Hi Neena,
When you render out of PyMOL using the button (not the command line), it just
renders out the view window. Therefore if you make the helix fill the entire
viewport rectangle, you will effectively render out a ‘cropped” image.
If you turn on transparency (in the background setting), yo
Thank you Thomas for all the help you have provided us over the years! You have
certainly made my experience with PyMOL far more useful and easier, with all of
the answers and shortcuts you have provided to this list!
Adam
> On Apr 30, 2021, at 9:14 AM, Thomas Holder
> wrote:
>
> Dear PyMOL
I also use this feature for illustrations and would love to find a better way
of controlling the outline thickness. Could anyone fill us in on the history of
this feature?
In Chimera black outline is just a simple slider and it’s super easy to use.
You just move the slider up and down and it sh
iv-paris-diderot.fr>
> caution: you need to submit each chain separately, since the server cannot
> deal with multi-chain models.
>
> Annemarie
>
>
> Today's Topics:
>
>1. incomplete secondary structure (h. adam steinberg)
>
>
>
Hi all,
When I open 3jav the backbone shows many helices, but Pymol doesn’t draw them
as helices when showing the cartoon. Clearly there is something that is not
perfect with the deposited cyro structure.
If I run the dss command, the cartoon structure isn’t fixed, and I get repeats
of the fol
https://www.ncbi.nlm.nih.gov/pubmed/27488983
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Rese
lt distance-based bonding doesn't pick it up.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
>
> From: h. adam steinberg
> <mailto:h.adam.steinb...@gmail.com>
> Reply: h. adam steinberg
> <mailto:h.adam.steinb...@gmail.com>
> Date: Ma
ooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
When you use the alter command, then rebuild, and then save the PyMOL session
as a .pse file, the changes will be written into the .pse file. They will not
be lost when you reopen the .pse file.
The alter command doesn’t do anything to the actual .pdb or .cif file. It’s my
understanding that wh
It’s the same command but just change the “S” to an “H”. Or you can use a “L”
if you want a loop (unstructured).
alter 3-10/, ss=‘H’
You also need to enter the command: rebuild, to redraw the structure on your
screen. Use rebuild after you enter the alter command.
> On Jun 4, 2019, at 10:37
Here is one way to do this:
change your mouse mode from “viewing” to “editing”.
left-click on the atoms at each end of the bond you wish to remove,
each atom will highlight with a gray ball around it,
In the command line type "unbond pkset” and hit the enter key,
your bond will be removed.
> On Ju
'+O5'
> unbond name OP2, name O3'+O5'
>
> PyMOL doesn't yet write bonds to mmCIF (it's on our TODO list, unfortunately
> the mmCIF spec doesn't make this straight forward). You could save to MMTF
> instead, it stores all bonds.
>
> Cheers,
&
hat helps.Cheers,JaredOn March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.adam.steinb...@gmail.com) wrote:On Mar 21, 2019, at 1:41 AM, Kevin Jude <kj...@stanford.edu> wrote:The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you
Hi All,
I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I
fixed those two breaks (add in the correct atoms and join them) how do I get
the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the
breaks.
Thanks!
Adam
___
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.
>
Hi All,
I’m doing a number of morphs for a project and have one example that includes
DNA.
I generated a second piece of straight DNA from scratch, and would like to show
it morph into the protein bound DNA.
PyMol 1.8 doesn’t seem to want to morph DNA. It goes through the exercise but
nothing
I get around this by rendering both items separately and then combining the two
images in photoshop.
Is there a way to do what Nasir is asking directly in PyMOL?
> On Feb 16, 2016, at 8:15 AM, Nasir Bashiruddin wrote:
>
> Hello!
>
> So, I've had this problem for a while now.
>
> I have a
_
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
---
RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>
ifying the protein and membrane.
>>>
>>> If you and your students would like to try it out, I can give some pointers
>>> and provide my scripts to get it done. The wiki will have to wait a bit,
>>> but it will come.
