[PyMOL] Preparation of the starting structure for the Gromacs simulation

Dear PyMol users! I want to prepare my pdb structure for MD simulation with gromacs 1- I want to place some CAP groups like ACE or NH2 to N and C termii of 1 and last residue of my protein, respectyally. I found possible option for this in the build- amono acids buit creted via this way ACE or N

[PyMOL] Work with pdb's enssemble

Dear Pymol Users! I want to solve one methodologycal problem via Pymol. I have 20 x-ray structures of one protein presented in different conformations. The main problem is that all those structures consist of Hen Lysozyme inserted in the protein for the improvement of the crystallographic proper

[PyMOL] Torsion angles

Dear PyMol Users! I wounder to know about posible ways to plot for my structures different torsion angles (phy, psi, chi ) on the ramachandran map via pymol. In particular I would like to obtain the next information 1- I d like to visualise and measure different torsions for my structure and pl

[PyMOL] Fwd: Torsion angles

php/Set_Dihedral<http://pymolwiki.org/index.php/Set_Dihedral> > http://pymolwiki.org/index.**php/Torsion<http://pymolwiki.org/index.php/Torsion> > > And you can modify torsion angles interactively using the mouse while in > editing mode (pick one atom, then CTRL-Drag). > >

Re: [PyMOL] Fwd: Torsion angles

Thanks, Thomas It works fine! Could you tell me in what strings the marker for the particular ss element is defined ( e.g I want to change from triangle to oval representation for alpha-helixes )? Thanks Rober I'll try investigate both of that programs, James 2011/11/17 Robert Immormino > Ja

Re: [PyMOL] Fwd: Torsion angles

gt; http://pymolwiki.org/index.**php/DynoPlot<http://pymolwiki.org/index.php/DynoPlot>to > enable postscript export (was quite easy). > > Cheers, > Thomas > > > On 11/18/2011 10:31 AM, James Starlight wrote: > >> Thomas, hello! >> >> In the past I'v

Re: [PyMOL] Work with pdb's enssemble

Jason, but as I've understood super did alignment only for two structures, Is there any way to do the same operation for ensemble ? (for CE as I understood this could be done by alignto command but it lack for seq alignment iin this case) James 2011/11/21 Jason Vertrees > Hi James, > > > set

Re: [PyMOL] Work with pdb's enssemble

l but for just one reference ( similar to the align ) so I'd like to obtain multiple sequence alignment on one reference based on the multiple structure alignment. Thanks James 2011/11/21 James Starlight > Jason, > > but as I've understood super did alignment only for two struct

[PyMOL] creating PDB structure

Dear PyMol Users! I wounder to know about possible ways of creation of the peptide structures via PyMol Builder module. In particular I need create a linear structure of my protein ( with fixed phi and psi angles) for futher folding molecular dynamics simulation of that peptide. But in builder mod

Re: [PyMOL] creating PDB structure

Thanks Thomas! Those scripts works fine. Could you tell me if there any way to install all of those scripts as the pymol plugins ( that I need not to load this scripts every time when I sttart pymol de novo )? James 2011/11/23 James Starlight > Thanks thomas > > Those scripts w

Re: [PyMOL] creating PDB structure

ow i could specify exactly location of that attachment if i want that ACE just be the first residue in my pdb ( linked with the actual first residue on the N term )? James 2011/11/23 James Starlight > Thanks Thomas! > > > Those scripts works fine. Could you tell me if there any w

[PyMOL] Questions about pymol plugins

Dear PyMol Users! I've decided to make this topic for all questions wich could be arrise during working in diffent PyMol plugins. So My first question about installation of the plugins wich are separate python modules ( installed not via PyMolf itself) E.g I have old PyMol wicj lack CEalign plug

[PyMOL] H-bonds representation

Dear PyMol users! As I've understood there are no posible ways to represent H-bonds in proteins in explicit manner. So I'm looking for possible way to do it via some plugin or another way. In particular I need 1) to visualize H-bonds in some structural motifs like coiled coil wich are dimers of

Re: [PyMOL] Editing of the pdb structure

he bottom right of the viewer. > > ** ** > > Joel**** > > ** ** > > *From:* James Starlight [mailto:jmsstarli...@gmail.com] > *Sent:* Thursday, 17 November 2011 7:52 a.m. > > *To:* Joel Tyndall > *Subject:* Re: [PyMOL] Editing of the pdb structure

