[Jmol-users] Jmol select chains in large structures

How to select chains in large structures? Testing on Jmol.jar 14.2.4_2014.08.03 2014-08-03 08:56 We are working on 4v8m, one of the ‘large structures’ ( ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF/4v8m.cif.gz ) . The asymmetric unit for this structure is composed of multiple PDB en

Re: [Jmol-users] IF for multiple frames

Hello Pshemak! "if" structures are not hard, at least if you have some experience e.g. with Javascript. But for your problem you don't need that; the "connect" command will set the bond type based on distance, very easily, for all frames at a time. > Let's say I have some "boundary" conditions

Re: [Jmol-users] IF for multiple frames

Thanks Angel, I have missed that in the manual, that is much simpler. PM On 8/14/2014 6:35 AM, Angel Herráez wrote: > Hello Pshemak! > "if" structures are not hard, at least if you have some experience e.g. with > Javascript. > But for your problem you don't need that; the "connect" command

Re: [Jmol-users] File paths in Jmol/Windows

thanks Rolf, the commands seem to be the right method for loading from a variable: 1)load DATA 2)load INLINE 3)Load "@jmol_variable" I could not get a result by VB programming. load INLINE "1 C 1 1 1" loads an atom from the command input line. Is more information available ? especially for a

Re: [Jmol-users] File paths in Jmol/Windows

On 08/14/2014 02:16 PM, Michael Marden wrote: > thanks Rolf, > > the commands seem to be the right method for loading from a variable: > 1)load DATA 2)load INLINE 3)Load "@jmol_variable" > > I could not get a result by VB programming. > load INLINE "1 C 1 1 1" loads an atom from the command inp

Re: [Jmol-users] Setting default colors

Ah, thanks. I was actually displaying a ribbon structure and now see that `color structure` is all I needed. I'd been reading the docs and hadn't realised that in 'color [object] structure', [object] was optional - I'd been a little confused about what I was supposed to have there! Chris ___

Re: [Jmol-users] bug fixes

St. Olaf server should be back now. Simone, how about a Skype? Something you are doing is very strange. Perhaps you can send me a zipped up version? You're not trying to run this from within Eclipse, are you? That does not work. notes below... On Wed, Aug 13, 2014 at 4:51 AM, Simone Sturniolo

Re: [Jmol-users] Jmol select chains in large structures

Unfortunately, the chain designations used by Jmol to create the complete model, _atom_site.label_asym_id are not the ones you refer to with "chain=", _atom_site.auth_asym_id For example, in 1vu4 we have: ATOM 68679 C CA . VAL MA 1 36 ? 215.540 621.913 480.029 1.00 0.00 ? ? ? ? ? ? 36 VA

Re: [Jmol-users] File paths in Jmol/Windows

that helped. the "Load data" example gives a bit more information, and shows a vertical line as separator. I was able to run that example in VB. I'll experiment with it. thanks, Michael Marden On 14/08/2014 14:56, Rolf Huehne wrote: > On 08/14/2014 02:16 PM, Michael Marden wrote: >> thanks Ro

Re: [Jmol-users] Building JMol from SVN on a Mac

should be some error messages there; probably something simple. We definitely build on Macs. On Wed, Aug 13, 2014 at 6:52 AM, Michael Florian Peintinger < michael.peintin...@gmail.com> wrote: > Dear all, > > I checked out the JMol source from svn. > On my Linux machine it builds fine, > on m

Re: [Jmol-users] File paths in Jmol/Windows

With load DATA just put the data following it as it would be in the file. Starting immediately on that line. No need for any special line fomatting. On Thu, Aug 14, 2014 at 8:32 AM, Michael Marden wrote: > that helped. the "Load data" example gives a bit more information, and > shows a vertical

Re: [Jmol-users] Building JMol from SVN on a Mac

Yes, I got it to build. Just for the record Had to set the JAVA_HOME directory manually. To version 1.7 - it does not build with 1.8 All the best Michael Am 14.08.14 um 15:34 schrieb Robert Hanson: > should be some error messages there; probably something simple. We > definitely build on Macs

Re: [Jmol-users] Jmol select chains in large structures

Dear Bob, Thank you for a prompt reply. It does work when using the proper chain identifier. Regards, Jaim On Aug 14, 2014, at 4:32 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: Unfortunately, the chain designations used by Jmol to create the complete model, _atom_site.label_asym_id

Re: [Jmol-users] Setting default colors

Chris, "atom" is the default object there, so when you omit it your color the atoms. All other renderings inherit from the atom unless a specific color has been applied to them. So you could have color structure; //colors everything or (dfferent) color red; //everything color ribbons structu