Re: [PyMOL] Source version?

2018-01-12 Thread David Hall
The source of 1.9.0.0 is likely the subversion repository, which also has the history that shows the changes. https://sourceforge.net/p/pymol/code/4184/log/?path=/trunk As for pymol 2.0 coming to open source, the announcement for 2.0 said the improvements would be pushed to the open source

Re: [PyMOL] Record and load coordinates

2018-01-11 Thread David Hall
The transform matrix you’re using is the identity matrix, so it won’t have any effect. -David > On Jan 11, 2018, at 6:54 PM, Benjamin Bailly wrote: > > Hi Thomas, > > Thanks for your reply. > > So if I am correct, for my protein get_coords fetches a very large matrix of

Re: [PyMOL] Combining views of different Pymol sessions in one single file ?

2017-12-28 Thread David Hall
You can use the partial argument of the load command to get two sessions together. load session1.pse load session2.pse, partial=1 > On Dec 28, 2017, at 6:03 PM, david gae wrote: > > Dear Maria, > > I don’t think there is a direct way to connect two sessions together. One

Re: [PyMOL] Help- PyMOL 1.8.7 on Python 3.6- Plugin Manager Issue

2017-08-22 Thread David Hall
See https://sourceforge.net/p/pmw/patches/7/ > On Aug 21, 2017, at 10:32 PM, Vijay Masand wrote: > > Dear Christoph > Thank you for the help. I followed your suggestion, but no success. > However, a new line is appearing now at

Re: [PyMOL] (no subject)

2017-07-31 Thread David Hall
For some reason, the people doing brew have decided to stop supporting compiling tcl-tk with X11 support. Not 100% sure, but I'm pretty certain pymol cannot use tcl-tk with aqua. If you already had pymol installed, this seems to eliminate the external gui. If you didn't, new installations of

Re: [PyMOL] Why does Pymol display the chain as disconnected?

2017-06-20 Thread David Hall
PyMol doesn’t display any atoms for a region of the protein for the same reason the rcsb doesn’t for that area. The crystallographer deposited a structure without coordinates for residues 25-38. http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=1AX8

Re: [PyMOL] Error aroused when install pymol from source

2017-06-08 Thread David Hall
I think if you install "msgpack-devel”, it will compile and install. Generally, header files (which is what is included in C++ files) are in *-devel packages. The regular msgpack package just contains the shared library for use by programs already compiled against msgpack. -David > On Jun 7,

Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

2017-06-01 Thread David Hall
PyMol does not use QM methods. It also does not "determine the structures of molecules". -David > On Jun 1, 2017, at 12:38 AM, Susmita/Rajib wrote: > > Thank you, Dr. Tyugashev, for replying to my query. > Doesn't PyMol also use those QM methods to determine the

Re: [PyMOL] show surface on pymol

2017-05-24 Thread David Hall
It sounds like you may need to change surface mode to include hets https://pymolwiki.org/index.php/Surface_mode -David > On May 24, 2017, at 4:45 AM, 刘艳超 wrote: > > > Dear Madem/Sir, > > I am a user of Pymol software. Pymol facilitates me a lot during my study. I >

[PyMOL] Packaging python3 version of pymol

2017-05-06 Thread David Hall
Hi, I maintain the pymol package for openSUSE. I'm considering packaging a python3 version alongside the python2 version. Are there maintainers of other distributions that have done so? Do you rename /usr/bin/pymol to /usr/bin/pymol3 for your python3 version? I'm looking to see if there is a

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

2017-05-02 Thread David Hall
When debugging, it is good to stop running pymol as a command line app and just run your script in a pymol gui and see what it is going on. In this case, you would find your selections have zero atoms. Why? Because you are basing them on something like "resn 102" , which is using the residue name

Re: [PyMOL] Calculating center of mass for the entire protein

2017-04-06 Thread David Hall
, Ahmad Abdelzaher <underoath...@gmail.com> >> wrote: >> >>> Well I'm assuming the selection goes in the argument of cmd.centerofmass(), >>> however, does it have to be an atom? How should I calculate the center of >>> mass for an entire protein? >>&