Re: [PyMOL] H-bonds representation

Thomas, thank you for so detailed explanation. This way works good but I'd like to ask you about possibe Hbonds in the protein chain. As I remember for protein physics courses the H atom is always donor for only ONE H-bond ( and O or N atoms could be akceptors for 1 or 2 Hbonds) But In my case t

Re: [PyMOL] H-bonds representation

hanks, James 2011/11/27 Edward A. Berry > Yes i think the strongest H-bonds are single acceptor and straight > (angle at H = 180*). but these other bonds have significant > strength also. > Sorry, I'm a complete beginner at pymol. I have no idea how to > do these things. >

Re: [PyMOL] H-bonds representation

omething like this: > > show spheres, resn LEU+ILE+VAL and not name N+O+C > set sphere_transparency, 0.5 > > > Cheers, > Thomas > > > On 11/28/2011 02:58 PM, James Starlight wrote: > >> Another question also linked with the non-covalent interaction. >> &g

Re: [PyMOL] H-bonds representation

er > >> > >> and eventually something like this: > >> > >> show spheres, resn LEU+ILE+VAL and not name N+O+C > >> set sphere_transparency, 0.5 > >> > >> > >> Cheers, > >> Thomas > >> > >> On 11/28/2011 02:58 PM

Re: [PyMOL] H-bonds representation

> >> > 2011/11/28 Thomas Holder > >> >> > >> >> Hi James, > >> >> > >> >> most trivial manner: > >> >> > >> >> as cartoon > >> >> show sticks, resn LEU+ILE+VAL > >> >> set cartoon_side_

Re: [PyMOL] Editing of the pdb structure

. I'm getting ready > for the PyMOL v1.5 release, so you'll get faster answers there. > > Cheers, > > -- Jason > > On Tue, Jan 10, 2012 at 6:22 AM, James Starlight > wrote: > > Hi Jason > > > > Thank you for help again. > > >

[PyMOL] Problems with FindSeq.py script

Dear PyMol Users, I need to search defined sequence motifs in my structures. For that purpose I've used http://www.pymolwiki.org/index.php/FindSeq script but when I've try to use it I've got error PyMOL>findSeq SYG, 1a3h Error: selName was not a string. There was an error with a parameter. Pl

Re: [PyMOL] Problems with FindSeq.py script

ext, SYG is not in that protein. If you search for "S.G" you find > SNG. You can double check this by: > > fStr = cmd.get_fastastr("1a3h") > > print "SYG" in fStr > > which return false. > > Cheers, > > -- Jason > > > On

Re: [PyMOL] Problems with FindSeq.py script

/16 Troels Emtekær Linnet > It depends on, if you run or import the script. The namespace will be > different. > > What do you do? > > This is no error. This is basic Python knowledge. > > Troels Emtekær Linnet > Slotsvej 2 > 4300 Holbæk > Mobil: +45 60210234

Re: [PyMOL] Problems with FindSeq.py script

e="4ins" (Your variable) > propka proteinname (will not work) > propka 4ins(will work) > propka.propka(proteinname) (will work) > > I hope this clarify a little. > > Read more about namespaces here: > http://www.pymolwiki.org/index.php/Running_Scripts > http://do

[PyMOL] Protein-ligand interactions

Dear PyMol users! I've decided create new topic about representation of the protein-ligand interactions via Pymol because of alot of questions wich have been emerged during last month. Commonly I use the PyMol built-in command a-> present->ligands sites-> cartoon for the representation of the po

[PyMOL] Mutagenesis wizard

Dear PyMol users! I've desided to make this topic for my questions linked with the mutagenesis wizard setup. First of all I've already tried to make some point mutations in my proteins and all worked perfect. I just want ask about definition of the new torsions for the mutated residue. E.g I hav

Re: [PyMOL] Protein-ligand interactions

Thanks Thomas I've just one extra question about ligand sites. As I've said previously I can obtain information about polar contacts between ligand and its surrounding residues via Present- ligand sites. On the next step I mask all other non relevant parts of the protein ( wich are represented a

