Re: [PyMOL] Center view on arbitrary coordinates

? (where there might not be an atom) origin position=[1.0,2.0,3.0] center origin At least it looked like it worked. -David Hall

Re: [PyMOL] PyMol initialization

Put the commands in your pymolrc file See http://pymolwiki.org/index.php/Launching_PyMOL#Windows -David Hall - Original Message From: Kelvin Luther klut...@ic.sunysb.edu To: pymol-users@lists.sourceforge.net Sent: Saturday, October 4, 2008 5:53:24 PM Subject: [PyMOL] PyMol

Re: [PyMOL] Error: unknown type

If people really like this git stuff, it might be interesting to move the scripts to using gist.github.com . I don't know how well that would work with the current repo that Justin created. Also, it might be useless as wikipedia already lets us track the history of the page. I could see

Re: [PyMOL] Error: unknown type

I could see some use in being able to see forks off from the scripts in the wiki to people's individual computers though. this can be readily done via the repo Can you show how I can clone a single file out of the repository? Or how I can fork a single file from the repository? Or

Re: [PyMOL] The List Archive is Back!

is it possible to put a link to these archives in the signature portion of the mailing list? I would find that very helpful. -David - Original Message From: Warren DeLano war...@delsci.com To: pymol-users pymol-users@lists.sourceforge.net Sent: Tuesday, April 28, 2009 11:52:28

Re: [PyMOL] RMS

pymol.cmd.align(%s % name_struct1, %s % name_struct2) should return a list, the first element of which is the rms, if I remember correctly. Warren can probably say what the rest of the elements are. On this note, maybe we could start documenting on the wiki what exactly all these commands

[PyMOL] Alignment Objects

Is there any documentation on getting information out of alignment objects into scripts? I tried looking around the wiki, but I didn't see anything. I'm just wondering things like if I have a residue in one object, finding the residue in another object that has been aligned. Thanks, David

[PyMOL] Jymol Question

I wanted to play around with Jymol free evaluation builds ( http://delsci.com/jymol/ ), but I'm having trouble with the instructions given in the README.txt for using javac to compile the examples. I know almost nothing about Java, so my problem may be something obvious. When I run: javac

Re: [PyMOL] Jymol Question

Problem solved: it looks like I just had to use javac from openjdk instead of javac from gcj. -David - Original Message From: David Hall dwash59_2...@yahoo.com To: pymol-users@lists.sourceforge.net Sent: Sun, November 22, 2009 2:22:18 PM Subject: [PyMOL] Jymol Question I

[PyMOL] Fw: why losing information about simulation box size in pdb file after edit it?

2. Is there any way to get the information about bonds, angles and dihedrals ? I found the following command can display the bonds information, but can't be assigned to a variable. cmd.select('all') atoms=cmd.get_model('sele') print atoms.list()

[PyMOL] List of Groups

How would someone get the list of groups in a pymol session? get_object_list doesn't have them and the only commands I can find in cmd that have the word group in them seems to be group and ungroup (if my quick regex search worked right). Thanks, David

Re: [PyMOL] get translation / rotation matrix from super

Matthias Haffke said: Is there a way to extract the translation / rotation matrix out of the super command or can I use another command to align both, protein B and A and to apply the function on every symmetry mate? In addition the commands mentioned by Jason, you can look at matrix_copy

Re: [PyMOL] New Feature Ideas

- Original Message From: Adrian Schreyer ams...@cam.ac.uk To: jason.vertr...@schrodinger.com; PyMOL-users@lists.sourceforge.net Sent: Wed, January 20, 2010 10:00:03 AM Subject: [PyMOL] New Feature Ideas Something more challenging: 3) Export scenes as webGL.This is a bit more

Re: [PyMOL] Feature Requests/Ideas (Sean Law)

That seems like a modification that makes it less flexible. Now I can't do: ray 2.5in, 20cm, dpi=300 Don't ask me why I might want to use two different units, I just don't see a reason to make it so I cannot. I'm frequently surprised by my desires. And resolution is inconsistent with the png

