[PyMOL] Cryo-EM file with modified residues + fetch issue

r your help, Pascal ----- Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr <mailto:p.auffin...@ibmc-cnrs.unistra.fr> - -- Dive into the World of Parallel Programmi

[PyMOL] saving cif files and atom numbering

ow to get this saving cif option to work ? Best, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr <mailto:p.auffin...@ibmc-cnrs.unistra.fr> -

[PyMOL] saving cif files and atom numbering

). Any clue on how to solve these issues ? Thanks a lot, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr <mailto:p.auffin...@ibmc-cnrs.unistra

[PyMOL] how to get a correct pdb output for atom names ?

Dear Thomas, Sorry for this posting, you are correct. There is no problem with pymol but rather with one of my scripts that process the files afterwards. Anyway, your reply helped me to correct my scripts. Thanks for that, Pascal ---

[PyMOL] how to get a correct pdb output for atom names ?

distinguish CA^^ as a calcium atom from ^CA^ which would be a C-alpha based solely on atom names. Are my settings OK ? Did I do something wrong ? Should I change them to get an output respecting pdb standards ? Thanks a lot for helping, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084

[PyMOL] python module in pymol

n, it works fine when I type in the command "cluster_count PO4" Any idea ??? Thanks for helping, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr -

[PyMOL] cross hair for non-bonded atoms

Hi, Just wondering how to remove the cross hair that is shown for each non-bonded atom (for example water molecules). Thanks, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr

[PyMOL] O1P versus OP1

Hi, What is the current status of Pymol with respect to O1P or OP1 atom labels in nucleic acid ? The current PDB convention is OP1 and OP2. Is there an option in pymol to save the coordinates with this convention ? Thanks, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084

[PyMOL] nucleic acid (one or two letter) residue names

Hi Jason, A more difficult one (at least for me) Pymol seems to write (through save command) nucleic acid residue names not as suggested by PDB convention. Here is an extract of a PDB file (any PDB file containing nucleic acid residues shows the same ­ try 100D for example) ATOM 1 O5' C

[PyMOL] set pdb_reformat_names_mode

Hi, The pymol manual indicates: pdb_reformat_names_mode (integer: 0-4, default: 0) affects how and whether or not PDB names are reformatted in order to attempt to meet alternate conventions. What are these four modes ? Is this working internally or does it have an effect on saved files? Thanks

[PyMOL] Set pdb_echo_tags, HEADER

Hi, Please can someone precise the syntax of: Set pdb_echo_tags, HEADER Since there is no documentation for this, I am not really sure about what I am doing. It doesn't seem to work. What is expected is to save the HEADER lines along with the pdb coordinates. Yet, when I save a PDB file the HEA