Re: [PyMOL] Calculating center of mass for the entire protein

2017-04-05 Thread David Hall
It returns the x, y, and z coordinates of the center of mass as a list of 3 floats, presumably in that order? Is there another question? The page describes the arguments and their defaults so I am unsure what is lacking. -David > On Apr 5, 2017, at 10:29 PM, Ahmad Abdelzaher

Re: [PyMOL] problems creating object using align method

2017-03-13 Thread David Hall
The error is due to you not surrounding AlnAB in quotes, so python treats it as a variable which has not been defined. That said, align modifies the coordinates of the existing object, the object created just shows the correspondence of residues used for alignment. To save the superimposed

Re: [PyMOL] Atom Order when Saving

2016-11-14 Thread David Hall
https://pymolwiki.org/index.php/Retain_order > On Nov 14, 2016, at 3:04 PM, Subha K wrote: > > Hi There, > > Just wondering if there is a way to have the same order of atoms (with that > of the initial loaded file) while saving a pdb file with pymol? > > I came across

Re: [PyMOL] loading StringIO

2016-10-26 Thread David Hall
https://pymolwiki.org/index.php/Read_Pdbstr -David > On Oct 26, 2016, at 3:55 AM, Albert Solernou wrote: > > Dear All, > I was wondering if there was a way to load a PDB file stored in memory > instead of disk, i. e., a memory file, defined through StringIO or >

Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

2016-10-12 Thread David Hall
Every time you loop through the list of files, you set X=1 ; you do your X=X+1 in a loop that will only run once ( because glob.glob(“lig.pdb”) is only going to return a list of length 1 that has lig.pdb) , so you set X=1 , then X=2, then back to X=1 before you process the next entry. That is

Re: [PyMOL] Modeling protein-dna complex

2016-08-13 Thread David Hall
Select the protein you want and the dna, then save the selection as a PDB. There are many ways to make a selection; visually, the easiest might be: You said you’ve removed the DNA from the protein-dna complex, so now you should have: (1) an object that has just your protein that you want in

Re: [PyMOL] Video in Ubuntu Linux

2016-07-08 Thread David Hall
Do you have the python code from freemol.org ? -David > On Jul 8, 2016, at 7:02 AM, Ioannis Michalopoulos > wrote: > >> On Friday 08 of July 2016 11:10:08 Folmer Fredslund wrote: >> Dear Ioannis, >> >>> On 2016-07-08 09:04, Ioannis Michalopoulos wrote: >>> Dear PyMOL

Re: [PyMOL] ABPS Tools 2.1 plugin error

2016-07-07 Thread David Hall
http://www.poissonboltzmann.org psize.py and pdb2pqr.py are part of pdb2pqr The others are part of apbs > On Jul 6, 2016, at 5:15 AM, Yanni wrote: > > Hello > > I'm using pymol 1.7 on OS X 10.11.5. > XQuartz version: 2.7.9 > python version: 2.7.12 > >

Re: [PyMOL] High Resolution Ray Tracing

2016-05-06 Thread David Hall
Feel free to send me the files off list. -David Hall > On May 6, 2016, at 1:54 PM, Stephen Kerry <stephen.kerr...@outlook.com> wrote: > > Dear All, > > I have a protein complex scene that I need to create a large, high resolution > (1200 dpi) ray traced image of, but

Re: [PyMOL] Bash scripting and pymol

2016-04-28 Thread David Hall
You need to add “,async=0” to your fetch calls. http://pymolwiki.org/index.php/Fetch > On Apr 28, 2016, at 4:51 AM, James Starlight wrote: > > Hi, > > My script is > > pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H") > pdb_array_store=$template/pymol > > > #

Re: [PyMOL] pymolrc location

2016-04-08 Thread David Hall
Make a file at ~/.pymolrc -David > On Apr 8, 2016, at 10:35 AM, harold steinberg > wrote: > > where in OS X is pymolrc located? > >> On Apr 7, 2016, at 2:39 PM, Thomas Holder >> wrote: >> >> pymolrc > > H. Adam Steinberg > 7904

Re: [PyMOL] running python scripts from within python loops in a pymol scripts

2016-04-01 Thread David Hall
I think you can use cmd.do cmd.do("com /DARPin2//A/37-135/CA, object=com2”) -David > On Apr 1, 2016, at 8:48 AM, Honegger Annemarie wrote: > > Hi! > > I am trying to automate some model building tasks > > this loop in my pml script works just fine, it generates models

Re: [PyMOL] why lib/python folder is missing?