Re: [PyMOL] Protein-ligand interactions

ose that error might be due to the HETATM ussage because when I check sequence of my structure I'vee found many repeates of the assigned residues like THR-THR-THR-THR-TYR-TYR-TYR-TYR-TYR-GLY-GLY-GLY instead of simple THR-TYR-GLY triplet What should I do? 2012/1/23 James Starlight > Tho

[PyMOL] Addition of the missing hydrogen atoms

Dear PyMol users! I have one extra question about addition of the missing Hydrogen atoms to my structure. I've found that I could do it via context Hydrogen command as well as via H_add command. Now I want to add only specific hydrogens to the specific residues of my proteins ( e.g only alympha

[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 qu

Re: [PyMOL] Distance measurement between atom groups

: > http://pymolwiki.org/index.**php/Distance<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 t

Re: [PyMOL] Protein-ligand interactions

e to use this for better prediction of the mutations wich will change the shape and geometry of the ligand binding pockets in the above cases. \ Thanks again, James 2012/1/23 James Starlight > Thanks Thomas > > The reversible convertion indeed solved problem. > > James &

[PyMOL] Set values for dihedral angles

Dear PyMol users! I'm looking for the possible way to change some backbone didedral values in my peptide and dont perturbe the secondary structure of the rest of the peptide. E.g I have alpha-helix with sequence x-S-T-G-xI want to make turn motif in the STG tripeptide only by cha

Re: [PyMOL] Set values for dihedral angles

# activate sculpting > > sculpt_activate all > > set sculpting > > > > # switch to edit mode > > edit_mode > > > > Now drag atoms with the mouse or pick bonds and use commands like > "torsion". > > > > Hope that helps. > > > &g

Re: [PyMOL] Editing of the pdb structure

Dear PyMol users! I need to create NEW covalent bond between two adjacent atoms. How this could be done in PyMOl? James -- Try before you buy = See our experts in action! The most comprehensive online learning library for

Re: [PyMOL] Editing of the pdb structure

emb ( like benzol) because of long distance between adj atoms. How I could optimise geometry of the new mollecule? Have pymol some built-in functions like conformational search be means of monte carlo or energy minimisation ? James 2012/1/27 Thomas Holder > On 01/27/2012 09:11 AM, James St

Re: [PyMOL] Set values for dihedral angles

election 1 doesn't contain a single atom/vertex. I suppose this error might be due to incorect definition of H atom in the first selection. By the way how I could define PHI in case if my structure lack for hydrogens at all ? James 2012/1/27 James Starlight > Dear Thomas, Jed! > >

[PyMOL] Creating of chmeric protein

Dear PyMol Users! I want to make simple chimeric mutant via PyMol by transferring specified group from one protein to another. E.g I have to proteins: 1 protein consist of triplet of TLG amino acids in the X place 2nd protein consist of specific group wich I w'd like to move in the X place of

Re: [PyMOL] Creating of chmeric protein

is were me though, I would use Biopython. > > Jordan > > > > > On Jan 28, 2012, at 11:41 PM, James Starlight wrote: > >> Dear PyMol Users! >> >> >> I want to make simple chimeric mutant via PyMol by transferring >> specified group from one prote

[PyMOL] Assignment of the secondary structure for the PDB ensemble

Dear PyMol users! I'm working with the big pdb ensemble wich lack information about the secondary structure ( deleated header region) I want to find possible way to assign secondary structure for all pdb's in my ensemble ( like A-> assign sec.str for specified pdb). Finally I want to deleate some

Re: [PyMOL] Editing of the pdb structure

tried set connect_mode, 1 but saved pdb still have not contained CONNECT :( Thanks for help James 30 марта 2012 г. 13:52 пользователь James Starlight написал: > Hi all :) > > > Recently I've been needed to parametrise my short protein mollecule by ATB > server for futher MD simu

[PyMOL] Polar interactions within selection

Dear PyMol users! I'm analysing polar interactions occured during MD simulation of my protein. In particular I have PDB file obtained from such trajectory where I'd like to check new polar contacts ( salt bridges first of all) within selection region. I've tried to select specified region and use

Re: [PyMOL] Polar interactions within selection

_raw_distances('**saltbridges', state) >print ' %2d charged contacts in state %d' % (len(sb), state) > python end > --** > > [1] > http://pymolwiki.org/index.**php/Get_raw_distances<http://pymolwiki.org/index.php/Get_raw_distances>

