Re: [PyMOL] Exporting data from PyMOL into OriginLab

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),

Re: [PyMOL] Farewell

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

Re: [PyMOL] Outlines thickness

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

Re: [PyMOL] incomplete secondary structure

ris-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) > > > --

[PyMOL] incomplete secondary structure

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

Re: [PyMOL] [EXTERNAL] Re: broken DNA cartoon

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 Research Center (BRC) Rm. 466

Re: [PyMOL] broken DNA cartoon

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: March 20, 2020 at 9:59:45 PM >

Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?

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

Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?

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

Re: [PyMOL] Unwanted bond formed in azetidine ring

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

Re: [PyMOL] fix cartoon backbone

> 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, > Thomas > > >> On Mar

Re: [PyMOL] fix cartoon backbone

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.

[PyMOL] fix cartoon backbone

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

Re: [PyMOL] query

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

Re: [PyMOL] visualizing a transparent surface within a transparent surface

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

Re: [PyMOL] auto_show_cartoon or similar

ation Performance > APM + Mobile APM + 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=/4140

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

Lipid Membranes." Structure. > > > vincent > > > On 03/02/2016 19:33, H. Adam Steinberg wrote: >> Thank you Tsjerk. What we do right now is just open VMD and use the membrane >> builder, then take that file back into PyMOL! >> >>> On Feb 3,

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

gt; > Cheers, > > Tsjerk > > On Feb 2, 2016 5:33 PM, "H. Adam Steinberg" <h.adam.steinb...@gmail.com > <mailto:h.adam.steinb...@gmail.com>> wrote: > Tsjerk, > > Can you add an example of generating a “real” membrane around a protein to

Re: [PyMOL] PyMOL-users Digest, Vol 116, Issue 15

nitor 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=267308311=/4140___ >

Re: [PyMOL] [BUG?] Selection by secondary structure - Pymol 1.8.0.0 r4144

gt; <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> H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 ---

Re: [PyMOL] JyMOL vs JSMol

d it would be great to collaborate on this 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 anymor

[PyMOL] JyMOL vs JSMol

? Or is JyMOL more equivalent to JMol? Thanks! H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page

[PyMOL] Brownian motion in movie?

<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

Re: [PyMOL] real time minization in Pymol

t) > 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

Re: [PyMOL] lipid membrane help

://www.mail-archive.com/pymol-users@lists.sourceforge.net > <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> > > > -- > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lis

Re: [PyMOL] PyMOLWiki: Quick Update

> _______ > 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 Lo

Re: [PyMOL] change electrostatic ramp color?

e Ramp_New <> > Wiki page? > > Cheers, > > Osvaldo. > > On Fri, Oct 16, 2015 at 9:10 PM, H. Adam Steinberg > <h.adam.steinb...@gmail.com <mailto:h.adam.steinb...@gmail.com>> wrote: > > > > I opened a complex .pse file I created back in 20

[PyMOL] change electrostatic ramp color?

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

Re: [PyMOL] secondary structure disappears

created by the split_states command before merging them all into one object. It worked for me when I tried that with 3ow9. Cheers, Rob On Thu, 2015-07-23 09:23 EDT, H. Adam Steinberg h.adam.steinb...@gmail.com mailto:h.adam.steinb...@gmail.com wrote: Hi All, If you fetch 3ow9

[PyMOL] secondary structure disappears

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

Re: [PyMOL] secondary structure disappears

record in the PDB file to the lost ones. Smith At 2015-07-23 22:23:24, H. Adam Steinberg h.adam.steinb...@gmail.com wrote: 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

[PyMOL] test message

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

Re: [PyMOL] test message

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. Adam Steinberg h.adam.steinb...@gmail.com wrote: Hi Thomas

Re: [PyMOL] bonding nucleic acid bases

/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 bond_hbonds.py On 23 Jun 2015, at 22:51, H. Adam Steinberg h.adam.steinb...@gmail.com wrote: Hi all, If I create a string of double-strand

[PyMOL] working with ccp4 maps

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 provide you

[PyMOL] bonding nucleic acid bases

and 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

[PyMOL] bonding nucleic acid bases

and 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

[PyMOL] Cryo-EM structures

://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 Bowman Rd Lodi, WI 53555 608/592-2366

Re: [PyMOL] Beginning with PyMol

: http://www.mail-archive.com/pymol-users@lists.sourceforge.net H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process

Re: [PyMOL] pymol crash when ray

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 h.adam.steinb...@gmail.com wrote: For an instantaneous rendering of any PyMOL

Re: [PyMOL] green rings

/ ___ 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

Re: [PyMOL] green rings

. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- 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

Re: [PyMOL] what color was used?

