[git-users] Git frozen at (main|merging)

While learning this I have my branch frozen in a state where instead of (main) or any other branch it always shows (main|merging). I've tried an abort instruction that Bing AI suggested and then reboot of my windows, but that odd (main | merging) line remains. I'm ready to reinstall Git. Are

Re: [Rdkit-discuss] 2018.03.1 RDKit release

On Tue, Apr 24, 2018 at 7:03 PM, Andrew Dalke wrote: > > By the way, how do I install RDKit into a specified location? I usually > expect something like --prefix /usr/local, and there's a > CMAKE_INSTALL_PREFIX which defaults to "/usr/local" but "make install" puts >

[ccp4bb] Principal Beamline Scientist Positions at Diamond Light Source

Dear all We currently have three vacancies to lead and develop three of our structural biology beamlines here at Diamond Light Source. Two MX beamlines: the in-situ serial crystallography beamline VMXi (http://www.diamond.ac.uk/Beamlines/Mx/VMXi.html): VMXi –

[ccp4bb] Call for applications for beamtime at Diamond Light Source

Dear all, The call for applications to use Diamond’s MX and BIOSAXS beamlines from October 2018 – March 2019 is now open for users – these beamlines use the BAG proposal system

Re: [PyMOL] Source version?

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

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

[Moo] MooTools in Maintenance Mode

It would appear that JavaScript has caught up with many of the things that MooTools was originally trying to do. I say this not as an expert but after reading this article from over two years ago: https://medium.com/@cpojer/breaking-the-web-with-javascript-48cc406ca98d It seems unlikely that

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

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: [ccp4bb] Charges for using synchrotron MX

Hi Access to Diamond is free to users who publish in the public domain (via peer review access) and chargeable for proprietary access. Please see: http://www.diamond.ac.uk/Users.html and http://www.diamond.ac.uk/industry/ for further information. Thanks Dave From: "ccp4bb@jiscmail.ac.uk"

Re: [Rdkit-discuss] RPM distros

apt install rpm should get you rpmbuild -David > On Nov 15, 2017, at 2:59 PM, Tim Dudgeon wrote: > > OK, makes sense, but I'm building on a Debian system. So neither 'yum install > rpm-build' nor 'apt-get install rpm-build' doesn't work. > > So (sorry for the stupid

Re: [Open Babel] extract a single compound from a multimolecular sdf

rote: > > Hi David, > > 9782 is not the 9782th molecule in the file. > I also will have to loop through sdf for various other numbers. I asked this > as an example. > > Thanks, > Sundar > > On Sun, Nov 5, 2017 at 7:13 PM, David Hall <li...@cowsandmilk.net >

Re: [Open Babel] extract a single compound from a multimolecular sdf

Assuming you want the 9782’th molecule in the file, using the -f and -l options to obabel is what you are looking for. obabel ../input/in-3D.sdf -O 9782.sdf -f 9782 -l 9782 > On Nov 5, 2017, at 7:49 PM, Sundar wrote: > > Hi, > > I was trying to extract a single

Re: [Rdkit-discuss] Conformer generation

Hi Paul, Your reuse of the variable num_confs inside the loop is causing that monotonic decrease. So, if a molecule returns 190 conformers, the next iteration has you only asking for 190 conformers. And so on. Best, David On Wed, Oct 25, 2017 at 12:36 PM, Paul Hawkins

Re: [Open Babel] gen3d doesn't convert all compounds

? > > I had several warnings on Stereochemistry of the molecules and using distance > geometry method instead. > > Thanks, > Sundar > > On Fri, Oct 13, 2017 at 5:56 PM, Sundar Jubilant <jubilantsun...@gmail.com > <mailto:jubilantsun...@gmail.com>> wr

Re: [Open Babel] gen3d doesn't convert all compounds

I assume your second command is actually using output2D.sdf as input? -David > On Oct 13, 2017, at 3:46 PM, Sundar wrote: > > Sure. > Here it goes. > > obabel input.smi -h -r -b -c --unique --gen2d --partialcharge mmff94 -O > output2D.sdf > obabel output3D.sdf

Re: [Rdkit-discuss] Using inchikey as entry

I believe InchiKey uses a 1 way hash (sha-256), so what you are asking for is basically impossible. That is, to go from InchiKey to molecule requires already having a table of molecules corresponding to the InchiKeys. There are various services online that have such lookup tables for a large

Re: [PyMOL] (no subject)

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: [Cdk-user] Computing the LogD

CDK has logP descriptors: ALOGPDescriptor, MannholdLogPDescriptor, and XLogPDescriptor > On Jul 9, 2017, at 5:08 PM, Yannick .Djoumbou wrote: > > Hey all, > > I am looking for a tool to compute the LogD for various compounds. I could > not find any function/module that

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

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

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: [Open Babel] how to use CMAKE_PREFIX_PATH with openbabel

since FindOpenBabel2.cmake uses pkg-config, you can do something like PKG_CONFIG_PATH=~/opt/lib/pkgconfig/ cmake .. That said, I believe there may a better way to link to openbabel with cmake using the files in: ~/opt/lib/cmake/openbabel2/ but I don't know what that is. On Jun 7, 2017, at

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

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

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 >

Re: [Open Babel] How to run readstring in pybel?