Re: [PyMOL] New Feature Ideas

1) I would love it if the PDB Loader Service Plugin would clean up what it left in /tmp on pymol exit. I have a feeling this might be complicated though. I just have a bad memory when I first entered this world and I had pymol open and I was trying to load a pdb and the plugin just would not

Re: [PyMOL] new ideas

In my incentive build, freemol is present with the following readme: This is a binary distribution of the FreeMOL Open-Source Compilation. The FreeMOL project home page can be found at: http://bioinformatics.org/freemol Complete source code for building FreeMOL and its various components

[PyMOL] Dynoplot/Get residues was:[Re: New Feature Ideas]

You would have to work with the DynoPlot author to improve this. So, I figured it would be nicer if I sent the author a patch instead of just complaining, so I went to look at the code. Right now, it uses integer math to try to find the residues before and after, but I know from my mistakes

Re: [PyMOL] PyMOL on the Mac

Alright, here's a feature request that might convince people who still don't believe, despite your first commit to pymol trunk post-acquisition including Fixed a GL build bug on OSX (see http://pymol.svn.sourceforge.net/viewvc/pymol?view=revrevision=3887 ) A Pymol Quicklook plugin. My primary

Re: [PyMOL] Feature Requests/Ideas (Sean Law)

On Thu, Jan 21, 2010 at 9:46 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Errm, that only makes sense if the viewport itself is resampled somehow when you don't do raytracing, but I don't think it is. I'm pretty sure it is resampled when you specify a width or height. All this below is with

[PyMOL] Whitespacing?

During my editing of dynoplot.py, I noticed that there were some whitespace issues. Normally I consider whitespace a bikeshedding topic, but in python, it is significant, so it matters. When tabs and spaces are mixed, our own personal settings for how tabs are displayed in an editor makes a huge

Re: [PyMOL] color by element

util.cbas for salmon util.cbay for yellow You can see how these are implemented in http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/modules/pymol/util.py?view=markup if you want to make your own custom versions. -David Hall On Tue, Feb 9, 2010 at 5:46 PM, Ariel Talavera talav...@cim.sld.cu wrote

Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 5

I don't think DynoPlot can't do this. Are there even callbacks to watch for things like changing state in the Pymol GUI? Maybe that should be a feature request as it would allow for a lot more powerful plugins. Callbacks that we can bind to through TKinter to watch for modifications in the

Re: [PyMOL] hi

If you would like to use a server for protein-protein docking, you can check out the nice list on the wikipedia page for CAPRI. http://en.wikipedia.org/wiki/Critical_Assessment_of_PRediction_of_Interactions#List_of_predictions_servers_participating_in_CAPRI If you're looking for actual pieces of

Re: [PyMOL] Fwd: succinct secondary structure 'readout'

Can Jason set up the list as the automatic Reply-To: header? Would make it a lot easier. -David On Mar 9, 2010, at 5:53 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: I never get used to Pymol doing reply-to-sender in stead of reply-to- list :| -- Forwarded message --

Re: [PyMOL] How to create pdb file within pymol?

What are you using to create the xyz file (and why can that software not write a pdb)? The command you have below is pretty simple. An alternative is also the xyzpdb program that comes as part of tinker. ( eg: xyzpdb graphite.xyz charmm22.prm gives you graphite.pdb ) -David On Tue, Mar 9, 2010

Re: [PyMOL] Fwd: succinct secondary structure 'readout'

while I agree with many of the points in that article, I've found it often penalizes members of a community who participate the most strongly by having them: a) receive a lot of private e-mail that should go to the list, meaning they have to explain to a lot of people the purpose of lists and what

