Re: [ccp4bb] Visualisation software supporting ChromaDepth

t; > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [ccp4bb] pymol fonts on gui

> options (A, SA, H ,L etc) or the primary sequence without a magnifying glass. > > Running Pymol 2.0.7 on Mac 10.12.6, I’ve attached an image showing the > problem. > > Any ideas? > > Thanks > Amir > > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [ccp4bb] RMSD between superposed structures without moving

to just calculate the all atom RMSD between two >>> already superposed structures in pymol or any other programm? >>> >>> Thanks in advance! >>> Johannes >>> > > -- > Johannes Sommerkamp > Ruhr-Universität Bochum > AG Röntgenstrukturanalyse an Proteinen, LS Biophysik, ND04/396 > Universitätsstraße 150 > 44801 Bochum > Tel: +49-(0)234/32-25754 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [ccp4bb] PyMOL question

object 1 that are different from > object 2? I know how to select residues that are similar ("select name, obj1 > like obj2") but can't figure out how to do the opposite. I am running PyMOL > on a Mac. > Thank you, > Lindsey -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [ccp4bb] Residues are missing in cartoon mode when dealing with virus capsid-like proteins in Pymol

went missing. Did anyone > come across the same problem and could you give me some suggestions? > > Thanks very much! > Best wishes, > Didi -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [ccp4bb] PyMOL v. Coot map 'level'

=hrPT -END PGP SIGNATURE- -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [ccp4bb] PyMOL v. Coot map 'level'

at a level I cannot interpret in PyMOL relative to Coot :-/ Regards, Emily. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [ccp4bb] PyMOL v. Coot map 'level'

PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlVo1L4ACgkQU5C0gGfAG10YkwCfROYPVXBK/pDS4z/zi5MNY1D+ nHIAnjOFiAkb6JbuIGWRWkBFDG5Xgc2K =hrPT -END PGP SIGNATURE- -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [ccp4bb] off topic: measuring angle between two nucleic acid helices

? Thanks a lot. Best, Almudena. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [ccp4bb] RMSD of dimers

superimposed the structures relative to Chain A. I have tried using Pymol though there are gaps/insertions so rms/rms_cur will not work. Does anyone else have any other suggestions? Thanks in advance, Dan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.

Re: [ccp4bb] CCP4BB Digest - 6 Aug 2014 to 7 Aug 2014 (#2014-213)

the same order in PyMol and how do I fix that? Thanks for any help, Remie -- Thomas Holder PyMOL Developer Schrödinger, Inc.

Re: [ccp4bb] [PyMOL] Farewell

(o) +1 (603) 374-7120 -- Thomas Holder PyMOL Developer Schrödinger, Inc.

Re: [ccp4bb] pymol multiple transparent surfaces

://www.strubi.ox.ac.uk - -- Thomas Holder PyMOL Developer Schrödinger, Inc.

Re: [ccp4bb] Tool for calculating RMSD

de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [ccp4bb] Finding N-term to C-term Distances

serious problem for such a statistic is that many PDB files do not contain the full-length protein and the last O atom is not actually the C-terminus (same with first N atom). Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [ccp4bb] Server or software for B factor analysis

to the residue?Or a server or software by which we can easily order the B factors of the atoms in the PDB file according to the B factor in decrease or in increase? Or to get the residues with the highest B factor and the lowest B factor? Cheers, Dialing -- Thomas Holder MPI for Developmental

Re: [ccp4bb] residuewise rmsd for multiple chain superposition

in advance, sreetama -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [ccp4bb] PyMol plugin

. For example my PyMOL+cctbx launcher looks like this: #!/bin/sh cctbx.python /opt/pymol-svn/modules/pymol/__init__.py $@ You could also symlink cctbx.python to python, like described here: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/cctbx/ Cheers, Thomas -- Thomas Holder MPI

Re: [ccp4bb] Symmetry Related molecules

-- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [ccp4bb] print cmd.align in PYMOL

are the meaning of those number? which one is RMSD? Many thanks! G -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [ccp4bb] Influence of symmetry related molecules on a protomer conformation in crystal structures

) interacting with a given chain in a crystal structure. Thanking you, suku NIBIO, Osaka -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [ccp4bb] generate large symmetry model

gratefully received, Dave *David Hargreaves* Associate Principal Scientist -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [ccp4bb] mutation and minimization

but you have to pick the best rotamer yourself. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [ccp4bb] PDB data mining

) +1 (603) 374-7120 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [ccp4bb] rmsd calculation for all atoms.

distances between atoms or residues that were not used in the alignment. Thanks, Mike. -- Thomas Holder AG Jekely MPI for Developmental Biology Spemannstr. 35 D-72076 Tuebingen