That is still the wrong pybel. You should uninstall it (i.e. pip uninstall pybel ) > On May 7, 2017, at 10:38 PM, Peng Yu wrote: > > Hi, I should have installed the correct one. But readstring() is not > available. > print pybel.__dict__.keys() > ['to_bel_path',

[PyMOL] Packaging python3 version of pymol

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

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

, 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

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

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

[ccp4bb] MX Support Scientist Positions at Diamond Light Source

Dear All Two Support Scientists positions are open to work with the MX group at Diamond Light Source, UK (closing date is 26th March). Details for the two posts can be found at: http://www.diamond.ac.uk/Careers/Vacancies/All/023_17_CH.html and

Re: [Open Babel] Using pybel.readstring() and using pybel in Python 2.7

Quoting from Matt Swain a couple weeks ago: > pip install pybel is not correct. That's an unrelated package. Instead, do > pip install openbabel -David > On Mar 9, 2017, at 8:29 AM, Quim Aguirre wrote: > > Hello, > > I am new at using Open Babel software. My

Re: [OpenBabel-Devel] Proposal to overhaul/replace OBElementTable

On Sat, Feb 25, 2017 at 6:06 PM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > 2. The GetAtomicNum() will be a compiled prefix tree using switch > > statements. Right now, if you ask what is the atomic number of Fermium > > (element 100), it will do 100 string comparisons. > > Fair

Re: [Open Babel] OpenBabel for Python 3?

My guess is that your python3 is not at /usr/bin/python3 . Are you sure it isn't at /usr/local/bin/python3 ? Based on your Python.framework information, that would seem to be likely where it is. On that note, we should consider printing an error if the detected version of python is 1.4 ; that

Re: [Open Babel] Batch minimization of ligands

I would iterate over the molecules using pybel, calling localopt on each molecule http://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html?highlight=pybel#pybel.Molecule.localopt On Wed, Dec 21, 2016 at 2:01 PM, ishan wrote: > Dear All, > > I have

Re: [Open Babel] Build a pdb molecule. problem to provide the atoms name

Residue->SetAtomId(atom, string) http://openbabel.org/api/2.3/classOpenBabel_1_1OBResidue.shtml#ad4945233e0066b2b6fbfbe0ed73ae7bc -David > On Nov 18, 2016, at 8:27 AM, ivan petit wrote: > > Hi, > > I’m trying to write a pdb file by using OBMol, OBAtom,... class in

Re: [PyMOL] Atom Order when Saving

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

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

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: [Open Babel] Java bindings for openbabel 2.4.0

I believe swig is needed for creating java (and python) bindings and it says swig was not found -David > On Oct 4, 2016, at 8:10 PM, Jason Ott wrote: > > Hello all! > > I have been trying all day to build the java bindings for open babel. I have: > installed through mac

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

What happens if you do this instead? cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DPYTHON_EXECUTABLE=/usr/bin/python3.4 .. That seems to work for me on Ubuntu 14.04, also, delete your entire build directory and make it again before running the command. -David On Mon, Oct 3, 2016 at 11:05 AM, Philip

Re: [Rdkit-discuss] The RDKit and modern C++

I've used Red Hat's developer toolset for years on RHEL5 to be able to build stuff there using gcc 4.8 and that software has seemed to run fine when shipping to people running RHEL5 and RHEL6. I have "source /opt/rh/devtoolset-2/enable" in my bash profile and that sets all the environment

Re: [Open Babel] Converting PDB to SMILES and matching atom orders

It is a bit of a hack, but for certain applications where I know it is likely fine, I use networkx to do subgraph isomorphism while considering only the elements and not looking at the order of the bonds. I can trivially draw a molecule where this does the wrong thing, but the majority of the

Re: [PyMOL] Modeling protein-dna complex

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: [Open Babel] OpenBabel for Python 3?

do you have python3-dev installed? > On Aug 9, 2016, at 12:57 PM, John wrote: > > PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7 -- What NetFlow Analyzer can do for you? Monitors network

Re: [Open Babel] OpenBabel for Python 3?