Re: [PyMOL] PyMOL on the Mac

To: Jason Vertrees Cc: pymol-users@lists.sourceforge.net; David Hall Subject: Re: [PyMOL] PyMOL on the Mac Hi Jason, Along those lines, would it be possible to have a 'default' which can be set to a list of settings related to appearance? That might be more concise than to have everything

Re: [PyMOL] frustrating rms command

See http://www.pymolwiki.org/index.php/Intra_Rms#USER_EXAMPLES.2FCOMMENTS comments that start with Fit, Rms, Rms_Cur are finicky and only work... as that likely explains your problem and a possible solution. But I agree that pymol's behavior with this command can be extremely annoying. -David

Re: [PyMOL] PyMOL on the Mac

I would be a fan of auto_show_cartoon. Also, if you set more than one of these, it will auto show more th one representation. Coolness. If anyone is curious, I just figured out what auto_show_selections appears to do (it is on by default), so I'll try to document that tomorrow. Thanks,

Re: [PyMOL] installing pumol on suse

Looks like you don't have the python-devel package. This provides the header files such as Python.h you need for compiling python modules. -David On Fri, Mar 19, 2010 at 5:50 PM, Tatsiana Kirys nus...@mail.ru wrote: Dear All, i'm trying to install pymol on suse. i've checked that i have

Re: [PyMOL] installing pumol on suse

2010/3/22 Tatsiana Kirys nus...@mail.ru: I've installed it. But i have even more errors now: nus...@linux-3mpg:~/Download/trunk/pymol python setup.py build install bunch of stuff /usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld: cannot find -lpng collect2: ld

Re: [PyMOL] getting Residue environment distances and residue-residue distances programatically

PyMol doesn't provide programmatic access to actual bond objects. Instead, you have to do what was suggested 5 days ago: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07745.html -David On Tue, Mar 23, 2010 at 3:48 PM, hari jayaram hari...@gmail.com wrote: Hi I want to write

Re: [PyMOL] compiled Pymol on MacOSX , The Pmw menu window does not open properly and Python Icon bouncing on dock

Do you know about the fink builds of pymol? http://pdb.finkproject.org/pdb/package.php/pymol-py26 . You might have more success modifying that package to pull the source from subversion. -David On Wed, Mar 24, 2010 at 11:48 AM, hari jayaram hari...@gmail.com wrote: Hi , Because I wanted to

Re: [PyMOL] Charged Surface Calculation at different pHs?

I know little of the apbs-pymol integration, but in general, you can use the PROPKA support built into PDB2PQR to assign protonation at different pHs and then feed your pqr to apbs. See http://www.poissonboltzmann.org/pdb2pqr/user-guide/using-pdb2pqr for the --with-ph option. There's also a

[PyMOL] Fedora Graphics Test Week

to be currently running Fedora or even Linux to participate. So, if you have some time to spare this week, you can run all the tests on your system and hopefully help move open source graphics on linux forward. Announcement and details can be found at: http://lwn.net/Articles/383156/ -David Hall

Re: [PyMOL] RMSD for ALL ATOMS against ALL ATOMS

rms and fit gave you different values? They have never given me different values. Example: from pymol import cmd cmd.fetch('1nmr') cmd.split_states('1nmr') for i in xrange(1,21): for j in xrange(1,21): prot_i = '1nmr_%04d' %i prot_j = '1nmr_%04d' %j rms_val =

Re: [PyMOL] pyMol executing python script: file path

I think you'll be saddened to discover that if you try what Petr (the original poster) was doing, sys.argv[0] won't work. $ cat test.py print sys.argv[0] $ pymol -qrc test.py PyMOLrun test.py,main /sw/lib/pymol-py26/modules/pymol/__init__.py This quite clearly gives the behavior that Petr had

Re: [PyMOL] how to install pymol in Mac?