Re: [PyMOL] Editing of the pdb structure

ow I could do it? James 1 апреля 2012 г. 15:04 пользователь James Starlight написал: > Thomas, > > > thank you I'll test your script with modeller after obtaining of this > software on my workstation and post here results :) > > > James > > 1 апреля 2012

Re: [PyMOL] Editing of the pdb structure

uot;, chain="A" > > See also > http://pymolwiki.org/index.**php/Alter<http://pymolwiki.org/index.php/Alter> > > Cheers, > Thomas > > James Starlight wrote, On 04/26/12 09:18: > > Dear PyMol users! >> >> >> I have some structure.pdb from the md si

Re: [PyMOL] Editing of the pdb structure

in my structure there are lack not only side chain atoms but also two backbone Oxygens in the Gly and Asn wich could be the main problem of such task. In any case I'll be very thankfull if you provide me with such server James 26 апреля 2012 г. 12:55 пользователь James Starlight напис

Re: [PyMOL] problems with mutagenesis wizard

On Fri, Jun 1, 2012 at 11:16 AM, James Starlight > wrote: > >> Dear PyMol users! >> >> >> I've tried to make 1 point mutation by means of pymol's mutagenesis >> wizard and obtain partially broken pdb. >> >> In my caseI've changed 27

Re: [PyMOL] problems with mutagenesis wizard

Oh, it seems that the problem was due to old version 1.3 of PyMol wich has been installed on my linux work-station. Today I've tried to make the same mutation on another win PyMol and the result was perfect. James 2012/6/1 James Starlight > I've sent another message with attache

Re: [PyMOL] Polar interactions within selection

. But what exaclty cutt-offs and addition python modules should I use? James 2012/4/17 James Starlight > Thanks, Thomas! > > Your script works fine. I've tested in one pdb structure and it finds all > polar and salt-bridges perfectly. > > As I've understood this scr

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Thomas, thanks this works perfect. Jason, I've tested this script on my system ( this is the membrane protein inserted in the bilayer surrounded by two water layers ( up and down ). During simulation individual water mollecules move into the protein interiour ( in that case protein like a water

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

maps? Thanks James 2012/6/15 James Starlight > Thomas, thanks this works perfect. > > > Jason, I've tested this script on my system ( this is the membrane > protein inserted in the bilayer surrounded by two water layers ( up and > down ). During simulation individual wa

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

/1-s2.0-S0005273610001707-g > > r4.jpg > > > > Could you tell me examples of software wich could produce such maps? > > > > > > Thanks > > > > James > > > > 2012/6/15 James Starlight > > > > > Thomas, thanks this works perfe

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Christian, Also I've found the same software- pose view (in that article I've also found link on it). Its very friendly but I've noticed some erorrs during representation of the non-covalent contacts partly in case of the vdw interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw but some

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

ow: > > http://pymolwiki.org/index.php/PoseView > > A LigPlot wrapper may follow... > > Cheers, > Thomas > > On 06/26/2012 10:13 AM, James Starlight wrote: > > Christian, > > Also I've found the same software- pose view (in that article I've also &

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

> Hi James, > > hm, looks like PoseView ignores all water molecules :( > > Have you tried LigPlot? It has a "-w" option to include waters. > > Cheers, > Thomas > > > On 06/26/2012 05:11 PM, James Starlight wrote: > >> Thomas, >> Its really grea

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

re or pymol modules for the analysis of protein-ligand interactions. In particular I'd like to obtain 3d surfaces of vdw as well as electrosctatics profiles of the active sites of my proteins as well as analysing of H-bonds ? James 2012/6/26 James Starlight > I'm still waiting for a

Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

Dear Christian, thank you for infromation- I'll examine this software. In particular I'm looking for possible modules for pymol because as I've found previously it's a good visualisation of the surfaces wich have been already included in PyMol. 2012/6/28 Christian Roth > > > By the way, there

Re: [PyMOL] Select crystal waters inside protein

ce area. For example: > > remove solvent beyond 3.5 of polymer > set dot_solvent > get_area solvent, load_b=1 > remove solvent and b > 20 > > Hope that helps. > > Cheers, > Thomas > > On 04/26/2012 10:55 AM, James Starlight wrote: > >> Another ques