If you use the version of openbabel from git (which I would recommend over for the 2.3.2 release), then you can just specify PYTHON_EXECUTABLE as the python3 and it should find everything correctly. $ git clone https://github.com/openbabel/openbabel.git $ cd openbabel $ mkdir build $ cd build $

Re: [Rdkit-discuss] Problems after installing rdkit release 2016_03_1

what does os.environ["PYTHONPATH”] show when you are in IDLE? > On Jul 19, 2016, at 12:26 PM, Jessica Krause wrote: > > Dear All, > > I installed the new release of Rdkit in Ubunutu 16.04. I am not able to > import rdkit module in my IDLE and Spyder after installing

Re: [Open Babel] GAFF2 in babel?

Is there documentation beyond the Amber source code? Do you know if the difference is just using gaff2.dat instead of gaff.dat? On Wed, Jul 13, 2016 at 4:58 PM, Albert wrote: > Hello: > > I noticed that GAFF2 is released in recent Amber 16. I am just wondering > how can

Re: [Open Babel] GAFF2 in babel?

, Jul 14, 2016 at 9:54 AM, David Hall <li...@cowsandmilk.net> wrote: > Is there documentation beyond the Amber source code? Do you know if the > difference is just using gaff2.dat instead of gaff.dat? > > > > On Wed, Jul 13, 2016 at 4:58 PM, Albert <mailmd2...@gmail.com&

Re: [Open Babel] Unable to import pybel in Python

The below is dependent on how you import pybel you did "import pybel", which imports the pybel functions with a "pybel." prefix as shown in your efforts to run things. Some of the examples in the documentation implicitly do "from pybel import *" so the functions are imported without a prefix.

Re: [PyMOL] Video in Ubuntu Linux

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

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

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

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: [Rdkit-discuss] GetMol and GetMolFrags in C++

When I want to replicate one of RDKit’s python functions in C++, I go to the source. RDKit has very readable wrappers that make this a surprisingly nice approach (many other pieces of software have pretty ugly wrappers, so this is a major compliment to RDKit). For this, I think the source is:

Re: [PyMOL] pymolrc location

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

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: [Open Babel] SMARTS query

I’m confused by why there is -!: Your description suggests this to me: [cH]1[cH]n[cH][cH]c1[r5] It at least looks nice on http://smartsview.zbh.uni-hamburg.de/smartsview/calculate?method=get > On Mar 29, 2016, at 6:33 AM, Gravestock David GBJH > wrote: >

Re: [Open Babel] - problem with PHP script

Have you tried setting enable_dl to on? http://php.net/manual/en/info.configuration.php#ini.enable-dl Or adding it as an extension that is loaded when PHP starts? http://php.net/manual/en/ini.core.php#ini.extension Note, with either options, you probably need to restart the web server after

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

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

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: [Talk-se] Operator på postlådor

Bring och PostNord är i och för sig de enda operatörer som har utdelning över stora delar av landet men det finns även lokala postoperatörer. Lista finns hos PTS ( https://www.pts.se/upload/Ovrigt/Post/postoperatorer-150930.pdf) men huruvida de har brevlådor eller inte anges inte. / David On

Re: [PyMOL] pdb edition

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: Eigenvalue solver

(I don't know anything spark specific, so I'm going to treat it like a Breeze question...) As I understand it, Spark uses ARPACK via Breeze for SVD, and presumably the same approach can be used for EVD. Basically, you make a function that multiplies your "matrix" (which might be represented

Re: [PyMOL] optimize and open babel troubles

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

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

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

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

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

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

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

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

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

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?

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: [Rdkit-discuss] cis/trans directional bond and smiles strings in python

That behavior appears to all be in python; as you’ve written it, your smiles string has a newline before rdkit ever sees it: >>> print 'C/C=C\n1nc(nn1)C' C/C=C 1nc(nn1)C >>> print 'C/C=C\\n1nc(nn1)C' C/C=C\n1nc(nn1)C > On Oct 12, 2015, at 4:37 PM, Michael Reutlinger wrote: >

Re: [ccp4bb] Advice for Structure Determination

Diamond and a variety of other SRs have these devices. Check out their webpages for available equipment or contact directly. Dave -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans Sent: 05 October 2015 09:59 To: ccp4bb Subject: Re:

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

[kde-doc-english] Documentation

Although I've been working with computers for 30 years I've found your description of how to use KWallet and KWallet Manager very confusing. You ramble though without mentioning important details. The KWallet Handbook - Introduction - Create a Wallet what exactly is a wallet Use the

Re: [Rdkit-discuss] NP-score and SA-score datas

This is the easiest way. python -c "import json,gzip,pickle; print json.dumps(pickle.load(gzip.open('publicnp.model.gz', 'rb')))" > publicnp.model.json Modify as appropriate for the other file. -David On Sun, Sep 6, 2015 at 11:48 AM, Guillaume GODIN < guillaume.go...@firmenich.com> wrote: >