The error below shows that you don't have gcc, which means you have to install Apple's Developer tools to compile pymol. That said, the easiest way right now is probably using macports. Follow the instructions at http://www.macports.org/install.php for installing macports, then you can run port

Re: [PyMOL] Automatic modification of structures in PyMOL

I think what you're asking for is one of the examples included in the PyMol source code. You can do this manually using the mutagenesis wizard, but it is possible to drive this wizard through scripts. The two examples can be found at:

[PyMOL] Load without bonding

Is it possible to load a pdb file and have pymol skip making bonds? There's a bunch of undocumented options to load, but I don't think any of them do what I want. I have a file where there's a bunch of jumbled atoms and there's no relation between them, just thousands in the same place and pymol

Re: [PyMOL] Load without bonding

actually, you can ignore this email, it seems pymol was having issues because there were a bunch of CONECT records, if I delete those, pymol actually loads it really fast. Kind of odd behavior, but interesting. -David On Thu, Apr 22, 2010 at 2:14 PM, David Hall li...@cowsandmilk.net wrote

Re: [PyMOL] Load without bonding

. -David On Thu, Apr 22, 2010 at 2:43 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi David, Check out the connect_mode setting: set connect_mode, 1 # no bonds fetch 1cll Cheers, -- Jason On Thu, Apr 22, 2010 at 2:14 PM, David Hall li...@cowsandmilk.net wrote: Is it possible

Re: [PyMOL] for evaluation only

The quick answer is Don't use an evaluation build. You have 3 main options: 1) become a sponsor and get builds of the latest code http://pymol.org/funding.html 2) use the free builds that are several years old http://pymol.org/rel/099/ 3) build pymol from source. There are instructions on

[PyMOL] Super Bug Report

In preparing my test for the odd request that I just sent, I came across what seems to be a bug in super. It has to do with this weird nucleic acid thing I was talking about. Here's the script this time: from pymol import cmd cmd.fetch('1acb', async=0) cmd.fetch('1acb', '1acb_2', async=0)

[PyMOL] Request: Change in behavior of super on nucleic acids?

I realize this is an edge case, where behavior is not always well defined in programs, but I have a request for a behavior (and the behavior actually seemed to change between 1.2 and 1.3) My example script: from pymol import cmd cmd.fetch('1acb', async=0) cmd.fetch('1acb', '1acb_2', async=0)

[PyMOL] OpenDX files from opendx.org

I have long been happy reading .dx files produced by apbs and my own programs into pymol. Everything works great. Interestingly, when I save a .dx file from OpenDX (http://opendx.org), pymol seems to not be able to read it. I've attached two files that come from OpenDX's samples directory where

Re: [PyMOL] OpenDX files from opendx.org

. If they support non-orthogonal DX maps out of the box, that might be a quick and easy solution. Cheers, -Michael On Fri, Oct 15, 2010 at 5:51 PM, David Hall li...@cowsandmilk.net wrote: I have long been happy reading .dx files produced by apbs and my own programs into pymol.  Everything works great

[PyMOL] label_size in pymol 1.3 on Mac

Has anyone else run into a problem with label_size in pymol 1.3 on Mac? For both my fink and macports build, it doesn't work. The baseline of the text moves, but the size doesn't change. It does work when I compile from pymol trunk on my linux box. I don't see anything in the changelog or svn

Re: [PyMOL] Start PyMOL session in web browser

Jmol certainly is not the only thing able to do that. In the applet world, you have at least OpenAstexViewer http://openastexviewer.net/web/ , but I also imagine it is possible to build a (jogl-accellerated) applet using jymol http://www.pymol.org/jymol , but I'm fairly certain it is not open

Re: [PyMOL] using pymol from python script

No idea if this will fix your problem, but what I've found is portable across binaries from Delano Scientific/Schroedinger and OS/self-compiled versions of pymol is to instead run: pymol -r examply.py -- mymolecule.xyz (or if I'm making pngs, usually pymol -qrck examply.py -- mymolecule.xyz )

Re: [PyMOL] Pymol no longer fetches from pdb

Resolves fine for me. -David On Mar 22, 2011, at 12:30 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Roger, On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett rrowl...@colgate.edu wrote: Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it is currently