>>>
>>> Cheers,
>>>
-archive.com/pymol-users@lists.sourceforge.net>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> --
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>
nth
> Monitor end-to-end web transactions and take corrective actions now
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e.net/lists/listinfo/pymol-users>
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> <http://www.mail-archive.com/pymol-users@lists.sourceforge.net>
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
-
s to improve it
> more. See, for example: http://noys3.weizmann.ac.il/a2jb/browse
> <http://noys3.weizmann.ac.il/a2jb/browse>
>
> I certainly don't claim to know anything about JyMOL, except I guess it uses
> JNLP. Does Chrome support JNLP anymore?
>
> Bob Ha
JyMOL more
equivalent to JMol?
Thanks!
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
--
___
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Info Page
<https://www.youtube.com/watch?v=aNl7z0MOAVM
<https://www.youtube.com/watch?v=aNl7z0MOAVM>>
Does anyone know how CompChemist made the Brownian motion in the movie? I would
really like to duplicate that effect!
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
--
Go from Idea to Many
https://lists.sourceforge.net/lists/listinfo/pymol-users
> <https://lists.sourceforge.net/lists/listinfo/pymol-users>
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> <http://www.mail-archive.com/pymol-users@lists.sourceforge.net>
> ----------
> __
; Wiki page?
>
> Cheers,
>
> Osvaldo.
>
> On Fri, Oct 16, 2015 at 9:10 PM, H. Adam Steinberg
> mailto:h.adam.steinb...@gmail.com>> wrote:
>
>
>
> I opened a complex .pse file I created back in 2007 and the electrostatic
> ramp is showing as green to blue
---
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-use
I opened a complex .pse file I created back in 2007 and the electrostatic ramp
is showing as green to blue. Any ideas how to change it back to red to blue?
The wiki seems to be down.
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
distinct chain
>> ID if you want the cartoon representation to work correctly.
>>
>> Unfortunately that means you have to use "alter" but to change the
>> chain IDs on the objects created by the split_states command before
>> merging them all into one object.
d in the PDB file to the lost
> ones.
>
> Smith
>
>
>
>
>
> At 2015-07-23 22:23:24, "H. Adam Steinberg"
> wrote:
> Hi All,
>
> If you fetch 3ow9 in PyMOL,
> split_states to get all six of the strands,
> select all, then copy to object
Hi All,If you fetch 3ow9 in PyMOL,split_states to get all six of the strands,select all, then copy to object,You only get the two strands, not all six, I need all six to be duplicated into one object so I can make a long amyloid fibril.If I open the pdb file for 3ow9 in text edit and remove all the
l-Scripts/Pymol-script-repo/raw/master/get_raw_distances.py
> run bond_hbonds.py
> fetch 1nz1, async=0
> bond_hbonds resi 1-12, resi 12-22
>
> Hope that helps.
>
> Cheers,
> Thomas
>
>
> On 23 Jun 2015, at 22:51, H. Adam Steinberg
> wrote:
>
>> Hi all,
or you if you want).
>
> I assume nobody replied to your message "bonding nucleic acid bases" simply
> because nobody had written such a script before (I think that's what you were
> asking for).
>
> Cheers,
> Thomas
>
> On 02 Jul 2015, at 15:36, H. A
setting set wrong. Do you have
any idea if there is a setting I have messed up with the listserv? Or if I’ve
been blacklisted for some reason?
Thanks,
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
hub) and EMDB-2330 (one triplet that I have to
show nine times).
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
--
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provid
manually create physical bonds where the
hydrogen bonds would be, and I’m guessing that would work, but I’m wondering if
anyone has a script or is there a function that I am unaware of?
Thanks!
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
manually create physical bonds where the
hydrogen bonds would be, and that would work, but I’m wondering if anyone has a
script or is there a function that I am unaware of?
Thanks!
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
.ebi.ac.uk/pdbe/ <http://www.ebi.ac.uk/pdbe/>>
<http://pdbj.org/emnavi/ <http://pdbj.org/emnavi/>>
Thank you for any help you can provide.
H. Adam Steinberg
7904 B
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
one more thing…
Delete all objects that you are not using for this particular rendering (save
it as a separate file). I have found this speeds up rendering times.
