Hello Team,
I need help in inserting ligand to base pair in DNA. I have a drug molecule and
want to insert in between the base pairs I am interested in ( it is 12-mer
dsDNA). I tried to follow the tutorials but cannot find something where I can
insert ligand into the custom DNA sequence I have
Hi Ankita,
set depth_cue, 0
http://pymolwiki.org/index.php/Depth_cue
Cheers,
Thomas
On 27 Apr 2016, at 11:06, H. Adam Steinberg wrote:
> Scrolling the mouse will not move the molecule, it will reduce the fog that
> pymol puts in the image, making it less gray.
>
> Sent from my iPhone
>
>
Scrolling the mouse will not move the molecule, it will reduce the fog that
pymol puts in the image, making it less gray.
Sent from my iPhone
> On Apr 27, 2016, at 6:45 AM, ankita mehta wrote:
>
> No, I can not do this becos i have to show the complex that is protein in a
> fix orientation.
>
No, I can not do this becos i have to show the complex that is protein in a
fix orientation.
Suggest some alternative..
Thanks!
On Wed, Apr 27, 2016 at 4:01 PM, Dheeraj Prakaash wrote:
> Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and
> down!
> Usually (if you have
Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and
down!
Usually (if you have not changed any settings), SCROLLING UP should solve
your problem.
Cheers.
On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta
wrote:
> Hii,
> I want to save the image in pymol
> I am using white back
Hii,
I want to save the image in pymol
I am using white background but it gives me dull colouring of the protein
which is at the background than the protein part at foreground.
I want a unified sceme for all protein .
pls suggest.
thanks!
Hello I know the plugin mentioned above (in the Subject) will work if I go to
Plugin > Manage Plugins > Install > contact_map_visualizer I get that. But
nothing happens if I run the plugin if I go to File > Run >
contact_map_visualizer.py I do this because I need it for my project,
preferab
I see!
Many thanks
Tsjerk! XD
> Date: Mon, 19 Mar 2012 20:59:08 +0100
> Subject: Re: [PyMOL] Query on 'Select group for analysis' for Contact Map
> Visualizer Plugin
> From: tsje...@gmail.com
> To: bell_beaut...@hotmail.com
>
> Hi Suheila,
>
> Th
bit confused what are those groups for? I mean I don't really need those. I
just need to plot on a chain. Many thanks,Suhaila> Date: Mon, 19 Mar 2012
19:37:12 +0100
> Subject: Re: [PyMOL] Query on 'Select group for analysis' for Contact Map
> Visualizer Plugin
>
Hi Suheila,
The CMV requires the contact map and the structure to match. So to get
what you want, it's easiest to load the structure in pymol, and save
only the part you want to analyze:
save helix.pdb, ss h
save sheet.pdb, ss s
Then you can run g_mdmat on each of those, and load the result back
Hello especially for those who are experienced using Contact Map Visualizer
Plugin. About generating a contact map, after typing the following command as
shown:
g_mdmat -f 2p31.pdb -s 2p31.pdb -mean contact-map.xpm
It gives us a list of group selection to analyze such as below: Select g
Hi Suhaila,
>From what I understand from the wiki, you have to have a match between
the PDB and the contact map. If your contact map was made on a
structure with multiple chains, all chains will be in there. If you
want to select a single chain, you have to extract that chain from
thhe PDB file, t
Hello guys,
Regarding the subject mentioned above, I'm wondering if PDB file has more than
one chain, will the generation of contact map using g_mdmat from Gromacs
still produce a map of all chains?
Don't I have a choice to choose one chain?
Refer the subject above for more details:
http://www
* "rjayashree13-scie...@yahoo.co.in"
>
> *Cc:* "pymol-users@lists.sourceforge.net" <
> pymol-users@lists.sourceforge.net>
> *Sent:* Sunday, 20 November 2011 1:57 PM
> *Subject:* Re: [PyMOL] query
>
> check this out:
> http://www.pymolwiki.org/index.php
check this out:
http://www.pymolwiki.org/index.php/InterfaceResidues
if you want faster and easier, but less reliable (in my opinion) way, you
can analyze your .pdb with PISA:
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
vitali
On Sun, Nov 20, 2011 at 1:51 AM, rjayashree13-scie...@yahoo.co
I have a PDB file for a dimeric protein. Is it possible to depict the
intersubunit contacts for any PDB file? Is Pymol alone sufficient for
this purpose or will it only help visualization?
Could you also tell
me which commands in Pymol can I use for this purpose? I have tried a
lot but could no
Hi Kumud,
I don't know,. Maybe because Warren wanted to label the end cap as residue
number 1. Anyone else know?
Regardless if you want to renumber your sequence, just type the following
or download the zero_residues script from the PyMOLWiki (
http://www.pymolwiki.org/index.php/Zero_residues):
hi
I built a peptide using pymol. When I labelled the residues they are numbered
fron 2 and not from 1 i.e. the first residues in my peptide is ALA and when I
labelled this residue it is labelled as ALA-2 and not ALA-1.
I want to ask why it is not labelled starting from 1 instead of 2?
Dear Sir,
* I want too assign the secondary structure of my protein according
to DSSP classification, I used the following commands*
* alter A/22:28/, ss='S'*
* or*
*alter A/45:50?, ss= 'H' *
*a
> I have recently downloaded Pymol and can't get the protein structure
> to display on the main screen, files are being uploaded and are
> visible in the side bar and if I try to randomly alter colours on the
> protein parts of it appear though I can't be sure of what I am
> looking at as the pro
Query
I have recently downloaded Pymol and can't get the protein structure to display
on the main screen, files are being uploaded and are visible in the side bar
and if I try to randomly alter colours on the protein parts of it appear though
I can't be sure of what I am looking at as the program
Olivier,
But how do I find out specular's (or ANY variable's) value without
changing it?
I wrote a little extension called 'grepset' that does what you want and it
is great for finding out about other settings.
It is available at the pymol wiki site:
http://www.pymolwiki.org/index.
PyExperts:
When inside PyMOL, how do I find out the value of a variable without
using 'set'?
For example, I can type:
set specular, 1
and then I know, specular = 1.
But how do I find out specular's (or ANY variable's) value without
changing it?
Thanks,
Olivier
Hello Olivier,
For PyMOL
PyExperts:
When inside PyMOL, how do I find out the value of a variable without
using 'set'?
For example, I can type:
set specular, 1
and then I know, specular = 1.
But how do I find out specular's (or ANY variable's) value without
changing it?
Thanks,
Olivier
--
Olivier Julien
PhD prov
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