2016-03-05 Thread David Hall
Doesn’t using --install-lib mean you are explicitly telling it to put the files in your modules directory instead of creating any lib/python type directories? > On Mar 5, 2016, at 2:50 PM, Albert wrote: > > Hello: > > I am using the following command line to compile

Re: [PyMOL] Filled rings on stick mode

2016-01-28 Thread David Hall
would something like these work for you? fetch 1rna, async=0 as cartoon set cartoon_ring_mode, 1 cartoon skip show sticks set cartoon_ladder_mode, 0 > On Jan 28, 2016, at 6:28 PM, COSTA Maria > wrote: > > Hi, > > I would like to know if it is possible to

Re: [PyMOL] pdb edition

2016-01-19 Thread David Hall
Well, yes, programs do use the CONECT records, including pymol http://pymolwiki.org/index.php/Connect_mode Removing bonds is http://pymolwiki.org/index.php/Unbond Atoms can be translated using the command line http://pymolwiki.org/index.php/Editing_atoms#Get_coordinates_from_Python Or in edit

Re: [PyMOL] optimize and open babel troubles

2016-01-06 Thread David Hall
Ubuntu’s universe repository has a 32-bit version of pymol? http://packages.ubuntu.com/precise/pymol Obviously, being a 4-year old distro, it is an older release, but it may still work with the plugin. -David > On Jan 6, 2016, at 2:39 PM, Joe Gauthier wrote: > >

Re: [PyMOL] Pymol issues for coloring ball and stick representation

2015-12-18 Thread David Hall
set_bond stick_color, color, selection For more info on what is used to create the ball and stick preset, see: http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/pymol/preset.py#l144 -David > On Dec 17, 2015, at 2:35 AM, ANURAG SANKHYAN wrote: > > Dear

Re: [PyMOL] Pymol under El Capitan

2015-12-11 Thread David Hall
Try the last comment on: https://github.com/Homebrew/homebrew-science/issues/2273 -David On Fri, Dec 11, 2015 at 3:39 AM, Chris Swain wrote: > Hi, > > I maintain a list of science applications that work under El Capitan ( >

Re: [PyMOL] on PDB

2015-11-25 Thread David Hall
http://pymolwiki.org/index.php/Save ?? -David > On Nov 24, 2015, at 9:45 PM, Smith Liu wrote: > > Dear All, > > Suppose the original PDB was not oriented. Once we have it oriented by pymol, > is any way we can save the new PDB oriented? > > Smith > > > > >

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

2015-11-18 Thread David Hall
Assuming you are ok with overwriting the B-factors stored.y=[] iterate_state 1, prot, stored.y.append(y) % prot here should be replaced with your pymol object name alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object name On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

2015-11-18 Thread David Hall
I forgot: spectrum b at the end. On Wed, Nov 18, 2015 at 8:11 AM, David Hall <li...@cowsandmilk.net> wrote: > Assuming you are ok with overwriting the B-factors > > > stored.y=[] > iterate_state 1, prot, stored.y.append(y) % prot here should be replaced > with your p

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

2015-11-18 Thread David Hall
he PDB and save it as another file? Can you introduce to me a server of software which can delete the original b-factors in the original PDB and have the ys pasted on the b-factors positions in the PDB file? Smith At 2015-11-18 21:13:05, "David Hall" <li...@cowsandmilk.ne

Re: [PyMOL] placing protein into lipid bilayer

2015-11-14 Thread David Hall
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] Pymol Morph movie error

2015-10-20 Thread David Hall
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 Morph movie error

2015-10-19 Thread David Hall
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 to webGL?

2015-10-18 Thread David Hall
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] Using cartoon putty-like command

2015-10-05 Thread David Hall
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

Re: [PyMOL] creation of a sphere

2015-08-28 Thread David Hall
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] Python from PyMOL or PyMOL from Python?

