 and 1.7 does not show

Dear PyMOL Experts, I did check on the mailing list and fond one email about my problem but it seems it was nor resolved: (http://sourceforge.net/p/pymol/mailman/message/31119931/) I use PyMol : PyMOL(TM) Molecular Graphics System, Version 1.7.0.0. and have the problem that the distance command

[PyMOL] Distance measurement between atom groups

Dear PyMol Users! In the PyMol Wizard I've found very userful option called distance measurements beyween selected atoms. I wounder to know how I could realize such operation via PyMol console in the simplest manner. My current task consist of making different point mutations and subsiquent

Re: [PyMOL] Distance measurement between atom groups

Hi James, use the distance command: http://pymolwiki.org/index.php/Distance For the potential h-bonds, use it with mode=2. Cheers, Thomas On 01/24/2012 05:15 PM, James Starlight wrote: Dear PyMol Users! In the PyMol Wizard I've found very userful option called distance measurements

Re: [PyMOL] Distance measurement between atom groups

Thanks Thomas! I've already tried use this command. I want just ask about Hbond representation between 2 selected regions. E.g I want to represent Hbonds beetween 2 helices Firstly I've added donor Hydrogens H_add donors and than distance 3sn6 and resi 197-220, 3sn6 and resi 275-298,

Re: [PyMOL] distance bug

Hi, My pymol 1.4.1 works fine. can you try to ray trace and see if your objects are available but just not displayed on the standard screen? cheers, 2011/9/29 Andreas Förster docandr...@gmail.com Hi all, Has anyone noticed that the distance command behaves oddly. Has this been recently

Re: [PyMOL] distance bug

Hi Andreas, It was a bug with the invalidation system. I just pushed a fix to source forge. Thanks for bringing this to our attention. Cheers, -- Jason 2011/9/29 Andreas Förster docandr...@gmail.com: Hi all, Has anyone noticed that the distance command behaves oddly.  Has this been

Re: [PyMOL] distance bug

Ah, indeed, the latest revision 3969 has a correctly working distance command. Thanks Jason. Andreas On 29/09/2011 3:08, Jason Vertrees wrote: Hi Andreas, It was a bug with the invalidation system. I just pushed a fix to source forge. Thanks for bringing this to our attention.

Re: [PyMOL] distance between two atoms in all the pdb files in a directory

Hi pkb bioinfo (which I do hope is not your real name), Did you actually paste the script or did you retype it? from pymol import cmd from glob import glob lst = glob(*.pdb) lst.sort() for fil in lst:     cmd.load(fil,tmp)    

Re: [PyMOL] distance between two atoms in all the pdb files in a directory

O, and just when I pressed send (which also made firefox crash for some reason), it struck me that you only load files, which means that you're only appending states. But you don't specify a state to calculate the distance, which means the first is taken again and again. You might want to add a

[PyMOL] distance between two atoms in all the pdb files in a directory

Hello Pymol users, I am new to pymol scripting and I want to calculate the distance between two points of all the pdb file in a directory. I tried to write the script but seems its not working. PLease help me. from pymol import cmd from glob import glob lst = glob(*.pdb) lst.sort() for fil in

Re: [PyMOL] Distance labels

An object whose name begins with an underscore will not appear in the menu. Perfect! But how can I change the name of one name in the Names Panel? -- Two of the most famous products of Berkeley are LSD and Unix. I don't think that this is a coincidence. http://servomac.blogspot.com

Re: [PyMOL] Distance labels

set_name oldname, newname On Feb 12, 2008 2:48 PM, Toni Pizà servo...@gmail.com wrote: An object whose name begins with an underscore will not appear in the menu. Perfect! But how can I change the name of one name in the Names Panel? -- Two of the most famous products of Berkeley are LSD

[PyMOL] Distance labels

Hi! When I create a distance in a pymol session, an object called dist n is created, and a label with there name is shown at the right of the screen, with the other objects loadeds. Can I create a dist, and render the dotted line at the screen, without having the label in the right menú? Thanks

Re: [PyMOL] Distance labels

An object whose name begins with an underscore will not appear in the menu. On Feb 11, 2008 3:13 PM, Toni Pizà servo...@gmail.com wrote: Hi! When I create a distance in a pymol session, an object called dist n is created, and a label with there name is shown at the right of the screen, with

Re: [PyMOL] Distance and scripts

On Monday 21 January 2008 23:51:15 Toni Pizà wrote: I'm not sure this is what you're asking, but I use scripts by typing: @script.pml Thanks for your response, but I'm asking how to pass arguments to pymol's scripts written in Python. I type run nameOfScript.py within pymol for this, but

[PyMOL] Distance and scripts

Hi guys! I hope you enjoy your time with Pymol, it's so nice ;) I have a few doubts; anybody know if it's possible to change the color of the dotted line drawn by the distance command? How can I pass an argument to a python script run with run script.py? Thank you!

