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

[David Hall]

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 there any alternatives?

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Re: [Rdkit-discuss] 2018.03.1 RDKit release

[David Hall]

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
> it in the build directory, like
>
>   /Users/dalke/ftps/rdkit-Release_2018_03_1
>
>
You need to turn off RDK_INSTALL_INTREE

-David
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[ccp4bb] Principal Beamline Scientist Positions at Diamond Light Source

[David Hall]

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 – http://www.diamond.ac.uk/Careers/Vacancies/All/038_18_KR.html

the tuneable variable microfocus MX beamline I04 
(http://www.diamond.ac.uk/Beamlines/Mx/I04.html):

I04 - http://www.diamond.ac.uk/Careers/Vacancies/All/045_18_KR.html

And B21 BIOSAXS beamline 
(http://www.diamond.ac.uk/Beamlines/Soft-Condensed-Matter/small-angle/B21.html):

B21 - http://www.diamond.ac.uk/Careers/Vacancies/All/044_18_KR.html 

For informal enquiries please contact Martin Walsh, Rob Rambo or myself.

Best wishes

Dave Hall
Diamond Light Source



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

[David Hall]

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 
(http://www.diamond.ac.uk/Users/UserGuide/Proposals/Access-Routes.html).  To 
ensure you can avail of beamtime at Diamond during the ESRF upgrade period we 
strongly advise that you submit a proposal within the current call deadline 
which is the 4th April at 17:00 hours – please note carefully this deadline in 
your diaries. Successful applications will then be able to access the Diamond 
MX and BIOSAXS beamlines from October 2018. Successful BAG proposals are valid 
for 2 years and the Diamond BAG system mirrors generally the ESRF BAG system. 
Hence, successfully peer-reviewed BAG applications that have been submitted in 
the current call will have access to Diamond MX and BIOSAXS beamlines for the 
entirety of the ESRF upgrade period.

To start your application as a Diamond user either log in to or as a new user 
simply register in our User Administration Software (UAS) - 
https://uas.diamond.ac.uk/uas/#register.
…..
Information on the beamline capabilities can be found at 
http://www.diamond.ac.uk/Beamlines.html. The MX beamlines are I03, I04, I04-1, 
I23 and I24 and the BioSAXS beamline is B21. Note most of the beamlines are 
highly automated and available via remote access.
…..
Access to Diamond for European users is supported through the H2020 iNEXT 
project http://inext-eu.org.

Informal inquiries can be directed to Dave Hall 
david.h...@diamond.ac.uk for MX specific 
questions, Rob Rambo 
robert.ra...@diamond.ac.uk for BIOSAXS 
queries and Martin Walsh 
martin.wa...@diamond.ac.uk for queries 
related to iNEXT and support.

Thanks

Dave Hall
Diamond Light Source


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Re: [PyMOL] Source version?

[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 repository in early 2018.

On Fri, Jan 12, 2018 at 4:48 PM, CAS IT Services  wrote:

> Disclaimer:  I am not a chemist, nor a PyMol user.  I am an IT guy trying
> to assist students and educators with installing PyMol.
>
> I am pretty sure I can figure out how to get PyMol working from the
> compiled source that Christoph Gohlke offers for download, but I thought I
> should try to compile it myself.
>
> Does anyone know why there is a discrepancy between the version of the
> downloadable source tarball found here (v1.8.6.0) and the version Christoph
> offers (v1.9.0.0)?
>
> Assuming that I trust Christoph's offering, what changed between 1.8.6.0
> and 1.9.0.0?
>
> Also, does anyone know if 1.9.0.0 is the end for open source PyMol?  Has
> Schrodinger completed a conversion to a fully commercial (and likely
> profitable) version with v2.0?
>
> Thanks.
>
> 
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Re: [PyMOL] Record and load coordinates

