[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

[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

[PyMOL] Fwd: Torsion angles

/Torsion And you can modify torsion angles interactively using the mouse while in editing mode (pick one atom, then CTRL-Drag). Hope that helps. Cheers, Thomas On 11/16/2011 06:50 PM, James Starlight wrote: Dear PyMol Users! I wounder to know about posible ways to plot for my structures

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

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

Re: [PyMOL] Work with pdb's enssemble

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 jmsstarli...@gmail.com Jason, but as I've understood super did alignment only for two structures

[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

[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

[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

Re: [PyMOL] Editing of the pdb structure

) at the 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 ** ** Another question about working

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

Re: [PyMOL] H-bonds representation

, James 2011/11/27 Edward A. Berry ber...@upstate.edu 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. ed James

Re: [PyMOL] H-bonds representation

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. In particular I wounder to know how i Could represent all hydrophobic ( Ley Ile Val

Re: [PyMOL] H-bonds representation

Cheers, Thomas On 11/28/2011 02:58 PM, James Starlight wrote: Another question also linked with the non-covalent interaction. In particular I wounder to know how i Could represent all hydrophobic ( Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd like

Re: [PyMOL] H-bonds representation

show sticks, resn LEU+ILE+VAL set cartoon_side_chain_helper 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, James Starlight wrote: Another question also

Re: [PyMOL] Editing of the pdb structure

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 jmsstarli...@gmail.com wrote: Hi Jason Thank you for help again. I've also question about representation of the polarr contacts between

[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 PyMOLfindSeq SYG, 1a3h Error: selName was not a string. There was an error with a parameter.

Re: [PyMOL] Problems with FindSeq.py script

you find SNG. You can double check this by: fStr = cmd.get_fastastr(1a3h) print SYG in fStr which return false. Cheers, -- Jason On Fri, Jan 13, 2012 at 1:25 PM, James Starlight jmsstarli...@gmail.com wrote: Dear PyMol Users, I need to search defined sequence motifs in my

Re: [PyMOL] Problems with FindSeq.py script

/16 Troels Emtekær Linnet tlin...@gmail.com 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 2012/1/16 James Starlight

Re: [PyMOL] Problems with FindSeq.py script

Best Troels 2012/1/16 James Starlight jmsstarli...@gmail.com Troels, Commonly I run pymol scripts by means of run script.py or @ script.py from PyMol shell! then I use script_command ( e.g findSeq ) and further script syntax for my tasks e.g findSeq s.g 1f88 works perfect

[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

[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

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

Re: [PyMOL] Protein-ligand interactions

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 jmsstarli...@gmail.com Thomas

[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

[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

: http://pymolwiki.org/index.**php/Distancehttp://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

Re: [PyMOL] Protein-ligand interactions

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 jmsstarli...@gmail.com Thanks Thomas The reversible convertion indeed solved problem. James 2012/1/23 Thomas

[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

Re: [PyMOL] Set values for dihedral angles

and use commands like torsion. Hope that helps. Cheers, Thomas James Starlight wrote, On 01/26/12 13:45: 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

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

Re: [PyMOL] Editing of the pdb structure

, James Starlight wrote: Dear PyMol users! I need to create NEW covalent bond between two adjacent atoms. How this could be done in PyMOl? you could have guessed it: http://pymolwiki.org/index.**php/Bondhttp://pymolwiki.org/index.php/Bond :-) The atoms must both be within the same

Re: [PyMOL] Set values for dihedral angles

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 jmsstarli...@gmail.com Dear Thomas, Jed! Firstly

[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

Re: [PyMOL] Creating of chmeric protein

a modeling program like everyone else suggested? for a nice graphical interface and bond satisfaction why not try and use MOE if you want a graphical interface. http://www.chemcomp.com/software.htm If this were me though, I would use Biopython. Jordan On Jan 28, 2012, at 11:41 PM, James

Re: [PyMOL] Editing of the pdb structure

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

[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

Re: [PyMOL] Polar interactions within selection

://pymolwiki.org/index.**php/Get_raw_distanceshttp://pymolwiki.org/index.php/Get_raw_distances [2] http://pymolwiki.org/index.**php/Psicohttp://pymolwiki.org/index.php/Psico Cheers, Thomas On 04/16/2012 03:22 PM, James Starlight wrote: Hi Thomas! Yes I'd like find possible way for quick

Re: [PyMOL] Editing of the pdb structure

do it? James 1 апреля 2012 г. 15:04 пользователь James Starlight jmsstarli...@gmail.comнаписал: 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 г. 12:30 пользователь Thomas Holder

Re: [PyMOL] Editing of the pdb structure

/Alterhttp://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 simulation wich consist of 1 chain not defined in the pdb file explicitly ( missing chain id in the pdb file). So the pymol

Re: [PyMOL] problems with mutagenesis wizard

? On Fri, Jun 1, 2012 at 11:16 AM, James Starlight jmsstarli...@gmail.comwrote: 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 276 residue from Leu to Tyr. As the consequence the resulted

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 jmsstarli...@gmail.com I've sent another message

Re: [PyMOL] Polar interactions within selection

exaclty cutt-offs and addition python modules should I use? James 2012/4/17 James Starlight jmsstarli...@gmail.com 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 script also is usefull

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

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

? Thanks James 2012/6/15 James Starlight jmsstarli...@gmail.com 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

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

of software wich could produce such maps? Thanks James 2012/6/15 James Starlight jmsstarli...@gmail.com 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

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

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

on the PyMOLWiki now: 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 found link on it). Its very friendly but I've

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 great ) Could you tell me if you find a possible way to take into account

