[PyMOL] Seeing more H-bonds than expected

Hello PyMOL users, Hydrogen bond finder on Pymol sometimes gave me unexpected observations like: more than 3 H bonds to Lysine, more than 1 to a carbonyl oxygen and so on. This is even after setting H-bond center cutoff to 3.0 A. Any insight would be appreciated. Thank you for sharing your

Re: [PyMOL] PyMOL command line scripts

Hi Manish, Thank you for building these amazing scripts! However, I was wondering how to install these scripts into Pymol. I tried copying the URL for PhiPsiAngles code in the Plugin manager of Pymol, however the plugin is not being installed. Please advise. Many thanks, Neena On Thu, 7 Feb

Re: [PyMOL] Seeing more H-bonds than expected

Also, a carbonyl oxygen has 2 lone pairs, so can accept 2 H-bonds. See > perhaps McDonald & Thornton, JMB (1994) > https://doi.org/10.1006/jmbi.1994.1334 for a more detailed discussion. > > Hope that helps. > > Cheers, > Jared > > > On April 4, 2019 at 11:25:17

[PyMOL] Skip Activation Window Remove

Hello PyMOL users, I have been using official PyMOL build which requires a license. I do not need any special features of pymol, is there a way to remove this 'No License File' window? Many thanks, Neena ___ PyMOL-users mailing list Archives:

[PyMOL] Align more than two structures

Hello PyMOL users, How to align more than two structures in pymol? Thank you, Neena ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe:

[PyMOL] RMSD-based clustering tool

Hello PyMOL users, I was wondering does PyMol have a RMSD based clustering tool. Many thanks, Neena ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe:

Re: [PyMOL] Protonated aspartic acid

Thank you Pedro! On Tue, 7 Jan 2020 at 20:17, Pedro Lacerda wrote: > Hi Neena, > > Check the builder. You can change the charge of a atom adding or removing > H. > > Cheers, > > [image: image.png] > > Em ter., 7 de jan. de 2020 às 20:29, Neena Susan Eappen < &g

[PyMOL] Protonated aspartic acid

Hello PyMOL users, How to change the protonation state of aminoacid in Pymol? Say from aspartic acid at deprotonated state to protonated state? Thank you, Neena ___ PyMOL-users mailing list Archives:

[PyMOL] Extract all phi and psi angles

Hello PyMOL users, How to extract all peptide dihedral angles (phi and psi) in PyMOL? Many thanks, Neena ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe:

Re: [PyMOL] Extract all phi and psi angles

DAnalysis (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 ph

Re: [PyMOL] Extract all phi and psi angles

ohn...@schrodinger.com> wrote: > Hi Neena, > > Is this command sufficient? > > https://pymol.org/dokuwiki/doku.php?id=command:phi_psi > > Best, > Jarrett J > > On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen < > neenasusan...@gmail.com> wrote: > >> Hello

[PyMOL] B-factor coloring scale

Hello PyMOL users, Where can I find the coloring scale used for B-factor in PyMOL? Many thanks, Neena ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe:

[PyMOL] Energy minimization in Pymol

Hello PyMOL users, I used gromacs (opls-forcefield) to simulate a peptide, attached here are two energy minimized structures. However, em5 was 40 KJ/mol higher in energy than em4 according to gromacs. When I minimized these two structures using clean function in pymol builder, these structures

[PyMOL] View two proteins from one pdb file

Hello PyMOL users, I have a PDB file with coordinates for two proteins listed one after another (attached). However, when i open the file on pymol, I only see one protein (shown below) or it might be a sum of those 2 coordinates. How to view both structures? [image: image.png] Many thanks, and

Re: [PyMOL] View two proteins from one pdb file

Thank Joel, that worked very well! On Sun, 7 Jun 2020 at 18:28, Joel Tyndall wrote: > Hi Neena, > > > > Use the command “split_states clusters”, just type it into the command line > > > > J > > > > *From:* Neena Susan Eappen > *Sent:* Monday

[PyMOL] Label charge sites, termini, check contrast

Hello PyMOL users, Is there a way to label charge sites and termini on PyMOL as I have shown in the below figure instead of using Paint? In addition, is there a way to check color contrast for this peptide structure for making it more accessible to the readers? [image: image.png] Many thanks,

Re: [PyMOL] Label charge sites, termini, check contrast

Hi Ali, Thank you for the brief and thorough explanation! All those commands gave exactly what I was looking for! Many thanks, Neena On Fri, 29 Jan 2021 at 18:36, Ali Saad Kusay wrote: > Hi Neena, > > A simple way to label in PyMOL is to simply select the atom you want and > enter the

Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

gt; > From: Kamil Steczkiewicz [kamil.steczkiew...@gmail.com] > Sent: Wednesday, July 07, 2021 2:29 AM > To: Neena Susan Eappen > Cc: Mooers, Blaine H.M. (HSC); zb2...@cumc.columbia.edu; pymol-users > Subject: Re: [PyMOL] [EXTERNAL] No cartoo

[PyMOL] Exporting structure from PyMOL

Hello PyMOL users, I have a question regarding structure exporting from PyMOL. I have a peptide that adopts two conformations in gas phase: compact globule and helical ( see below). I was wondering how to best export these structures from two different PDB files with the same scale. [image:

[PyMOL] No cartoon view for custom PDB file

Hello PyMOL users, I performed a geometry optimization of a peptide on gaussview and then saved the output log file as a PDB. However, when I open this PDB file (attached hereby) in Pymol, I cannot enable the cartoon view of the secondary structure; I can only enable the line and stick

Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

Thank you Blaine and Zuben for your insights and troubleshooting the problem! I understood the formatting issue with the current PDB file, will do the necessary changes. Regards, Neena On Sat, 3 Jul 2021 at 09:59, Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> wrote: > Hi Neena, > > Thank

Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

insights on what could be wrong in the opt21 PDB file?* Many thanks, Neena On Sat, 3 Jul 2021 at 23:38, Neena Susan Eappen wrote: > Thank you Blaine and Zuben for your insights and troubleshooting the > problem! I understood the formatting issue with the current PDB file, will > do the

Re: [PyMOL] Label charge sites, termini, check contrast

set label_offset, [0,0,5], myobject > > Hope that helps. > > Cheers, > Jared > > > On Sat, Jan 30, 2021 at 2:52 AM Neena Susan Eappen < > neenasusan...@gmail.com> wrote: > >> Hi Ali, >> >> Thank you for the brief and thorough explanati

[PyMOL] Exporting data from PyMOL into OriginLab

Hello PyMOL users, I have some issues exporting images from PyMOL into a data analysis software called OriginLab (https://www.originlab.com/). If there is anyone in this mail list who integrates figures from PyMOL into Origin, please email me. I need some insights for data representation. Many

Re: [PyMOL] Custom zoom settings

gt; where "i" would be 15 in your case. > > On Tue, Jul 27, 2021 at 10:56 AM Neena Susan Eappen < > neenasusan...@gmail.com> wrote: > >> Hello PyMOL users, >> >> In addition to the current PyMOL interface for zoom settings (shown >> below),

[PyMOL] Custom zoom settings

Hello PyMOL users, In addition to the current PyMOL interface for zoom settings (shown below), is there a command to get a zoom setting like say 15 Angstrom sphere? [image: image.png] Many thanks, Neena ___ PyMOL-users mailing list Archives:

Re: [PyMOL] Exporting data from PyMOL into OriginLab

the helix > on transparency. > > Adam > > On Jul 23, 2021, at 11:57 AM, Neena Susan Eappen > wrote: > > Hello PyMOL users, > > Let me clarify my question. Shown below is one example figure. There is no > way to crop any images on Origin graphing software. For this fi

Re: [PyMOL] Extract H-bond angle

:10, Neena Susan Eappen wrote: > Hello PyMOL users, > > With "list_hbonds analyte" command, PyMOL gives the list of all H-bonds > with distances in a protein. > I was wondering how to also extract H-bond angle information for those > h-bonds. Is there a command line fo

[PyMOL] Extract H-bond angle

Hello PyMOL users, With "list_hbonds analyte" command, PyMOL gives the list of all H-bonds with distances in a protein. I was wondering how to also extract H-bond angle information for those h-bonds. Is there a command line for this? Thank you so much, Neena

[PyMOL] H-bond data extraction

Hello PyMOL users, This is not a question related to PyMOL, but I was wondering if someone can help me or guide me to the appropriate resource. I extracted two types of H-bond occupancy data (donor: Lysine side chain and backbone amide NH, with backbone carbonyl CO as acceptor) from two

[PyMOL] Extract relative helical character

Hello PyMOL users, I was wondering how to extract the total extent of helicity between two peptide structures on Pymol. [image: image.png] [image: image.png] Any insight would be appreciated. Many thanks, Neena ___ PyMOL-users mailing list Archives:

Re: [PyMOL] Extract relative helical character

Hello PyMOL users, Could I please get some insights on this? Thank you, Neena On Wed, 7 Sept 2022 at 12:06, Neena Susan Eappen wrote: > Hello PyMOL users, > > I was wondering how to extract the total extent of helicity between two > peptide structures on Pymol. > > &

Re: [PyMOL] Extract relative helical character

guide & ss H") > count_all = cmd.count_atoms("guide") > print("Number of helix residues:", count_helix) > print("Relative helix content:", count_helix / count_all) > > Cheers, > > Thomas > > > > On Sat, Sep 10, 2022 at 1:37 PM Neena Susa

Re: [PyMOL] Question on residue selection in multiple PDB

Hello PyMOL users, Can I get some insight on how to approach this analysis? Many thanks, Neena On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen wrote: > Hello PyMOL Team, > > I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38 > NMR structures deposited in

Re: [PyMOL] Question on residue selection in multiple PDB

sele1, sele2) >> print(dist) >> >> print("") >> >> # Approach 2: Without splitting states >> >> for i in range(cmd.count_states('1L2Y')): >> sele1 = "/1L2Y/A/A/ILE`4/O" >> sele2 = "/1L2Y/A

[PyMOL] Question on residue selection in multiple PDB

Hello PyMOL Team, I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38 NMR structures deposited in it. Using split_states command, I can see all 38 structures. I want to find polar contacts between same 3 residues in all these 38 structures and extract corresponding distance