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] 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: [Open Babel] pybel.write() produces truncated pdbqt? (R. K. Belew)

It seems I can reproduce the segfault on OS X Yosemite, but not on Ubuntu 14.04. -David On Aug 4, 2015, at 8:02 PM, R. K. Belew rbe...@ucsd.edu wrote: update, if anyone is interested: it seems quite clear the bug is in the PDBQT output filter: obabel file1.pdbqt -O file2.pdbqt

Re: [ccp4bb] Off-topic: Transfering data from Diamond

We'd much rather you connected to Diamond and pushed data back though: http://www.diamond.ac.uk/Beamlines/Mx/Common/Common-Manual/Data-Backup/Remote-Backup.html Thanks Dave -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jonathan Davies Sent:

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: [Open Babel] Partial charge on OSX system

As far as I know, the current ibabel ( http://www.macinchem.org/ibabel/ibabel3.php http://www.macinchem.org/ibabel/ibabel3.php ) requires that you install openbabel first. Have you checked that the command line openbabel has the qeq charges? -David On Jul 3, 2015, at 1:34 AM, Guoyi Li

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] 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: [Rdkit-discuss] Memory management during conformer generation

On Jun 27, 2015, at 6:05 AM, Dmitri Maziuk dmaz...@bmrb.wisc.edu wrote: On 6/26/2015 9:48 AM, az wrote: Thanks Jean-Paul You're right that I eat up a lot of memory with large files but I think its not the whole story. If it were, my memory should come back each time a new file is being

Re: [Rdkit-discuss] rdkit can not read sodium hexaflourophosphate molfile

See this commit if you want to know how it has been fixed in the development code. https://github.com/rdkit/rdkit/commit/672f8ea2008ca88ee4c9dc91eab74894916a https://github.com/rdkit/rdkit/commit/672f8ea2008ca88ee4c9dc91eab74894916a -David On May 21, 2015, at 4:26 AM, Contact

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] 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: [Open Babel] Protonation issues in 2.3.2 version

both these molecules perform as expected in the latest code on github. https://github.com/openbabel/openbabel -David On Thu, Mar 19, 2015 at 9:42 AM, ggbs luigi.capofe...@gmail.com wrote: Dear Users, I repropose a problem I already mentioned some time ago. I am using openbabel to

Re: [Open Babel] error by installing open babel for mac

Can you tell us what is in ob-src? Presumably it does not have CMakeLists.txt ... That is, what does $ ls ../ob-src say? -David On Mon, Mar 16, 2015 at 1:08 PM, Allassane Camara allassane.cam...@minddivision.net wrote: I used this link for my installation:

Re: [mllib] Is there any bugs to divide a Breeze sparse vectors at Spark v1.3.0-rc3?

. Thanks. Deb On Mar 15, 2015 9:39 PM, David Hall david.lw.h...@gmail.com wrote: snapshot is pushed. If you verify I'll publish the new artifacts. On Sun, Mar 15, 2015 at 1:14 AM, Yu Ishikawa yuu.ishikawa+sp...@gmail.com wrote: David Hall who is a breeze creator told me that it's a bug

Re: [mllib] Is there any bugs to divide a Breeze sparse vectors at Spark v1.3.0-rc3?

ping? On Sun, Mar 15, 2015 at 9:38 PM, David Hall david.lw.h...@gmail.com wrote: snapshot is pushed. If you verify I'll publish the new artifacts. On Sun, Mar 15, 2015 at 1:14 AM, Yu Ishikawa yuu.ishikawa+sp...@gmail.com wrote: David Hall who is a breeze creator told me that it's a bug

Re: [mllib] Is there any bugs to divide a Breeze sparse vectors at Spark v1.3.0-rc3?

snapshot is pushed. If you verify I'll publish the new artifacts. On Sun, Mar 15, 2015 at 1:14 AM, Yu Ishikawa yuu.ishikawa+sp...@gmail.com wrote: David Hall who is a breeze creator told me that it's a bug. So, I made a jira ticket about this issue. We need to upgrade breeze from 0.11.1

Re: [OpenBabel-Devel] I installed open babel 2.3.90, but I still can't import pybel

Not sure what you mean by “python was disabled”, if you cannot run python on a mac, there is probably some major issue. As described in the python documentation, OS X comes with python installed already ( https://docs.python.org/2/using/mac.html https://docs.python.org/2/using/mac.html ).

Re: [OpenBabel-Devel] I installed open babel 2.3.90, but I still can't import pybel

What version of CMake are you using? -David -- 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 things parallel

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