Well, for me at least it is a good think Lina asked, because
there were two different answers from the experts and i learned from each.
I don't think we want to discourage or intimidate new users from
asking questions. It is very easy to ignore or delete a silly email.
Marius Retegan wrote:
> Dear
While the single acceptor H-bond is most common, bifurcated (or three-centred)
H-bods are
not uncommon in crystal structures, as described starting page 22 of GA
Jeffrey's book:
http://www.amazon.com/Introduction-Hydrogen-Bonding-Physical-Chemistry/dp/0195095499/ref=sr_1_2?ie=UTF8&qid=1322331503
Have you tried opening a dos window and:
ftype pdbfile=C:\wherever\pymol.exe %1
assoc .pdb=pdbfile
If that doesn't work you can make the associations directly in the registry,
but its more complicated.
Jacob Keller wrote:
> Dear List,
>
> I have v.1.41 running on windows 7 64 bit, an
Jason Vertrees wrote:
> Hi Troels,
>
> I've run into this problem a few times, too, but never took the time
> to solve it correctly.
>
> A quick plan might look like:
>* cmd.orient on the selection
>* store the view vector (http://www.pymolwiki.org/index.php/Get_View)
>* let C1 = count
The electron density we usually display with an atomic model is based on
experimental diffraction data (usually x-ray). The purpose of the density map
is usually to validate the model, i.e. show it is consistent with the map
calculated using experimental data. Even for many structures that are at
t
Bachar Cheaib wrote:
> This record "REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC" does
> not tell us if a structure is really multi
> or monomeric in the pdb file.
>
Right, that tells you what it is in vivo.
To see what it is in the pdb file, i.e. contents of the asymmetric unit,
look
Due to the possibility of insertion codes and non-sequential residue numbering,
I believe there is no way to avoid aligning the residues in the ATOM records
with the sequence in SEQRES in order to find gaps. I don't know of a program
to do this.
The structure validation server at RCSB ADIT2 makes t
That would seem to violate rule #1 of macromolecular depiction:
Never change the coordinates!
But then I can't imagine why one would want to not draw a disulfide bond
in a real protein structure, so maybe this is some kind of exercise
where it is not important to adhere to the experimental results,
On 04/19/2015 02:08 AM, leila karami wrote:
> Dear Marcelo
>
> Thanks for your quick answer.
>
> Unfortunately, I can't open the link (https://www.pymol.org/citing) you
> suggested me.
perhaps your firewall or browser is blocking the https: connection or rejecting
the certificate?
Try http: in
On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote:
> Hi Pascual,
>
> The PDB file does not really have information on bonds. If atoms are closer
> than some cutoff a bond is drawn. Unbonding and saving will not change the
> distance, so the bond will be drawn again when loaded again. What is your
e
>
>
> But honestly, the description sounds like something that would be infinitely
> easier to do using some plain python code rather than in pymol.
>
> -David
>
>
>> On Jan 19, 2016, at 4:59 PM, Edward A. Berry > <mailto:ber...@upstate.edu>> wrote:
>
Jakob Nielsen wrote:
> Dear Pymol users,
> I would like to modify a protein pdb file with a "crankshaft" flip,
> which is the anti-correlated double change: psi(i-1) += delta and phi(i)
> -= delta. Such a change should leave the protein coordinates unchanged
> effecting only atoms in residues i-1 a
David A. Horita wrote:
> Hi,
> How does one change directories in Windows when the directory name has a
> space in it? I've tried double and single quotes as well as backslash
> space (I'd like to run a script that's in such a directory).
> Thanks
> David
These all work for me:
>cd \"program file
'
>
>
> cd \progra~1 does work, however.
> Pymol 1.1r1 running on Vista (32-bit) Business.
>
> -David
>
> -Original Message-
> From: Edward A. Berry [mailto:ber...@upstate.edu]
> Sent: Mon 9/20/2010 2:03 PM
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re
Is this the library described in:
Curr Opin Struct Biol. 2002 Aug;12(4):431-40.
Rotamer libraries in the 21st century.
Dunbrack RL Jr1.
J Mol Biol. 1993 Mar 20;230(2):543-74.
Backbone-dependent rotamer library for proteins. Application to side-chain
prediction.
Dunbrack RL Jr1, Karplus M.
?
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