Thanks a lot Tsjerk,
It iw really going to be helpful. I will update you when I play with it.
best,
Abhi
On Sat, Nov 9, 2013 at 12:46 PM, Tsjerk Wassenaar wrote:
>
> Hey :)
>
> I thought there was a post recently about showing secondary structure in
> C-alpha only models. I can't find it anym
can you give us the exact pdb/code so that we can reproduce the problem ?
On Fri, Jun 1, 2012 at 11:16 AM, James Starlight wrote:
> Dear PyMol users!
>
>
> I've tried to make 1 point mutation by means of pymol's mutagenesis wizard
> and obtain partially broken pdb.
>
> In my caseI've changed 276
Great!!
Thanks to all !!.. and specially Takanori!!
Cheers,
Abhi
On Wed, Feb 1, 2012 at 6:09 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Hi Thomas,
>
> > alternate locations and multi-state objects should not be an issue, the
> > script on the PyMOLWiki can handle both! The o
acts"
> option with the PyMOL built-in "distance" command. E.g.
>
> distance hbonds, all, all, 3.2, mode=2
>
> The problem is that you cannot set the A-H-D angle which is important for
> the definition of the H-bond.
>
>
>
> On 30 January 2012 18:45, Abhina
Hi,
I am trying to get the list of hbonds formed using
Apply-find-polarcontacts.
I searched and found some scripts, but they never give me the same result
as the one by default pymol.
Any ideas how I can get the hbonds as a list.
Thanks,
Abhinav
-
Hi,
My pymol 1.4.1 works fine.
can you try to ray trace and see if your objects are available but just not
displayed on the standard screen?
cheers,
2011/9/29 Andreas Förster
> Hi all,
>
> Has anyone noticed that the distance command behaves oddly. Has this
> been recently introduced?
>
>
As Tsjerk pointed out!!.. it is exactly 8.3
ATOM604 OG SER A 77 37.493 60.526-103.507 1.00 26.47
O
123456781234567812345678
cheers,
Abhi
On Mon, Apr 25, 2011 at 12:59 PM, kanika sharma wrote:
> in the y-z coordinate the 8.3% format is not there..
>
>
Hi Jason & Tsjerk ...
Just for the info that I just downloaded, compiled and tried it on
OpenSuse 11.4 and it ran without any problems:
PyMOL>load ../../3lzt.pdb
HEADERHYDROLASE 23-MAR-97 3LZT
TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
COM
Thanks a lot Jason!!
Will try it out today!!
On Fri, Apr 1, 2011 at 11:34 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Greetings PyMOLers,
>
> I got back from my trip last night and immediately started putting the
> new features into the open source branch as promised. I've fin
Hi Jason,
many thanks for your reply and efforts. I hope you have a good time at the
meetings.
Keep up the good work !!
cheers,
Abhi
On Wed, Mar 23, 2011 at 8:06 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Hi Stephen,
>
> > I would like to know if, and when, 1.4 will be avai
r the incentive builds seems
> to be hardly different from what Warren had started doing.
>
> -David
>
> On Mar 23, 2011, at 6:33 AM, Abhinav Verma wrote:
>
> And why would that be? I thought that pymol is open source and till Warren
> was there all updates were available in
And why would that be? I thought that pymol is open source and till Warren
was there all updates were available in the open source domain and incentive
builds were limited to windows executable and involving support!!
On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij
wrote:
> > Is the 1.4 ver
How do I download pymol 1.4 from the svn.
I used
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol
but i still got the 1.3 version.
Is the 1.4 version restricted to incentive downloads only??
Thanks,
set label_color, black
can help you.
Abhi
On Tue, Aug 31, 2010 at 6:31 AM, Craig Smith wrote:
> Hello,
>
> I'm to make the color of my label different from the color of the residue.
> For example, I have my carbons colored yellow but its label is hard to see
> and I want to change the color to
Hello,
I wish to show one chain in cylindrical helices, while the other one in
ribbon representation. How can I achieve this with pymol.
thanks in advance,
Abhi.
--
___
PyMOL-
ense there's
> no need to really do it. The big question is really what do you want
> to see and what do get instead?
>
> Cheers,
>
> Tsjerk
>
> On Mon, May 18, 2009 at 4:53 PM, Abhinav Verma
> wrote:
> > Hi Tsjerk,
> > Thanks a lot for reply.. All I
way, you only sent this mail this afternoon. Don't expect
> > instant replies or assume something didn't come through just because
> > you didn't get an answer within a few hours :)
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Mon, May 1
I am trying to use povray tracer with pymol. I got povray and installed it
and tried to follow the instructions for the patch.. The patch seems too old
written in 1999 and the current povray code is cpp and not c. so I skipped
that part.. and now when I set smooth_color_triangle = 1, I get the
foll
or if B' is residues M to N in prot1 and B'' is residues L to K in prot2,
its as simple as
load prot1.pdb
load prot2.pdb
align prot1 and i. M-N, prot2 and i. L-K
look at "help selections" and you can try to align any two selections..
cheers,
Abhi.