Re: [PyMOL] Show Sticks - Turns Molecule Blue

Assuming you're using a recent version of openSUSE (11.3, 11.4, or Factory), feel free to grab the svn compiled version from http://software.opensuse.org/download.html?project=devel:languages:pythonpackage=pymol -David 2011/9/11 Troels Emtekær Linnet tlin...@gmail.com: This should get you on

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

the builds on https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython for opensuse 11.3 and 11.4 use gcc4.5 successfully. I blame ubuntu or linux mint. -David On Dec 2, 2011, at 10:21 AM, Marius Retegan marius.s.rete...@gmail.com wrote: Could you please

Re: [PyMOL] Using super correctly

I think super does not handle nucleic acid sequences well. super ec-5s, hm-5s, seq=-1 works. I'll leave it to someone else to say what that does. I just noted that align works, super doesn't, guessed it had to do with sequence and noted that for align, the default value of seq was -1 and for

Re: [PyMOL] cmd.do(png filename) error

On Fri, Jan 13, 2012 at 4:34 AM, tusi t...@enzim.hu wrote: Dear All, After updating to Ubuntu natty (11.04), cmd.do('png filename') does not work. When I execute the following commands in pymol I get the wanted png picture: load tmp.pdb tmp png tmp.png but, if I execute the following

Re: [PyMOL] Using super correctly

about invalid selections because it thinks the selections are empty. -David On Fri, Jan 13, 2012 at 8:37 AM, David Hall li...@cowsandmilk.net wrote: I think super does not handle nucleic acid sequences well. super ec-5s, hm-5s, seq=-1 works. I'll leave it to someone else to say what that does

Re: [PyMOL] Open Source PyMOL v1.5.0.1

On Mon, Feb 13, 2012 at 2:27 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Greetings, It is my pleasure to announce the release of open source PyMOL v1.5.0.1. The source code has been committed to the open-source repository. It is revision 3976. An svn tag and downloadable bz2

Re: [PyMOL] Little coordinate cross in Pymol?

http://pymolwiki.org/index.php/Axes -David On Feb 27, 2012, at 5:38 AM, Gudrun Lotze gudrun.lo...@gmx.net wrote: Dear all, is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please? I have a protein made from dummy atoms and there is no

Re: [PyMOL] Editing of the pdb structure

On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Thomas, 'Wrong', certainly in the context it was given in, is a statement of judgment. It suggest that there is a failure in the functioning, and is a criticism to the developer, becoming a wrongdoer. My argument

Re: [PyMOL] GUI to improve interaction between user and PyMOL

Hi Suhaila, Correct me if I'm wrong but you want create *new* GUI elements for pymol to enhance your application, right? To my knowledge, there is not a great tutorial on this, but I can give you some pointers to plugins that do this currently and hopefully you can backfill some knowledge. The

Re: [PyMOL] Is there or should there be a pymol annotation server?

The main technology I've seen used for interactive publications is ActiveICM (see http://www.molsoft.com/activeicm.html#aipub ). In my lab, we regularly include pymol sessions as supplementary material to help people understand our results. -David On Friday, July 13, 2012 at 6:41 AM, Troels

[PyMOL] Pymol Rotated Screen

, the same thing happens. Interestingly, while the desktop background and any app on the screens are impacted, the mouse cursor is not. Note, the incentive build PyMolX11Hybrid does not have this problem. Thanks for any help, David Hall

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb.