[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 
> thousands and thousands of rows. This could prove very impractical if I want 
> to stores those coordinates in a script.
> 
> To circumvent this issue I tried the following but it did not seem to work:
> 
> print cmd.get_object_matrix('%prot')   # to obtain my coordinates in a 4X4 
> format
> 
> PyMOL>cmd.transform_selection("su", [[1.0,0.0,0.0,0.0], [0.0,1.0,0.0,0.0], 
> [0.0,0.0,1.0,0.0], [0.0,0.0,0.0,1.0]], homogenous=1)
> CmdTransformSelection-DEBUG: bad matrix
> 
> PyMOL>cmd.transform_selection("su", 
> [1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0], 
> homogenous=1)  # In that case nothing happens
> 
> What do you think I am doing wrong?
> 
> Many thanks,
> 
> Ben
> 
> --
> 
> Dr Benjamin Bailly | Research Scientist – von Itzstein group
> 
> Institute for Glycomics
> Griffith University | Gold Coast campus | QLD 4222 | Institute for Glycomics 
> (G26) Room 4.30
> 
> 
> 
> ___
> 
> Benjamin Bailly 
> +61 479 17 66 34 (Australia)
> 
>> On 11 January 2018 at 17:26, Thomas Holder  
>> wrote:
>> Hi Ben,
>> 
>> The coordinates argument must have a Nx3 shape, that means:
>> len(coordinates) = number of atoms
>> len(coordinates[0]) = 3
>> 
>> You can use numpy's reshape() function:
>> 
>> import numpy
>> coordinates = numpy.asfarray(coordinates).reshape((-1,3))
>> cmd.load_coords(coordinates, '%prot')
>> 
>> I recommend to prefix the object name with "%" to unambiguously address a 
>> named object or selection. I mention this because I just ran into a common 
>> selection language ambiguity problem myself: I named my object "obj01" and 
>> then pasted your code without changing the object name. The error message 
>> was "atom count mismatch" instead of "invalid selection name". Why? Because 
>> "prot" was evaluated as the selection keyword "protected", so it was a valid 
>> (but empty) selection expression.
>> 
>> Cheers,
>>   Thomas
>> 
>> > On Jan 11, 2018, at 7:43 AM, Benjamin Bailly  wrote:
>> >
>> > Hi everyone,
>> >
>> > I have been scratching my head quite a bit on this one, I am sure there 
>> > must be a simple solution but I can't seem to figure it out.
>> >
>> > In short, I would like to record the spacial coordinates of a protein so 
>> > that when I run my script I can fetch it from the PDB and place it exactly 
>> > where I would like it to be.
>> >
>> > I used this command to obtain the coordinates, and here is the output I 
>> > get:
>> >
>> > PyMOL>print cmd.get_coords('prot')
>> > [[159.402 258.709 204.556]
>> >  [159.932 259.514 204.223]
>> >  [158.951 258.206 203.792]
>> >  ...
>> >  [117.662 263.108 309.314]
>> >  [115.591 265.038 307.88 ]
>> >  [116.386 259.713 306.195]]
>> >
>> > To load the position in my script I know that I should be able to use the 
>> > following command however I can not figure out the format required:
>> >
>> > cmd.load_coords(coordinates, 'prot')
>> >
>> > I tried to use all the floats the ones after the other like [1.1, 2.2, 
>> > 3.3,...] and I was close to making it work, but it said the numbers of 
>> > atoms did not match. I read that I should probably used a numpy array but 
>> > I am not sure of its format.
>> >
>> > Your help would be much appreciated,
>> >
>> > Many thanks
>> >
>> > Ben
>> 
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>> 
> 
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[Moo] MooTools in Maintenance Mode

[David Hall]

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 MooTools will be updated again. 

Over time we will move on and use later generation frameworks but for now 
we still have websites using MooTools.

I assume it is likely with the rapid development of browsers that our sites 
using MooTools may become broken in similar ways described in the article.

Do we think there are still people who are willing and able to maintain 
MooTools in such a situation?

As a diminishing group of users it must be in our own interests to ensure 
MooTools can be maintained by ourselves being or learning to be those 
maintainers?

What do other current users think?

