Re: [Jmol-users] PDB and crystallography

ah, one more comment. I don't have CIF set up yet for nonfractional coordinates. I guess I had better do that. [EMAIL PROTECTED] wrote: >On Fri, September 8, 2006 2:12 pm, G. Jones wrote: > > >>PDB is fine, I don't know the format of cif files but if I did, or if you >>know a link where I

Re: [Jmol-users] PDB and crystallography

also _symmetry_space_group_name_H-M 'P 1' is necessary for propagating to multiple unit cells. [EMAIL PROTECTED] wrote: >On Fri, September 8, 2006 2:12 pm, G. Jones wrote: > > >>PDB is fine, I don't know the format of cif files but if I did, or if you >>know a link where I can find it then th

Re: [Jmol-users] PDB and crystallography

On Fri, September 8, 2006 2:12 pm, G. Jones wrote: > PDB is fine, I don't know the format of cif files but if I did, or if you > know a link where I can find it then that would be fine to. CIF files are very easy to write since they are free-format in a dataname datavalue style with not very many

Re: [Jmol-users] PDB and crystallography

PDB is fine, I don't know the format of cif files but if I did, or if you know a link where I can find it then that would be fine to. On Sep 8 2006, Bob Hanson wrote: >re recent message -- can you make do with PDB files? Or, changing XYZ >files to CIF files would be quite easy, although I don't

Re: [Jmol-users] PDB and crystallography

re recent message -- can you make do with PDB files? Or, changing XYZ files to CIF files would be quite easy, although I don't know of anyone who is doing this. All you do is add a short header and a little trailer line. You could just add the appropriate symmetry information as "boilerplate" a

Re: [Jmol-users] jmol and space groups

show is not new. Maybe "hide and seek" :) Timothy Driscoll wrote: >On Sep 8, 2006, at 12:27 PM, Bob Hanson wrote: > > > >>Alan Hewat wrote: >> >> >> The doc says that "restrict" just hides the atoms, so I can still select them, but how do I unhide them ? >>>

Re: [Jmol-users] unit cell

10.9.54 adds the capability to use space group information with Cartesian coordinate files. Right now, just PDB, but there is no longer any reason it couldn't also be done with XYZ files and, perhaps, a data statement. So Glenn, if you can write those files in PDB format, you can do what you w

Re: [Jmol-users] jmol and space groups

On Sep 8, 2006, at 12:27 PM, Bob Hanson wrote: > Alan Hewat wrote: > >>> The doc says that "restrict" just hides the atoms, so I can still >>> select them, but how do I unhide them ? >>> >>> >> >> "spacefill 20%" does it of course. (I knew it was a dumb question >> - sorry). Alan. >> >> >> > a

Re: [Jmol-users] jmol and space groups

Alan Hewat wrote: >At 17:49 07/09/2006, Bob wrote: > > >>This {-1 -1 -1} is meant to be a check for the space group listed in the CIF >>file. In particular, some Hermann-Mauguin symbols return ambiguous results, >>as happens for my quartz.cif file. >> >> > >OK, now I understand the differ

Re: [Jmol-users] jmol and space groups

Alan Hewat wrote: >>The doc says that "restrict" just hides the atoms, so I can still select >>them, but how do I unhide them ? >> >> > >"spacefill 20%" does it of course. (I knew it was a dumb question - sorry). >Alan. > > > actually, not. True "unrestrict" is not possible, since "restri

Re: [Jmol-users] jmol and space groups

>The doc says that "restrict" just hides the atoms, so I can still select them, >but how do I unhide them ? "spacefill 20%" does it of course. (I knew it was a dumb question - sorry). Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMA

[Jmol-users] Pause or wait in jmol scripts

Hi! I just found out that I very much miss an equivalent to the "pause" or "wait" command of rasmol in jmol, that is, a command that I can place in a script to make the script execution pause until I have had time to examine the representation of my molecule, and then allows me to continue

Re: [Jmol-users] jmol and space groups

At 17:49 07/09/2006, Bob wrote: >This {-1 -1 -1} is meant to be a check for the space group listed in the CIF >file. In particular, some Hermann-Mauguin symbols return ambiguous results, as >happens for my quartz.cif file. OK, now I understand the difference. {1 1 1} means use the SG symbol and

Re: [Jmol-users] PDB and crystallography

What I am interested in (which I currently use a bit of fortran to do) is taking a set of coordinates(absolute or fractional) and unit cell vectors and repeating them periodically. It would just be handy in jmol when making images or examining a structure to either click on a button or type in t

[Jmol-users] PDB and crystallography

Q1: Is there interest in Jmol reading unit cell/symmetry information from PDB files and working with that? (Or is CIF sufficient?) Q2: Is there interest in being able to take any Cartesian data set, indicating a unit cell and space group, and then being able to apply symmetry to that? B

Re: [Jmol-users] Proposing "set labelsFront group"

set labelsGroup # labels appear just in front of the atoms of their group. is in 10.9.53. Very simple implementation. Thanks for the suggestion, Eric. For file types that do not support protein/nucleic acid groups, set labelsGroup is the same as set labelsFront, since for those files all atoms

Re: [Jmol-users] unit cell

Jmol currently only supports periodicity in the context of a unit cell. In order to replicate, you need: 1) a file format that supports defining the unit cell (CIF, RES) 2) to define all atom positions in fractional coordinates 3) to define the unit cell parameters 4) to provide a space group nam

[Jmol-users] unit cell

Hi, I have calculated structures in the form of xyz files, and would like to repeat them periodically, I if have found a menu in jmol which allows you to draw a unit cell but can't find where to specify the dimension of the unit cell or the repeat periodicty in the x y or z direction . Is ther