On Thu, Mar 20, 2008 at 12:34 PM, DeLano Scien
you can try to use a "pick-color tool" of corel draw.. I am not sure what it
is actually called in corel, but you might be able to pick the exact colors
with that tool...
hth,
Abhi.
On Wed, Mar 5, 2008 at 2:17 PM, Patrick Loll wrote:
> I'm making a figure that contains both an actual molecular
play with
set dash_gap, 0.3 (or choose your value)
cheers,
Abhi
On Tue, Mar 4, 2008 at 10:15 AM, JunJun Liu wrote:
> Hello everybody,
>
> I want to make a picture on which two close atoms are connected by a
> dashed line. I use the "distance" command to make the dashed line.
> However, there's
set_name oldname, newname
On Feb 12, 2008 2:48 PM, Toni Pizà wrote:
> > An object whose name begins with an underscore will not appear in the
> menu.
>
> Perfect! But how can I change the name of one name in the Names Panel?
>
> --
> "Two of the most famous products of Berkeley are LSD and Unix.
there is something on the menu, file->save->molecule
after the alignment, choose the molecule you want to save and just save.
pymol saves the pdb with new coordinates.
cheers,
Abhi
On Jan 25, 2008 10:29 PM, Lu Lin wrote:
> Hi Hally,
> Thank you for your reply! Could you tell me how to save the
use wizard->mutagenisis..
On Dec 19, 2007 5:43 PM, wang,guojun wrote:
> hi, everyone, I want to make an image to show some structual differences
> between wild-tye ribosomal protein S12 and mutant type in bacteria. Does
> anybody know how to substitute wt aa residue with mutant type in
> an pub
>
> -----Original Message-
> From: Abhinav Verma [mailto:abhinav1...@gmail.com]
> Sent: Mon 11/26/2007 7:35 PM
> To: Mayer, Mark (NIH/NICHD) [E]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] sphere diameter
>
> set sphere_scale should scale the sph
set sphere_scale should scale the spheres, but they should be
proportionate and they are van der waal spheres I guess, so chlorine
is smaller than soduim..
http://pt.chemicalstore.com/
227 vs 175 pm for na and cl respecively.
On Nov 26, 2007 4:15 PM, Dr. Mark Mayer wrote:
> hello,
>
> Can't fin
there is set cartoon_highlight_color, command to set the highlight
color to grey or something, so you can use that to color the other side of
the secondary structure.
On 10/10/07, Omar Davulcu wrote:
>
> Hi everyone,
>
> I've noticed that in some PDB files, not all, when I attempt to color a
>
AFAIK setting connect_mode=1 strictly uses the CONECT records from pdb file
to draw bonds.
Cheers,
Abhi.
On 9/6/07, Mark A Saper wrote:
>
> This was previously discussed in an archived email but I can't find it
> right now. Does the setting connect_mode=0 use the CONECT records in the
> PDB f
Dear Nicole,
I can orient and zoom with the newpdb file I downloaded from the pdb
databank. (there was no attachment in your email for the old one, but it
wast needed as the orient and zoom works)
Atleast I cannot reproduce anything you mentioned.
Abhi
On 9/5/07, Nicole Lewis-Rogers wrote:
although maybe out of context (as I am talking about the older pymol
0.99rc6 on windows), but the same happens with windows 2003 server .
If you do
not touch anything, the screen keeps updating.
On 8/30/07, DeLano Scientific wrote:
>
> Roger,
>
> This isn't so much a PyMOL bug as a flaky characte
hi
one of doing this would be, to load ur file and then type the follwing
for i in range(200): cmd.mset(str(i),str(i))
cmd.mdo(1, "color yellow")
cmd.mdo(101, "color red")
mplay
cheers,
Abhi
Abhinav Verma
Postdoc,
University of Washington,
Seattle WA
On 8/29/07, Nicola Gi
I want to align different models of a multimodel pdb file.
How can I do that without extracting models as identical pdb.
cheers,
Abhi
lectionname","r. na\+")
>
> which actually works, but probably shouldn't.
>
> Cheers,
> Warren
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:del...@delsci.info
>
> > -Original Message-
> > Fr
Hallo,
I have an annoying problem. I have pdb file with Na+ atoms defined as
ATOM 1 Na+ Na+53 -1.106 7.854 52.244 1.00 0.00
Na
ATOM 2 Na+ Na+54 -0.106 3.854 27.244 1.00 0.00
Na
ATOM 3 Na+ Na+55 1.894 -6.146 62.244 1.00 0.00
Na
ATOM
1CRN for example has disulphide bonds which are covalant and thats why
set_dihedral does not work. I think its the bug, which tells you that it has
been setted to zero. So you have to remove the disulphide bonds before
setting the dihedral angles.
you can do so by
unbond r. cys and n. sg, r. cys
Hello,
pymol finds the disulphide bonds very nicely when you load a pdb file.
What I want is, to tell him not to do that. I need it for the fact that I
need to set new values of dihedrals to the protein, and if there is a
disulphide bond, then pymol just doesnt set the dihedrals. One way is to
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