> On Apr 14, 2015, at 7:49 PM, H. Adam Steinberg
> wrote:
>
> For an instantaneous rendering of any PyMOL scene that
--
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
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urceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
--
Dive in
> HTH,
> Matt Baumgartner
>
>
> On 2/27/2015 4:28 PM, H. Adam Steinberg wrote:
>> I am creating a new PyMOL session and I have to match the colors that
>> someone else used in a different PyMOL session. Is there any way to identify
>> what colors they used for an
I am creating a new PyMOL session and I have to match the colors that someone
else used in a different PyMOL session. Is there any way to identify what
colors they used for an obj or sele?
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
tnership with Slashdot Media, is your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/
> ______
if you have access to Gimp or photoshop and want to do this in just a few
minutes… clip and render the surface how you want it, then without moving
anything, unclip and render just the ligand. In any bitmap editing program
layer the ligand image over the clipped surface image and merge the two i
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H.
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
--
gt;
> PyMOL> unset cartoon_oval_length, *
>
> That clears the setting on all objects and falls back to using the global
> setting.
>
> Cheers,
> Thomas
>
> On 25 Aug 2014, at 12:26, H. Adam Steinberg
> wrote:
>> 1) Go to Settings in the menus and choose E
www.mail-archive.com/pymol-users@lists.sourceforge.net
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
--
Slashdot TV.
Video for Nerds. Stuff that matters.
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THANK YOU, that was it!
On Jun 16, 2014, at 5:22 PM, Sampson, Jared wrote:
> set cartoon_ring_color, blue, my_selection
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
--
HPCC Systems Open Source Big D
anyone help?
Sample image attached…
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
--
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with
Works perfectly! Thank you so much!
On Dec 9, 2013, at 2:43 PM, Thomas Holder wrote:
> Hi Adam,
>
> alter all, vdw*=0.5
> rebuild
>
> Cheers,
> Thomas
>
> On 09 Dec 2013, at 14:51, H. Adam Steinberg
> wrote:
>
>> I can show an atom as a sphere, and
I can show an atom as a sphere, and then scale that sphere to 0.5.
I can show an atom as dots, but then cannot scale the volume of those “dots” to
0.5. There is no dot_scale command in PyMOL.
Is there anyway to scale the volume of the dots in some way?
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI
gt; --
> Tsjerk A. Wassenaar, Ph.D.
>
>
> --
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced pro
how any change.
> Have you meet such circumstance? The pymol (version 1.5.0.1) is installed in
> centos5.9 system and other functions seem well. Thanks.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
H.
It would be great if we could control PyMOL with a Leap Motion control
<https://www.leapmotion.com>.
I see it supports molecules.
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
--
See everything fr
that allows you to see the hidden files. I used TinkerTool.
This works and solved the problem! Thanks!
On Jan 30, 2013, at 12:59 PM, Nat Echols wrote:
> On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg
> wrote:
>> You are correct, if I put the pymolrc.pym file in the user fold
o_zoom = 0
^
SyntaxError: invalid syntax
On Jan 30, 2013, at 12:46 PM, Nat Echols wrote:
> On Wed, Jan 30, 2013 at 10:43 AM, H. Adam Steinberg
> wrote:
>> This is great, but looks like it's only for Windows? Where would one put
>> this pymolr
This is great, but looks like it's only for Windows? Where would one put this
pymolrc.pym file on a Mac?
<http://www.pymolwiki.org/index.php/Pymolrc>
On Jan 30, 2013, at 12:12 PM, Nat Echols wrote:
> On Wed, Jan 30, 2013 at 8:33 AM, H. Adam Steinberg wrote:
>> Is there
ing MacPyMol on 10.8.
Thanks
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http
affected, so you still can generate high quality
> figures with correct colors:
>
> PyMOL> ray
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> H. Adam Steinberg wrote, On 11/20/12 03:40:
>> Hi all,
>>
>> If you run the script below to get a nice blob
script to make this work in 1.5? or is this now broken in 1.5.0.4?
---
set surface_quality, 1
alter all, b=50
alter all, q=1
set gaussian_resolution,5
map_new mapA, gaussian, 1, sele or pdb, 6
isosurface surfA, mapA
-
Thanks in advance for the help!
H. Adam Steinberg
ne else having problems?