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

[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 
> thought I had is that you could save coordinates from one session and then 
> same coordinates from the other session.
> 
> lastly, open an another session and do the following:
> 
> load state1.pdb 
> load state2.pdb, state1
> 
> cheers,
> David 
> 
>  
>> On Dec 28, 2017, at 10:16 AM, COSTA Maria > > wrote:
>> 
>>  
>> Dear PyMOL users,
>>  
>> I would like to do a movie showing a conformational change of my molecule. I 
>> guess that for that purpose I need to store the views of the two states but 
>> the problem is that my two states are in two different pymol sessions. Is 
>> there a way to combine the two views in the same pymol file ? or I need to 
>> redo the views in the same pymol session from the beginning ?
>> I hope I’m being clear enough….
>>  
>> Thank you so much for any help !
>>  
>> Maria Costa
>>  
>> I2BC – UMR9198
>> 91198 Gif-sur-Yvette cedex
>> France  
>> --
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>> 
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>> )
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>> 
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Re: [ccp4bb] Charges for using synchrotron MX

[David Hall]

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"  on behalf of KL Ho 
<05c3a58110fa-dmarc-requ...@jiscmail.ac.uk>
Reply-To: KL Ho 
Date: Thursday, 28 December 2017 at 02:37
To: "ccp4bb@jiscmail.ac.uk" 
Subject: [ccp4bb] Charges for using synchrotron MX

Dear All,

I have a quick question about the charges of using the MX station (eg. I03 in 
Diamond). Assuming that the cost is not covered by Diamond, how much do you 
think the charges would be? Thank you.

Happy New Year.

Best wishes,
Kok Lian

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Re: [Rdkit-discuss] RPM distros

[David Hall]

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 question) can DEBs only be built on a Debian based 
> system and RPMs om a Red Hat based system? 
> 
>> On 15/11/2017 19:31, Paolo Tosco wrote:
>> Hi Tim,
>> 
>> It looks like you are missing the rpmbuild binary on the machine where you 
>> are trying to build the RPM.
>> Issuing a
>> yum install rpm-build
>> as root should get it installed.
>> 
>> Cheers,
>> p.
>> 
>>> On 11/15/17 19:00, Tim Dudgeon wrote:
>>> So this now seems to have been merged to master so I gave it a try:
>>> 
>>> root@f083c3e3b6a1:/rdkit/build# cmake -DRDK_BUILD_INCHI_SUPPORT=ON 
>>> -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/ ..
>>> -- Could NOT find InChI in system locations (missing:  INCHI_LIBRARY 
>>> INCHI_INCLUDE_DIR)
>>> CUSTOM_INCHI_PATH = /rdkit/External/INCHI-API
>>> -- Found InChI software locally
>>> -- Boost version: 1.62.0
>>> -- Found the following Boost libraries:
>>> --   python
>>> Python Install directory /usr/lib/python2.7/dist-packages
>>> -- Could NOT find Eigen3 (missing:  EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) 
>>> (Required is at least version "2.91.0")
>>> Eigen3 not found, disabling the Descriptors3D build.
>>> -- Boost version: 1.62.0
>>> -- Found the following Boost libraries:
>>> --   thread
>>> --   system
>>> --   chrono
>>> --   date_time
>>> --   atomic
>>> -- Boost version: 1.62.0
>>> -- Found the following Boost libraries:
>>> --   serialization
>>> == Using strict rotor definition
>>> == Updating Filters.cpp from pains file
>>> == Done updating pains files
>>> -- Boost version: 1.62.0
>>> -- Found the following Boost libraries:
>>> --   regex
>>> -- Configuring done
>>> -- Generating done
>>> -- Build files have been written to: /rdkit/build
>>> 
>>> 
>>> root@f083c3e3b6a1:/rdkit/build# cpack -G DEB
>>> CPack: Create package using DEB
>>> CPack: Install projects
>>> CPack: - Run preinstall target for: RDKit
>>> CPack: - Install project: RDKit
>>> CPack: -   Install component: runtime
>>> CPack: -   Install component: base
>>> CPack: -   Install component: data
>>> CPack: -   Install component: docs
>>> CPack: -   Install component: dev
>>> CPack: -   Install component: python
>>> CPack: -   Install component: extras
>>> CPack: Create package
>>> CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Development.deb 
>>> generated.
>>> CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Extras.deb 
>>> generated.
>>> CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Python.deb 
>>> generated.
>>> CPack: - package: /rdkit/build/RDKit-2018.03.1.dev1-Linux-Runtime.deb 
>>> generated.
>>> 
>>> 
>>> root@f083c3e3b6a1:/rdkit/build# cpack -G RPM
>>> CPack: Create package using RPM
>>> CPack: Install projects
>>> CPack: - Run preinstall target for: RDKit
>>> CPack: - Install project: RDKit
>>> CPack: -   Install component: runtime
>>> CPack: -   Install component: base
>>> CPack: -   Install component: data
>>> CPack: -   Install component: docs
>>> CPack: -   Install component: dev
>>> CPack: -   Install component: python
>>> CPack: -   Install component: extras
>>> CPack: Create package
>>> CMake Error at /usr/share/cmake-3.7/Modules/CPackRPM.cmake:1573 (message):
>>>   RPM package requires rpmbuild executable
>>> Call Stack (most recent call first):
>>>   /usr/share/cmake-3.7/Modules/CPackRPM.cmake:2442 
>>> (cpack_rpm_generate_package)
>>> 
>>> 
>>> CPack Error: Error while execution CPackRPM.cmake
>>> CPack Error: Error while execution CPackRPM.cmake
>>> CPack Error: Error while execution CPackRPM.cmake
>>> CPack Error: Error while execution CPackRPM.cmake
>>> CPack Error: Problem compressing the directory
>>> CPack Error: Error when generating package: RDKit
>>> 
>>> So it looks like the building the debs works OK (I didn't test them) but 
>>> building rpms fails.
>>> 
>>> I'm probably doing something stupid here as I'm not that familiar with 
>>> cmake and cpack. 
>>> 
>>> 
 On 10/11/2017 00:03, Francois BERENGER wrote:
> On 11/08/2017 08:47 PM, Tim Dudgeon wrote: 
> There is mention of RPM distributions of RDKit 
> (https://copr.fedorainfracloud.org/coprs/giallu/rdkit/). 
> 
> But on trying these: 
> 
> 1. the distro is based on the 2017_03_1 release 
> 2. it fails due to missing libinchi.so.1 dependency. 
 