You don't need a license for the open source version. If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. -David On Oct 4, 2012, at 9:22

Re: [PyMOL] Custom menus and shortcuts?

http://pymolwiki.org/index.php/Set_Key http://pymolwiki.org/index.php/Extend is also useful. -David On Tuesday, October 23, 2012 at 6:02 AM, Boris Kheyfets wrote: Hello PyMOL users, Menus = Is there a way I can add custom menu in PyMOL? Ideally I'd like to be able to call

Re: [PyMOL] iPad pymol questions

Hi Steve, I'll suggest a workaround to having pymol cache the files: (1) Install the DropBox app (2) Favorite your PDB files in that app, this will cache those files locally within the DropBox app for offline access (3) From the dropbox app, you can open PDB files in Pymol using the button in

Re: [PyMOL] Pymol error in Mac OS X 10.8.2

what method did you use for installation? -- David Hall On Wednesday, May 1, 2013 at 11:53 AM, Rhitankar Pal wrote: I am having some issues after installing pymol in Mac OS 10.8.2. It seems the program is installed but when I try to open in using command line pymol it doesn't show

Re: [PyMOL] Pymol error

by default, macports installs tcl with the +corefoundation variant (see http://guide.macports.org/#using.variants ) if you do: sudo port install tcl -corefoundation that will solve the problem. -David On Mon, May 6, 2013 at 8:26 PM, Rhitankar Pal rhitan...@gmail.com wrote: Dear Thomas,

Re: [PyMOL] Pymol error

? Are these issues happening because OSX 10.8.2 comes with preinstalled tcl and tk ? Thanks Rhitankar On Tue, May 7, 2013 at 12:30 PM, David Hall li...@cowsandmilk.net wrote: by default, macports installs tcl with the +corefoundation variant (see http://guide.macports.org/#using.variants

Re: [PyMOL] PyMOL 1.6 pre-release announcement

, 2013-04-26 19:15 EDT, David Hall li...@cowsandmilk.net wrote: Hi Thomas, I'm running into issues with color compatibility between 1.6 and earlier versions when opening pses (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like: Setting-Error: type read mismatch (color

Re: [PyMOL] Leap motion control

Jason can fill you in if there's an update, but the latest status update I'm aware of was: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11572.html -David -David On Monday, July 29, 2013 at 11:04 AM, H. Adam Steinberg wrote: It would be great if we could control PyMOL

Re: [PyMOL] How to move/turn CGO

For a definition of TTT , see http://pymolwiki.org/index.php/Object_Matrix You'll notice that set_object_ttt takes a 16-member list that corresponds to this matrix. -David On Aug 12, 2013, at 11:48 AM, Павел Томашевский croov...@gmail.com wrote: Thank you Thomas, translate and rotate works

Re: [PyMOL] using pymol commands in a script

I couldn't reproduce the exact error message you received, but I will note: (1) your splitting of lines leaves out the chain, so chain is never defined (2) line 9 of your python is missing an opening quotation mark before (resi matching the closing quotation mark right before the % sign (3) line

Re: [PyMOL] Still need help with fetch and pymol 1.7

I think there's a bug in python's code, not pymol's In the file that it describes at the end ( C:\Python27\lib\mimetypes.py ) , you should change line 250 from: except UnicodeEncodeError: to except (UnicodeEncodeError,UnicodeDecodeError): keeping the indentation in the file and so on. Then the

Re: [PyMOL] Color starting midway between adjacent chains

set_bond line_color, color_name, n. CA+CB will color all bonds between CA and CB whatever color you put in as color_name If you're doing sticks instead of lines, you should use set_bond stick_color, color_name, n. CA+CB -David On Mon, Mar 3, 2014 at 10:01 PM, I-Ji Jung u5205...@anu.edu.au

Re: [PyMOL] Pymol wrl output

Have you tried doing show as surface It appears the wrl file has a bunch of extra information from the cartoon representation, which could confuse shapeways? -David On Sun, May 4, 2014 at 4:49 AM, Grateful Frog gratefulf...@gmail.comwrote: Hi Jared everyone, First, thanks for all your

Re: [PyMOL] need help

I am very unsure of your question, but I believe you're asking if you have a PDB id, how to load that into pymol. For that, you can use the fetch command ( http://www.pymolwiki.org/index.php/Fetch ) You type: fetch 1acb into the pymol interface and it will download pdb id 1acb and load it into