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

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 jmsstarli...@gmail.com I'm still waiting

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

Re: [PyMOL] Select crystal waters inside protein

. 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 question- I have my protein.pdb with some inserted crystall waters within protein

[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

[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

Re: [PyMOL] Coordinates of ligand-binding site

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. Jordan On Jul 18, 2012, at 2:23 AM, James Starlight

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 jmsstarli...@gmail.com: 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

[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

[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

[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

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 jmsstarli...@gmail.com: Dear PyMol users! I want to create chimeric protein

[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

[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

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 jmsstarli...@gmail.com: Recently I've tried to find pymolrc but couldn't do it ( I have pymol 1.5 installed from

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 jmsstarli...@gmail.com: Dear PyMol users! I've forced with the problem during superimposition of two identical proteins. First of all I've

[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

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

Re: [PyMOL] Electrostatic potential surface

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

Re: [PyMOL] Electrostatic potential surface

at once ? James 2013/3/28 James Starlight jmsstarli...@gmail.com 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 and when I've started

[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

Re: [PyMOL] loadDir script

try, after 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 name like 001.pdb 002.pdb ... 055.pdb but when the sotring have been still

[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

[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

[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

[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

Re: [PyMOL] Automatic mutation introduction

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 pymol source would introduce selected mutations in the defined PDB file and produce PDB output

[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 jmsstarli...@gmail.com

Re: [PyMOL] Caver 3.0 pugin

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, James Starlight wrote: This issue have been solved. Caver works fine. Does anyone

[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

[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

[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

are cations because of the symbol in the last column. By default, PyMOL doesn't make bonds to cations. But this will work: PyMOLunset pdb_unbond_cations, PyMOLload example.pdb Hope that helps. Cheers, Thomas On 06 Dec 2013, at 11:04, James Starlight jmsstarli...@gmail.com wrote: Thomas

Re: [PyMOL] Working with the pdb ensemble

212-263-7898 http://kong.med.nyu.edu/ On Dec 6, 2013, at 12:03 PM, James Starlight jmsstarli...@gmail.com wrote: 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

[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

[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

[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

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 jmsstarli...@gmail.com: 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

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

occurs (I have not this in case of ONE model from the ensemble) James 2014-08-27 13:10 GMT+02:00 Thomas Evangelidis teva...@gmail.com: split_states NMR-ensemble object name alignto 1st NMR model name, method=cealign On 27 August 2014 13:28, James Starlight jmsstarli...@gmail.com wrote: also

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

is it working here? https://www.sendspace.com/file/8i0aqo James 2014-08-27 14:58 GMT+02:00 Justin Lecher j.lec...@fz-juelich.de: On 27/08/14 07:56, James Starlight wrote: Hi both of them are present in my ensemble. the problem is not here- if it possible i could upload

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

tools (software) for the processing of the ensembles with such options for the analysis? James 2014-08-27 15:05 GMT+02:00 Thomas Evangelidis teva...@gmail.com: On 27 August 2014 15:43, James Starlight jmsstarli...@gmail.com wrote: and than how to quick merged aligned conformers back

Re: [PyMOL] Access to pymol commands from the terminal

To remove NA+/CL- too grep -v ATOM.*\(SOL\|NA+\|CL-\) in.pdb out.pdb The fitting is a bit more cumbersome :) Hope it helps, Tsjerk On Thu, Sep 4, 2014 at 10:19 AM, James Starlight jmsstarli...@gmail.com wrote: Dear PyMol users! I'd like to find possibilities for running of some

Re: [PyMOL] Access to pymol commands from the terminal

of this using pymol ref.pdb tarr.pdb -cd super tarr ref but eventually obtained error James 2014-09-04 15:47 GMT+02:00 James Starlight jmsstarli...@gmail.com: Thanks Guys! I'll check the tutorials. All the best, James 2014-09-04 13:15 GMT+02:00 David Hall li...@cowsandmilk.net

Re: [PyMOL] Access to pymol commands from the terminal

thanks! and do I need to pipe the below command to smth grep -h '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb if I need to change 'END' to 'TER' in the merged.pdb ? 2014-09-04 16:54 GMT+02:00 James Starlight jmsstarli...@gmail.com: thanks! and do I need to pipe the below

Re: [PyMOL] Access to pymol commands from the terminal

(tarfile, 'tar') cmd.align('ref', 'tar') cmd.save(outfile, 'ref') Then on the command line call it like: python my_align.py reffile.pdb target.pdb output.pdb On 09/04/2014 11:06 AM, James Starlight wrote: thank you very much! so now only my question regarding the usage of the pymol

Re: [PyMOL] Access to pymol commands from the terminal

should to add than I've used both TMalign and mammoth utilities but didn't understand how to obtain superimposed output as the full-atomic pdb's. I will be thankful if someone could share with me its experience :) James 2014-09-05 12:00 GMT+02:00 James Starlight jmsstarli...@gmail.com

Re: [PyMOL] Access to pymol commands from the terminal

a light version for fitting gromacs' gro files. No time to adapt that now for PDB, but it's not too hard. ./qfit.py source.gro target.gro output.gro Hope it helps, Tsjerk On Fri, Sep 5, 2014 at 12:31 PM, James Starlight jmsstarli...@gmail.com wrote: should to add than I've used both

[PyMOL] Shell utilities for structural bioinformatics

Dear Pymol users! I've decided to open new topic focused on the implementation of the common shell utilities like grep awk and sed for the structural bioinformatics tasks like processing and editing of the large sets of pdbs. In my current task I need to copy all lipids from one pdb (called it

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