2015-08-14 Thread David Hall
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] How to find RMSD values using fitting.py using Shell script

2015-07-11 Thread David Hall
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

2015-07-10 Thread David Hall
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

2015-07-10 Thread David Hall
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] how can we rotate torsion angle of a molecule?

2015-07-06 Thread David Hall
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] opensource for commercial use?

2015-07-03 Thread David Hall
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] PyMOL ball stick representation of imatinib in 2HYY

2015-04-23 Thread David Hall
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] APBS plugin not working on both Ubuntu Windows 7

2015-04-14 Thread David Hall
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] green rings

2015-03-10 Thread David Hall
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] Ball and stick model

2015-02-01 Thread David Hall
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] The problem of save molecule to PDB after mutagenesis wizard

2015-01-27 Thread David Hall
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

2015-01-23 Thread David Hall
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] MacPyMOL fink download

2015-01-19 Thread David Hall
(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] sulfated tyrosine's losing connection

2014-12-23 Thread David Hall
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] CGOs

2014-12-22 Thread David Hall
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] DNA representation

2014-12-14 Thread David Hall
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] select state not working

2014-11-05 Thread David Hall
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] CONECT table

2014-10-06 Thread David Hall
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] need help

2014-09-09 Thread David Hall
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] Pymol wrl output

2014-05-04 Thread David Hall
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] Color starting midway between adjacent chains

2014-03-03 Thread David Hall
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] Still need help with fetch and pymol 1.7

2014-01-20 Thread David Hall
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] using pymol commands in a script

2013-09-04 Thread David Hall
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] How to move/turn CGO

2013-08-12 Thread David Hall
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] Leap motion control

2013-07-29 Thread David Hall
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] PyMOL 1.6 pre-release announcement

2013-06-19 Thread David Hall
, 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] Pymol error

2013-05-07 Thread David Hall
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

2013-05-07 Thread David Hall
? 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 error in Mac OS X 10.8.2

2013-05-01 Thread David Hall
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] iPad pymol questions

2012-11-28 Thread David Hall
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] Custom menus and shortcuts?

2012-10-23 Thread David Hall
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] I just built pymol, comes up but hangs on any attempt to view a test pdb.

2012-10-04 Thread David Hall
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

[PyMOL] Pymol Rotated Screen

2012-08-14 Thread David Hall
, 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] Is there or should there be a pymol annotation server?

2012-07-13 Thread David Hall
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

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

2012-03-23 Thread David Hall
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] Editing of the pdb structure

2012-03-20 Thread David Hall
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] Little coordinate cross in Pymol?

2012-02-27 Thread David Hall
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] Open Source PyMOL v1.5.0.1

2012-02-14 Thread David Hall
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] Using super correctly

2012-01-13 Thread David Hall
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

2012-01-13 Thread David Hall
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

2012-01-13 Thread David Hall
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] Installation PyMOL failure in Linux (CentOS)

2011-12-02 Thread David Hall
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] Show Sticks - Turns Molecule Blue

2011-09-11 Thread David Hall
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] Pymol no longer fetches from pdb

2011-03-22 Thread David Hall
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] using pymol from python script

2011-02-17 Thread David Hall
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] Start PyMOL session in web browser

2010-12-19 Thread David Hall
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

[PyMOL] label_size in pymol 1.3 on Mac

2010-12-14 Thread David Hall
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] OpenDX files from opendx.org

2010-10-18 Thread David Hall
. 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] OpenDX files from opendx.org

2010-10-15 Thread David Hall
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

[PyMOL] Super Bug Report

2010-09-22 Thread David Hall
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?

2010-09-22 Thread David Hall
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)

Re: [PyMOL] for evaluation only

2010-04-29 Thread David Hall
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] Load without bonding

2010-04-22 Thread David Hall
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

2010-04-22 Thread David Hall
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

2010-04-22 Thread David Hall
. -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] Automatic modification of structures in PyMOL

2010-04-19 Thread David Hall
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:

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

2010-04-15 Thread David Hall
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?

2010-04-15 Thread David Hall
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] RMSD for ALL ATOMS against ALL ATOMS

2010-04-14 Thread David Hall
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 =

[PyMOL] Fedora Graphics Test Week

2010-04-13 Thread David Hall
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

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