Re: [PyMOL] CONECT table

http://www.pymolwiki.org/index.php/Connect_mode -David On Oct 6, 2014, at 6:35 PM, Markus Heller mhel...@cdrd.ca wrote: Hello, How can I get PYMOL to use the CONECT table from a PDB file? My protein is glycosylated, and I'd like to properly and automatically display the glycosides

Re: [PyMOL] select state not working

I'm a little confused by what PDB assemblies you are talking about that are distributed as multi-state structures, but assuming they are similar to NMR models... you can use intra_fit ( http://www.pymolwiki.org/index.php/Intra_fit ) For example, with 2kgx, we start out with chain a in state 1 and

Re: [PyMOL] DNA representation

colored by chain set cartoon_ladder_radius, 2 set cartoon_tube_radius, 2 set ray_trace_mode, 1 -David On Dec 13, 2014, at 1:22 AM, Jacob Lewis jl...@uowmail.edu.au wrote: Hi, Does anyone know how to show DNA like this in pymol? PastedGraphic-1.tiff Cheers, Jacob

Re: [PyMOL] CGOs

where are you getting this from? I don’t see a LINE command in pymol/modules/cgo.py -David On Dec 22, 2014, at 11:40 AM, Robert Hanson hans...@stolaf.edu wrote: OK. I will look at the PyMOL code if I need to. For instance: LINE has eight parameters. I don't know what the first two

Re: [PyMOL] sulfated tyrosine's losing connection

my experience shows that when you have two HETATM residues one after another, pymol never shows this bond because the crystallographer never put a CONECT record for it, which pymol wants. eg for 1674, there is not CONECT showing 1676 as being bonded and since they are HETATM , pymol decides to

Re: [PyMOL] MacPyMOL fink download

(2) assuming you didn't change it when installing fink, fink will install pymol in the /sw/bin directory. (4) this is fink setting environment variables such as PATH. You can add a line to your .bashrc to source it so it will be sourced every time you open a terminal. On Mon, Jan 19, 2015 at

Re: [PyMOL] The problem of save molecule to PDB after mutagenesis wizard

This occurs when retain_order is set before loading a protein. You have to: unset retain_order Then load your protein again. You might say: I didn't set retain_order. This is likely true. Some very popular pymol plugins set it when loaded, most famously the autodock plugin. -David On Tue, Jan

Re: [PyMOL] Compilation problem with Pymol v1.7.4.0

On Jan 23, 2015, at 7:32 PM, McCully, Dwayne (NIH/NIAMS) [C] dmccu...@mail.nih.gov wrote: When running python setup.py build in the pymol directory of version 1.7.4.0, I get an error that stops pymol from compiling (see below). Does anyone know how to fix this problem. Dwayne

Re: [PyMOL] Ball and stick model

http://pymolwiki.org/index.php/Ball_and_Stick ? You used the handmade method on that page. Generally, I like using the preset better. On Sun, Feb 1, 2015 at 11:42 PM, Seera Suryanarayana paluso...@gmail.com wrote: Dear Pymol Users I would like to represent the protein what I have in ball and

Re: [PyMOL] green rings

you can set cartoon_ring_color ? On Mar 9, 2015, at 11:20 AM, Quentin Vicens qvic...@unistra.fr wrote: Hi folks, I'm wondering how to get rid of the default green shine that's present in the middle of every ring (see attached snapshot) following commands such as: spectrum

Re: [PyMOL] APBS plugin not working on both Ubuntu Windows 7

There is an INSTALL file that provides instructions. The first step, calling ./configure , generates pdb2pqr.py from pdb2pqr.py.in If you want to manually do it, it just changes the first line in the file to point to your python installation. But, since there's a whole bunch of other things

Re: [PyMOL] PyMOL ball stick representation of imatinib in 2HYY

preset.ball_and_stick('r. STI’) On Apr 23, 2015, at 12:52 PM, Brenton Horne brentonho...@ymail.com wrote: Hi, I recently read this reply (http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13248.html

Re: [PyMOL] opensource for commercial use?

