On 27 August 2014 16:10, James Starlight wrote:
> *Q: My structure has multiple chains. Which one will be used for the
> calculation? *
> A: Generally, all of them. Be careful, though. While most chains are
> "legitimate" chains corresponding to subunits of the whole multi-mer (as in
> e.g. hemog
*Q: My structure has multiple chains. Which one will be used for the
calculation? *
A: Generally, all of them. Be careful, though. While most chains are
"legitimate" chains corresponding to subunits of the whole multi-mer (as in
e.g. hemoglobin), some PDB files use chain identifier "A", "B", etc. t
is it working here?
https://www.sendspace.com/file/8i0aqo
James
2014-08-27 14:58 GMT+02:00 Justin Lecher :
> On 27/08/14 07:56, James Starlight wrote:
> > Hi
> >
> > both of them are present in my ensemble. the problem is not here- if it
> > possible i could upload the ensemble.pdb to some serv
On 27/08/14 07:56, James Starlight wrote:
> Hi
>
> both of them are present in my ensemble. the problem is not here- if it
> possible i could upload the ensemble.pdb to some server if someone could
> check it.
>
> James
>
Hi,
Go for some paste bins or do a gist on github.
Justin
--
Justin
Hi
both of them are present in my ensemble. the problem is not here- if it
possible i could upload the ensemble.pdb to some server if someone could
check it.
James
2014-08-27 14:52 GMT+02:00 Justin Lecher :
> On 27/08/14 07:43, James Starlight wrote:
> > and than how to quick merged aligned co
On 27/08/14 07:43, James Starlight wrote:
> and than how to quick merged aligned conformers back to the NMR ensemble
> including TER record between each model in it?
>
>
Hi James,
in addition you need the "MODEL #" [1] - "ENDMDL" [2] entry.
Justin
1)
http://wwpdb.org/documentation/format33/sec
and than how to quick merged aligned conformers back to the NMR ensemble
including TER record between each model in it?
Actually I'm looking for the possibility to load this ensemble to the
http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states for
the titrable residues in case of
split_states
alignto <1st NMR model name>, method=cealign
On 27 August 2014 13:28, James Starlight wrote:
> also please tell me how is it possible to include ter record at the end of
> each model.
>
> James
>
>
> 2014-08-27 11:58 GMT+02:00 James Starlight :
>
> Dear Pymol users!
>>
>> Using be
also please tell me how is it possible to include ter record at the end of
each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight :
> Dear Pymol users!
>
> Using below script I can load all pdbs from the work dir into 1 nmr-like
> object. Could you suggest me how this script could be modi
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file
from pymol import cmd
import sys,glob
def ge
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