>
> Cheers,
>
> -- Jason
>
> On Thu, Jul 5, 2012 at 3:04 PM, H. Adam Steinberg wrote:
>> Is the wiki still in turmoil? every time I try to access a page via the
>> search field on the wiki, or via a Google search I get back "connect
list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
---
Hi all,
A friend of mine is looking to hire a structural biologist. With the tight job
market I though I would try and get this out to as many people as possible.
> I am looking to hire a PhD structural biologist to join the team I manage at
> Myriad Genetic Laboratories in Salt Lake City, Uta
default. :P
Why can't PyMol show the traditional cartoon like JMol does? and if JMol is
faking the traditional cartoon, why can't we get PyMol to also fake the
traditional cartoon? :)
Thanks for any insight.
Adam
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
60
6 Dunedin 9054
> New Zealand
> Skype: jtyndall
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> Pouaka Poutapeta 56 Otepoti 9054
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>
> Ph / Waea +64 3 4797293
> Fax / Waeawhakaa
Hi all,
Does anyone know of a pdb that was created for the structure of water molecules
in ice? I have not been able to find one and am not looking forward to creating
one! :)
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
> pplanes selection[, color[, alpha[, state[, name
>
> Hope it helps,
>
> Tsjerk
>
>
> On Thu, Aug 25, 2011 at 5:34 PM, H. Adam Steinberg wrote:
>> Hi all,
>> Can anyone help me with a problem that I am having trying to run a python
>> script?
>> I am
ur email and it worked
> fine. There are, however two spaces on line 14--maybe the parser
> thinks it found a block indent? Try erasing line 14 (the line
> following "from chempy import cpv") and re-running the script.
>
> Cheers,
>
> -- Jason
>
> On Thu, Aug 25,
= map(lambda x: x[1], angles)
vorder = [ verts[0], verts[1], verts[2],
verts[1], verts[3], verts[2] ]
# fill in the vertex data for the triangles;
for i in vorder:
obj.append(VERTEX)
obj.extend(pos[i])
# finish the CGO
obj.appe
(o) +1 (603) 374-7120
>
> --
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu
rge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
artforscience
H. Adam Steinberg
Artist, Scientist, Developmental Editor
www.artforscience.com
7904 Bowman Rd
Lodi, WI 53555
608/729-5944
have bought this new
Mac if I would have known this. Is there anything I can do to make this new
machine work?
I see a 64-bit version is on the horizon, will this address Radeon performance
or should I go back to my old MacPro with it's nVidia 7300 video cards?
H. Adam Steinberg
7904 Bowm
rystal Reports now. http://p.sf.net/sfu/bobj-july
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-use
itrogen back to the 1st alpha carbon.
These planes are what make up the strands and the alpha helices when you
show a protein as "cartoon" in PyMOL.
Thanks in advance for any help!
Adam
--
_______
H. Adam Steinberg
Designer, Artist, Scientist
<http://ad
anything you can offer,
Adam
--
___________
H. Adam Steinberg
Artist, Scientist
<http://adam.steinbergs.us>
Information Technology and Media Center
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI 53706
608/265-4982
___
It is especially difficult to remember which scene is which when you
open a pse file that you haven't looked at for a few months. Would it be
simple or easy to just let us name the scenes like we name the objects
and selections in the pane on the right?
Sarina Bromberg wrote:
I find it difficu
users
--
___
H. Adam Steinberg
Artist, Scientist
<http://adam.steinbergs.us>
Information Technology and Media Center
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI 53706
608/265-4982
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H. Adam Steinberg
Arti
lists/listinfo/pymol-users
--
___
H. Adam Steinberg
Artist, Scientist
<http://adam.steinbergs.us>
Information Technology and Media Center
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI 53706
608/265-4982
___
settings that might be relevant but
couldn't see any. I'm on 0.99rc6, if that makes any difference.
Thanks in advance for your help
Daniel
--
___
H. Adam Steinberg
Artist, Scientist
<http://adam.steinbergs.us>
Information Te
Use my hydrophobicity script... Please build this in as preset as I use
it all the time.
# Written by H. Adam Steinberg
# 08/22/2007
###set custom colors for each amino acid based on hydrophobicity scale
(scale derived by S. D. Black and D. R.
Mould):
set_color ala, [0.525490196, 0.792156863
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