Re: [PyMOL] Distance and scripts

I'm not sure this is what you're asking, but I use scripts by typing: @script.pml Thanks for your response, but I'm asking how to pass arguments to pymol's scripts written in Python. I type run nameOfScript.py within pymol for this, but I would pass some arguments, such as run script.py arg0

[PyMOL] Distance Label Format

Hi Folks, When using the distance wizard is there a way to change the number of decimal places output to the label from 2 to 1? Thanks, Tony Anthony A. Armstrong Department of Biophysics and Biophysical Chemistry Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD

Re: [PyMOL] Distance Label Format

Hi, Hmm. Not very easily. The measurement wizard just calls a distance method, which makes the dashed line and the label internally. Other wise it would be simple to say: cmd.label_dash(%0.1f % d) assuming that there was such a command... :) Oh, and that command would need a dash object as a

Re: [PyMOL] Distance Label Format

...@lists.sourceforge.net] On Behalf Of gilleain torrance Sent: Friday, February 23, 2007 2:16 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Distance Label Format Hi, Hmm. Not very easily. The measurement wizard just calls a distance method, which makes the dashed line and the label

Re: [PyMOL] distance atom-protein surface

I needed to have a measurement of the actual physical long dimension of a protein model to compare with x-ray scattering data. I activated the surface mesh feature and at the extreme ends of the longest axis, right at the surface boundary, created a carbon atom at each position, then simply

[PyMOL] distance atom-protein surface

Dear Pymol users, I would like to measure the distance between an atom and a specific point (not another atom) in the surface of the protein. Is it possible with pymol? do I need additional scripts? Thanks in advance, Giacomo Bastianelli

Re: [PyMOL] distance atom-protein surface

Hi Giacomo, you can either create an atom at that position (see eg. http://www.rubor.de/bioinf/tips_python.html#chempy) and than use the distance command (or wizard). Or you can get the position of your first atom and simply calculate the distance of the two positions, sth. like: class

RE: [PyMOL] distance between aromatic residues

Hi Sara, I don't think this is directly possible, since the centers of the aromatic rings are not declared per se. But I see another way to obtain the result you want, maybe this can be written as a small Python script (sorry I never wrote any Python scripts, so I can't translate my idea!!). The

Re: [PyMOL] distance from plane

Gareth Stockwell wrote: Hi Kristl, I'm not sure if PyMOL can do it, but it's not too hard to do a bit of vector algebra which gives the answer. Let the coordinates of the nitrogens be A, B, C, D, and the iron atom F. Compute the centre of your nitrogens: X = (A + B + C + D) / 4 Then you

[PyMOL] distance from plane

Hi Pymolers! Is there a way for me to define a plane of atoms say 4 Nitrogens in a heme complex and then determine how far out-of-plane the Fe atom is? If so either in Pymol or another program I'd love to know the secret. Thanks, Kristl kri...@physics.purdue.edu

Re: [PyMOL] distance from plane

Hi Kristl, I'm not sure if PyMOL can do it, but it's not too hard to do a bit of vector algebra which gives the answer. Let the coordinates of the nitrogens be A, B, C, D, and the iron atom F. Compute the centre of your nitrogens: X = (A + B + C + D) / 4 Then you work out a normal to the

RE: [PyMOL] distance parameters

From: Jules Jacobsen [mailto:jo...@hermes.cam.ac.uk] you can change most of the parameters using set dash_n where n= length, width, gap, radius. Unfortunately dash_color doesn't exist. ...but you can change the color of a distance object color red,dist01 Warren

[PyMOL] distance parameters

Hi, I'd like to know if it's possible to change the parameters of the DISTANCE command (color, radius, ...) Thanks, Franck Coste.