PyMol's License can be found at: http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/LICENSE Generally, this is considered a permissive license ( https://en.wikipedia.org/wiki/Permissive_free_software_licence ). If you plan to use it in a commercial tool, you should pay for a couple hours

Re: [PyMOL] how can we rotate torsion angle of a molecule?

On Jul 6, 2015, at 10:44 AM, Albert mailmd2...@gmail.com wrote: Hello: I am just wondering is it possible to rotate the torsion angle of a molecule in Pymol? I search in pymolwiki, and I only find how to translate a molecule or move the atom positions, but I didn't find anything

Re: [PyMOL] Python from PyMOL or PyMOL from Python?

I vastly prefer calling the python program from pymol You can call any python program using pymol as: pymol -r program.py — arg1 arg2 arg3 Or, my full preferred method is: pymol -qrck program.py — arg1 arg2 arg3 These make it quieter, stay on the command line, and not read the .pymolrc file

Re: [PyMOL] Pymol Morph movie error

there is no mpeg_encode.exe binary. mpeg_encode, as far as I am aware, has long been abandoned. You can find what I believe is the last version of the source code (1.5c) at https://build.opensuse.org/package/show/home:cowsandmilk/mpeg_encode , you can download by clicking the files with the up

Re: [PyMOL] Pymol Morph movie error

able from http://freemol.org <http://freemol.org/> > > Hans, what Windows version do you use? I can't reproduce this problem on > Windows 7 or 8. > > Cheers, > Thomas > > -Original Message- > > David Hall <li...@cowsandmilk.net <mailto:li...@c

Re: [PyMOL] pymol to webGL?

You can set: pse_export_version to the 3-part version of pymol you would like to use as an export version. -David > On Oct 18, 2015, at 3:48 AM, Takanori Nakane > wrote: > > Hi, > > It looks like the structure of PyMOL session (what > we got from

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

PyMOLrun fitting.py,main Do I need to import Pymol module in the shell script to use the pymol scripts like you did in python? Am I missing something? ​Thanks​ -- ​Gazal​ On Fri, Jul 10, 2015 at 11:36 PM, David Hall li...@cowsandmilk.net mailto:li...@cowsandmilk.net wrote: http

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

http://www.pymolwiki.org/index.php/Command_Line_Options http://www.pymolwiki.org/index.php/Command_Line_Options see the -c and -r options. I also use -q pymol -qcr script.py — arg1 arg2 arg3 On Jul 10, 2015, at 8:44 AM, Gazal gazal...@gmail.com wrote: Hi, I'm trying to find the RMSD

Re: [PyMOL] Problem with loadBfact.py on windows

This is the problem. Pymol’s working directory is not where you have this file. So, the script never loads. On Jul 10, 2015, at 12:20 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: No such file or directory: './loadB2Fact.py'

Re: [PyMOL] placing protein into lipid bilayer

I would disagree with your assertion that they use pymol to "insert" the protein into the membrane. They use the program they wrote, g_membed, to insert the protein. They used pymol to overlap them for the beginning of the simulation. That is, they use pymol to place the atoms of the protein on

Re: [PyMOL] creation of a sphere

What version of PyMol are you using? On Aug 27, 2015, at 7:50 AM, Christian Trindler christian.trind...@unibas.ch wrote: Hello, I’ve been trying to make a pseudoatom/sphere simply by typing: pseudoatom name into the command line of Pymol, but it only gives me the following error

Re: [PyMOL] Using cartoon putty-like command

presumably: http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/pymol/preset.py#l164 On Mon, Oct 5, 2015 at 5:42 AM, Clavel wrote: > Hello everyone, > > I would like to create my own command within the pymol environement. > > I have currently a set of points in

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