[PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!

Dear PYMOL users, I have done a homology modelling using swiss model. Template pdb file contain 3 chains (A, B, C). I used only chain A for homology modelling as template. There is a symmetry operator in template pdb file (temp.pdb). I want to use symexp to obtain dimeric structure for modeled pd

[PyMOL] Finding the surface residues using code

Dear Pymol users, I am using Pymol v 1.7.x. I want to obtain and show the surface residues in my protein. I found the following link: http://www.pymolwiki.org/index.php/FindSurfaceResidues#Usage How to run the code being in this link? Best, -

[PyMOL] -- selection --

Dear all I have a complex (protein-ligand). I want to have only those residues (from protein) with special distance relative to ligand. How to do that? Any help will highly appreciated -- Site24x7 APM Insight: Get Deep V

[PyMOL] superimposition of 2 ligand molecules

Dear pymol users, I have 2 ligand molecules having similar backbone. There is little difference between them. When I load them in pymol, I have following figure: https://www.dropbox.com/s/k4g53p0qoxp58zs/pymol.png?dl=0 I want to have these 2 ligands in superimposed form such as following: https:/

[PyMOL] visualize autodock vina results

I am sure that I am in working directory. To prevent this mistake, I selected desktop as working directory. (I put out.pdbqt and pr.pdb files in desktop and then load them). I am using pymol-0_99rc6-bin-win32 on windows 7. My input files are as follows: https://www.dropbox.com/s/hx94orra4pumx82/

[PyMOL] visualize autodock vina results

Dear Osvaldo, I used 2 following ways: 1) load out.pdbqt,obj1 load pr.pdb, obj2 split_states obj1 create obj3, (obj1_0001, obj2) save obj3.pdb, obj3 2) load out.pdbqt,obj1 load pr.pdb, obj2 split_states obj1 save obj3.pdb, (obj1_0001, obj2) Unfortunately, in both cases, when I open obj3.pdb fil

[PyMOL] visualize autodock vina results

Dear pymol users, I am visualizing autodock vina results using PyMOL: I open out.pdbqt (containing 9 docked conformations of ligand) I open pr.pdb (containing protein structure) I want to have 1 pdb file containing one of conformations of ligand (for example number 1 which is the best pose) + pr

[PyMOL] visualize autodock vina results

Dear PyMOL users, I am visualizing autodock vina results using PyMOL: I open out.pdbqt (containing 9 docked conformations of ligand) I open pr.pdb (containing protein structure) I want to have 1 pdb file containing one of conformations of ligand (for example number 1 which is the best pose) + pr

[PyMOL] how to connect to atoms?

Dear pymol users I have one pdb file containing two peptides. Based on experimental data, I should connect two peptides to obtain one new peptide in pdb file. This connection is as follows: CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from peptide 2. How to make this connecti

[PyMOL] (no subject)

Dear Marcelo Thanks for your quick answer. Unfortunately, I can't open the link (https://www.pymol.org/citing) you suggested me. Thanks in advance. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop

[PyMOL] (no subject)

Dear all How to cite pymol in my paper? Thanks. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bo

[PyMOL] mutation of the one basepair in dna

Dear pymol users I want to mutate one basepair in dna. For example: GC > AT Number of residues are as follows: G69 , C78. How to do that. Any help will highly appreciated. -- Keep Your Developer Skills Current wit

[PyMOL] change label position

Dear pymol users my system contains 2 residues. I labeled them. Now I want to change the position of one of labels as position of other be fixed. how do I do that? any help will highly appreciated. -- Magic Quadrant for

[PyMOL] ball and stick representation of water molecule

Dear pymol users how to show water molecules as ball and stick representation (O atom: ball and H atoms: stick)? any help will highly appreciated. -- AppSumo Presents a FREE Video for the SourceForge Community by Eric

[PyMOL] how to load two separate pdb files simultaneously

Dear all very thanks for your time and attention. my problem was solved by load A.pdb load B.pdb -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of appli

[PyMOL] how to load two separate pdb files simultaneously

Dear Hongbo very thanks for your attention. None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not help me. I need to load two separate pdb files simultaneously. -- All of the data generated in your IT inf

[PyMOL] how to load two separate pdb files simultaneously

Daer users I want to know how to load two separate pdb files simultaneously. any help will highly appreciated. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive re

[PyMOL] pymol homepage/error message

homepage or it is my problem only? best regards. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- Benefiting from Server Virtualization: Beyond

[PyMOL] Atom Selection Macros : /object-name/segi-identifier/ chain-identifier/resi-identifier/name-identifier

770 28.870 1.00 0.00 what is *segi-identifier *in com.pdb? please guide me about that. best wishes. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group ---

[PyMOL] change of color of dashed line in distance command

Dear João Rodrigues thanks for your quick reply. I want to know how to change color of dashed line. (color of dashed line is yellow by default). any help will highly appreciated. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical

[PyMOL] labeling dna residues

or: Malformed selection. ( ( name ca+C1*+C1' and ( byres ( b )<-- how to fix it? I want to know how label dna residues by command line? please guide me. best wishes -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Phy

[PyMOL] (HB) dotted line with out distance number

distance between two atoms. I don't need to distance number (I just need to dotted line). how to do that? how to remove distance number? please guide me. best regards. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry

[PyMOL] obtaining of protein-dna complex by pymol

Hi pymol users I want to generate an initial model structure (PDB file) for the PRH homeodomain-DNA complex for doing md simulation calculation. There is PDB file for my PRH homeodomain protein (PDB ID code: 2E1O), but there isn't PDB file for PRH homeodomain-DNA complex. also, there are PDB fil