[PyMOL] Restoring of atom number order

Dear Pymol Users! I've forced with the problem of missing correct atom numbering order during processing of my pbd structure. E.g I had a mollecule of caffein where each atoms had its own number ( e.g N1 or N3 etc) HETATM 2252 N1 CFF A 330 9.174 -33.156 -31.881 1.00147.73 N H

[PyMOL] Coordinates of ligand-binding site

Dear PyMol users! Some of docking servers (e.g swiss dock) which I'm using need in explicit definition of the coordinates (in XYZ) of the docking region as well as coordinates of its COM. How I could obtain such coordinates of intrested pdb file based on the knowing protein-ligand interaction sit

Re: [PyMOL] Coordinates of ligand-binding site

copy those selected aa's and atoms to another object: > save -> model -> copied_object as output.pdb > > output.pdb will then contain all the x,y,z coordinates of only what was > selected. > > Then just get those columns and upload them to swiss dock. >

Re: [PyMOL] Editing of the pdb structure

Dear all! I have input multi state structure consisted of protein in one state and ligand in the second state generated by Chimera. I want to merge both of that objects in one common object. How I could do it? James 2012/7/18 James Starlight : > Dear all! > > > I have input

[PyMOL] Creation of single nmr-like structure from separate pdb's

Dear PyMol users! I have big pdb ensembles consisted of 20-100 X-ray structures of different conformers of common protein solved by X-ray. I want to obtain single pdb files for such ensembles in NMR-like format. Firstly I can load all that pdbs into pymol by means of loadDir script. Now I'd like

[PyMOL] Algorithms for protein shape comparison

Dear PyMol users! In this topic I'd like to discuss different algorithms of the structure superimposition included in PyMol. First of all I've already noticed that some of such algorithms like CE or TMalign (part of the PSICO) have been already included in PyMol. It's known that such algoritms mai

[PyMOL] Preparation of the pdb for MD simulation

Dear PyMol users! I have pdb structure wich I'd like to prepare for my MD simulation. In that case this structure consist of some non-standart residue ( chromophore) wich is covalently bonded to the protein's backbone. The main problem is that this structure has some missing residues on both of t

[PyMOL] Creation of chimmeric protein

Dear PyMol users! I want to create chimeric protein (merge the N term of the second protein to the C term of the first protein) from two initial pdb's. How I could do this for further processing of that chimeric protein for MD simulation ? Thanks for help, James --

Re: [PyMOL] Creation of chimmeric protein

atom number in the sequence was mixed ( e.g like abababababababab,, where I need to obtain sequenctial order ). What I've done wrong and how I could obtain desired sequence ? James 2012/8/14, James Starlight : > Dear PyMol users! > > I want to create chimeric protei

[PyMOL] Saving setting in PyMol

Dear PyMol users! I wounder to know about possible way to save settings of the PyMol after LogOut from it. E.g I've defined some basic settings like fetch_host and fetch_patch for uploading of new pdb files as well as set new background colour. Also I've changed some advanced settings - e.g I de

[PyMOL] Building of the Carbon lattice

Dear PyMol users! I'd like to build simple 2D lattice model consisted of the Carbon atoms connected by the single bonds. Could you provide me with some script which can build such lattices of the desired dimensions ? Thanks for help James --

Re: [PyMOL] Saving setting in PyMol

ng for detailed options of the possible settings in that file ( e.g I didnt find how to set maximum quality of images as the default option ) Thanks for help James 2013/1/26 James Starlight : > Recently I've tried to find pymolrc but couldn't do it ( I have pymol > 1.5 installed

Re: [PyMOL] Changing of atom order after superimposition

hmm using TMalign method of superimposition I've solved that problem ( the atom order of ligand have been unchanged). James 2013/2/7 James Starlight : > Dear PyMol users! > > I've forced with the problem during superimposition of two identical > proteins. First of all

[PyMOL] Installing DSSP/Stride plugin

Dear PyMOl users! I've forced with the problem during installing of the DSSP/STRIDE plugin. In particular I've download pymol's plugins (and installed it via the plugin's meny) as well as DSSP binaries. then I've add DSSP_bin to the bash.rc so in the terminal I can launch it own@starlight ~/Do

