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
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
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
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
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
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
___
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
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
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
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
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
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
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
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
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