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 obj or sele? H. Adam Steinberg 7904 Bowman Rd Lodi, WI

[PyMOL] what color was used?

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

Re: [PyMOL] cartoon_highlight_color for specific regions of structure?

@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

Re: [PyMOL] Clip surface only

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

Re: [PyMOL] Cartoon_oval_length

H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL

Re: [PyMOL] Cartoon_oval_length

would be: 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 h.adam.steinb...@gmail.com wrote: 1) Go to Settings in the menus and choose Edit all

[PyMOL] filled rings

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

Re: [PyMOL] filled rings

THANK YOU, that was it! On Jun 16, 2014, at 5:22 PM, Sampson, Jared jared.samp...@nyumc.org wrote: set cartoon_ring_color, blue, my_selection H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- HPCC

[PyMOL] Sphere_scale vs Dot_scale

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

Re: [PyMOL] Molecular models with LEGO

@lists.sourceforge.net H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced

Re: [PyMOL] set line_width command doesn't work

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. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366

[PyMOL] Leap motion control

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 from

[PyMOL] default settings

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://p.sf.net/sfu

Re: [PyMOL] default settings

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 nathaniel.ech...@gmail.com wrote: On Wed, Jan 30, 2013 at 8:33 AM, H. Adam Steinberg a...@steinbergs.us

Re: [PyMOL] default settings

^ SyntaxError: invalid syntax On Jan 30, 2013, at 12:46 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Wed, Jan 30, 2013 at 10:43 AM, H. Adam Steinberg a...@steinbergs.us wrote: This is great, but looks like it's only for Windows? Where would one put this pymolrc.pym file

Re: [PyMOL] default settings

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 nathaniel.ech...@gmail.com wrote: On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg a...@steinbergs.us wrote: You are correct, if I put

Re: [PyMOL] MacPyMOL 1.4 vs 1.5 problem with color

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 type surface (great for illustrations) in 1.4 it all works perfectly, and you can color the new map

Re: [PyMOL] PyMOLWiki is Down

@lists.sourceforge.net H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how

Re: [PyMOL] PyMOLWiki is Down

problems? Cheers, -- Jason On Thu, Jul 5, 2012 at 3:04 PM, H. Adam Steinberg a...@steinbergs.us 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 connection reset in Firefox and server dropped

[PyMOL] Structural biologist job

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,

[PyMOL] cartoon from c-alphas JMol vs PyMol

as the 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 608/592-2366

Re: [PyMOL] pdb of ice

://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -Original Message- From: H. Adam Steinberg [mailto:a...@steinbergs.us

[PyMOL] bbPlane script SyntaxError: invalid syntax

the CGO obj.append(END) # update the UI newName = cmd.get_unused_name(backbonePlane) cmd.load_cgo(obj, newName) cmd.set(cgo_transparency, transp, newName) cmd.extend(bbPlane, bbPlane) artforscience H. Adam Steinberg Artist, Scientist, Developmental Editor

Re: [PyMOL] bbPlane script SyntaxError: invalid syntax

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, 2011 at 11:34 AM, H. Adam Steinberg a...@steinbergs.us wrote: Hi all, Can anyone help me with a problem that I am having trying to run

Re: [PyMOL] bbPlane script SyntaxError: invalid syntax

, Tsjerk On Thu, Aug 25, 2011 at 5:34 PM, H. Adam Steinberg a...@steinbergs.us wrote: Hi all, Can anyone help me with a problem that I am having trying to run a python script? I am trying to run the bbPlane script from the PyMOLWiki http://www.pymolwiki.org/index.php/BbPlane I have

Re: [PyMOL] How to color in a different way different helix types?

/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 -- Xperia(TM) PLAY It's a major breakthrough

Re: [PyMOL] How to color in a different way different helix types?

-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 artforscience H. Adam Steinberg Artist, Scientist, Developmental Editor www.artforscience.com 7904

[PyMOL] New MacPros and PyMOL - Radeon only?

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 Bowman Rd Lodi

Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand

-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ___ H. Adam Steinberg Artist, Scientist http://adam.steinbergs.us Information Technology and Media Center Department of Biochemistry University of Wisconsin-Madison 433 Babcock

[PyMOL] Showing Si and Re faces

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://adam.steinbergs.us The Media Center

[PyMOL] nice DNA pdb and ring options

-- ___ 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 ___

Re: [PyMOL] feature request

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

Re: [PyMOL] PyMOL crashes under Vista Home Premium Ubuntu 8.04 LTS

-- ___ 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 ___

Re: [PyMOL] surface properties

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