[PyMOL] Electrostatic potential surface

Dear PyMol users! I wounder to know about built-in PyMol option for electrostatic potential visualisation. For example I have pdb coordinates of my protein as well as its electrostatic potential distribution (calculated by another software). Using MolMol with both of that files I can visualize t

Re: [PyMOL] Electrostatic potential surface

As I understood the APBs plugin which already exist in PyMol is the very efficient device for electrostatic potential calculations. 2 questions have been arisen: 1- How I could change cut-off distances for the electrostatic? E.g I'd like to consider only interactions within 5 A between any charg

Re: [PyMOL] Electrostatic potential surface

arguments! argv: ['/usr/share/pdb2pqr/pdb2pqr.py'], args: [] should I provide some addition paths to the bash? James 2013/3/27 James Starlight : > As I understood the APBs plugin which already exist in PyMol is the > very efficient device for electrostatic potential calculations. &

Re: [PyMOL] Electrostatic potential surface

at once ? James 2013/3/28 James Starlight > by the way have someone had problems with the pdb2pqr usage with APBS in > pymol? > > > I've tried to install pdb2pqr from source as well as via packages > then I've add usr/bin/pdb2pqr to the APBs plugin window >

[PyMOL] loadDir script

Dear PyMol users! I've forced with the problem of the loading of the my structural ensemble (pdb files of the protein listed as 1.pdb 2.pdb 3.pdb ..;. 100.pdb) into pymol via loadDir.pml script. In particular after loading of my ensemble in the right contex pymol's window I want to preserve struc

Re: [PyMOL] loadDir script

100.pdb) > it might be easier rename your pdb files so that the default string sorting > from glob matches the numerical order you want. Using the same example, > the filenames would change to 001.pdb, 002.pdb, ... 100.pdb. > > Pete > > James Starlight wrote: > >&g

Re: [PyMOL] loadDir script

er loading the files: > > PyMOL> order *, yes > > Cheers, > Thomas > > James Starlight wrote, On 04/02/13 19:28: > > Pete, > > > > thanks for suggestion. > > > > I've tried to use loadDir with the pdb's subset where each file had

[PyMOL] Visualization of the protein-ligand interactions

Dear Pymol users! I want to examine protein-ligand interactions observed in the md trajectory using Pymol. For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save

Re: [PyMOL] Visualization of the protein-ligand interactions

Thomas, thanks for help! As I understood fconv can be used for the split several mol2 (or pdb) files which was placed in 1 model to the several pdb files, doesnt it ? In past I forced with some problems with g_hbond. Is there any other way to monitor h bonds along the trajectory (e.g in vmd) ?

Re: [PyMOL] Fwd: Visualization of the protein-ligand interactions

Thomas, actually I used very routine way. Firstly I've extract conformers of protein-ligand complexes from the trajectory. Than I've loaded it into pymol and visualize possible interactions. Than I've selected most representative conformers and loaded it separately into pose view to obtain 2D map

[PyMOL] sorting pdb ensembles based on rmsd

Dear PyMol users! I have a set of conformations extracted from the MD trajectory (on the equal time-steps). After loading of all that pdb's into pymol (each conformer= separate pdb file) I want to sort that structures based on the RMSD relative to the reference conformer (e.g step0.pdb ) in the s

[PyMOL] Cartoon transparency

Dear PyMol users! I want to set transparency on the selected carton region of my protein ( I have closed GFP barell with the chromophore inside it so I'd like set transparency of some beta-shits to make chromophore easily visible ). In PyMol I've selected region corresponded to that Beta-sheets

[PyMOL] Automatic mutation introduction

Dear PyMol users! I'm looking for the possible python script which using the pymol source would introduce selected mutations in the defined PDB file and produce PDB output containing such protein with the selected substitution residues. It would be also good if rotamers for mutation residues woul

Re: [PyMOL] Automatic mutation introduction

ed.unc.edu/), since the installation and > compilation can take some time. > > Best, > -Ron > > On Nov 10, 2013, at 2:27 PM, James Starlight wrote: > > > Dear PyMol users! > > > > > > I'm looking for the possible python script which using the pym

[PyMOL] Caver 3.0 pugin

Dear Pymol Users! In the latest 3.0 releases of the CAVER plugin lack the source path for the caver.jar launch file. Could you tell me how I could define this path manually from pymol shell? I've try to make calculations with thus plugin having Caver 3.0 dir in the work folder but obtained error

Re: [PyMOL] Caver 3.0 pugin

This issue have been solved. Caver works fine. Does anyone tried to include path information obtained by caver to the NAMD steered md simulation? I'm looking for the protocol for guiding namd forces along the direction obtaned from CAVER. James 2013/11/15 James Starlight > Dear Pym

Re: [PyMOL] Caver 3.0 pugin

jar > > Both Carver2_1_2.py and Carver2_1_2.pyc are in the startup subdirectory. > Also other plugins are working without complaint. > > This is exactly the way the plug was working the last time that I > attempted its installation and use. > > > On 11/15/2013 03:14 PM, J

[PyMOL] RMSD calculation for the pdb ensemble

Dear PyMol users! I'm looking for python script which would perform the 1- loading ensemble of the pdbs to the pymol (assuming that it could be done by loadDir script) 2- Perform structural alighnemnt of all loaded structures against reference 0.pdb by means of buit-in TMalighn module this coul

[PyMOL] Rendering in pymol

Der Pymol users! I wounder to know if it possible to increase rendering rate mainly at the expense of the GPU usage. At my desktop with core i7 and 6 cpu (12 cpus in the hyper-threading mode) I've spend ~ 2 hours to render image consisted of ensemble of conformations (~ 30 aligned pdbs) using onl

[PyMOL] AutoDock plugin

Dear PyMol users! I've forced with the problem of the installation of AutoDock plugin pymoawiki.org/index.php/Autodock_plugin in recent pymol version. I've tried to install it manually from the downloaded py script but at the starting of pymol below error has bbeen appeared Unable to initialize

Re: [PyMOL] AutoDock plugin

> For the missing bonds in your example, PyMOL thinks those atoms are > cations because of the symbol in the last column. By default, PyMOL doesn't > make bonds to cations. But this will work: > > PyMOL>unset pdb_unbond_cations, > PyMOL>load example.pdb > > Hop

[PyMOL] Working with the pdb ensemble

Dear PyMol users! I'd be thankfull if you provide me with the easliest way how I could save selection to the separate pdbs. For example I've loaded 10 pdbs of the receptor and selected from in each 10 ligands. This selection is defined in one object (extracted or coppied from sele). How I could sa

Re: [PyMOL] Working with the pdb ensemble

Center > 550 First Avenue > New York, NY 10016 > 212-263-7898 > http://kong.med.nyu.edu/ > > > > > > > On Dec 6, 2013, at 12:03 PM, James Starlight > wrote: > > Dear PyMol users! > > I'd be thankfull if you provide me with the easliest wa

[PyMOL] python scripting in pymol

Dear PyMol users! I'm learning of the python scripting for the solution of typical structural bioinformatics problems. This time I'd like to integrate in pymol simple script which will search for the selected motifs (just several amino acids situated in adjacent positions along the sequence) and m

[PyMOL] Saving trajectory outputs

Dear Pymol Users! I wounder whether it will be possible to save big ensemble of the loaded into pymol Pdb's files as the trajectory output (like dcd format) what are actually can be performed by vmd (e.g by means of http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/). The pro

[PyMOL] Making nmr-like ensemble from several pdbs

Dear Pymol users! Using below script I can load all pdbs from the work dir into 1 nmr-like object. Could you suggest me how this script could be modified to make alignment (or it's better structural alignment) of all pdbs against first loaded pdb file from pymol import cmd import sys,glob def ge

Re: [PyMOL] Making nmr-like ensemble from several pdbs

also please tell me how is it possible to include ter record at the end of each model. James 2014-08-27 11:58 GMT+02:00 James Starlight : > Dear Pymol users! > > Using below script I can load all pdbs from the work dir into 1 nmr-like > object. Could you suggest me how this scr

Re: [PyMOL] Making nmr-like ensemble from several pdbs

why this error occurs (I have not this in case of ONE model from the ensemble) James 2014-08-27 13:10 GMT+02:00 Thomas Evangelidis : > split_states > alignto <1st NMR model name>, method=cealign > > > On 27 August 2014 13:28, James Starlight wrote: > >> also please tel

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