 In the bugtracker, there is an issue about the .deb: 
 
 https://github.com/rdkit/rdkit/issues/911 
 
 and there is a pull request by Patrick Avery 
 to fix them: 
 
 https://github.com/rdkit/rdkit/pull/1580 
 
 Maybe you can read the pull request, replace DEB by RPM and see 
 if that produces usable RPMs for your distro. 
 
> This is presumably no longer being maintained? 
> 

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

[David Hall]

It appears there is a bug where numeric titles do not work with string 
comparisons. Leave out the single quotes and it works (on my machine).

obabel ../input/in-3D.sdf -O 9782.sdf --filter "title=9782"


> On Nov 5, 2017, at 8:17 PM, Sundar <jubilantsun...@gmail.com> wrote:
> 
> 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 
> <mailto:li...@cowsandmilk.net>> wrote:
> 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 <jubilantsun...@gmail.com 
> > <mailto:jubilantsun...@gmail.com>> wrote:
> >
> > Hi,
> >
> > I was trying to extract a single molecule from a multimolecular sdf.
> > I used the following but it didn't work.
> >
> > obabel ../input/in-3D.sdf -O 9782.sdf --filter "title='9782'"
> >
> > Let me how can I do this.
> >
> > Thanks,
> > Jubilant
> > --
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> > engaging tech sites, Slashdot.org! 
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> > <https://lists.sourceforge.net/lists/listinfo/openbabel-discuss>
> 
> 

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

[David Hall]

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 molecule from a multimolecular sdf.
> I used the following but it didn't work.
> 
> obabel ../input/in-3D.sdf -O 9782.sdf --filter "title='9782'"
> 
> Let me how can I do this.
> 
> Thanks,
> Jubilant
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Re: [Rdkit-discuss] Conformer generation

[David Hall]

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 
wrote:

> Hello,
>
>
> I have run into a problem with using the RDKit to generate conformers of
> molecules. I am using the following code:
>
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
> from timeit import default_timer as timer
>
>
>
> def GenerateDGConfs(m,num_confs,rms):
> start_time = timer()
> ids = AllChem.EmbedMultipleConfs(m, numConfs=num_confs,
> pruneRmsThresh=rms, maxAttempts=200,enforceChirality=True)
> for id in ids:
> AllChem.MMFFOptimizeMolecule(m, confId=id)
>
> end_time = timer()
> time_diff = end_time - start_time
> #print ("Normal DG = %0.2f" % time_diff)
>
> return m, list(ids), time_diff
>
>
> w = Chem.SDWriter("%s/%s" % (rootdir,"My_conformers.sdf))
>
>
> suppl = Chem.SDMolSupplier("%s/%s" % (rootdir,"My_molecules.sdf"))
> num_confs = 200
> rmsd = 0.5
>
>
> for mol in suppl:
>
> if mol is None: continue
>
> Chem.AssignAtomChiralTagsFromStructure(mol)
> mol1 = Chem.AddHs(mol)
>
> conf_mol, id_list, time_diff = GenerateDGConfs(mol1,num_confs,rmsd)
> num_confs = conf_mol.GetNumConformers()
> for id in id_list:
> w.write(conf_mol, confId=id)
>
>
>
> w.flush()
> w.close()
>
>
> What I see from this is as I go through the molecules in the input file
> the number of conformers returned declines monotonically, starting close to
> the 200 I set as a maximum to around 10 after a few thousand molecules have
> been processed (this applies whether I use 'normal' DG or the ETKDG method.
> As I am a new user of RDKit I am sure I missed something obvious but I
> cannot see it.
>
> Also, once I generate the conformers what is best way to cluster them by
> RMSD so that each conformer has a minimum RMSD to all the others in the set?
>
>
> Any help would be gratefully received.
>
>
>
> Paul.
>
> 
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Re: [Open Babel] gen3d doesn't convert all compounds

[David Hall]

Are you able to provide files that show this? Or reduce it to single compounds 
that are being eliminated that can be shared?


> On Oct 24, 2017, at 8:53 PM, Sundar <jubilantsun...@gmail.com> wrote:
> 
> Hi,
> 
> I am refreshing this thread for an answer.
> 
> obabel input.smi -h -r -b -c --unique --gen2d --partialcharge mmff94 -O 
> output2D.sdf
> obabel output2D.sdf --gen3d -O output3D.sdf
> 
> output2D.sdf contains 7581 compounds exactly as in input.smi but
> output3D.sdf only has 881 compounds.
> 
> Can someone tell me why this happens?
> 
> 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>> wrote:
> Yes. 
> 
> Sundar Thangapandian
> 
> On Oct 13, 2017, at 3:08 PM, David Hall <li...@cowsandmilk.net 
> <mailto:li...@cowsandmilk.net>> wrote:
> 
>> I assume your second command is actually using output2D.sdf as input?
>> 
>> -David
>> 
>> On Oct 13, 2017, at 3:46 PM, Sundar <jubilantsun...@gmail.com 
>> <mailto:jubilantsun...@gmail.com>> wrote:
>> 
>>> Sure.
>>> Here it goes.
>>> 
>>> obabel input.smi -h -r -b -c --unique --gen2d --partialcharge mmff94 -O 
>>> output2D.sdf
>>> obabel output3D.sdf --gen3d -O output3D.sdf
>>> 
>>> output2D.sdf contains 7581 compounds exactly as in input.smi but
>>> output3D.sdf only has 881 compounds.
>>> 
>>> Thanks,
>>> Sundar
>>> 
>>> 
>>> On Fri, Oct 13, 2017 at 2:18 PM, Noel O'Boyle <baoille...@gmail.com 
>>> <mailto:baoille...@gmail.com>> wrote:
>>> I'm a bit confused. Can you write out in full the commands you used?
>>> 
>>> On 13 Oct 2017 6:53 p.m., "Sundar" <jubilantsun...@gmail.com 
>>> <mailto:jubilantsun...@gmail.com>> wrote:
>>> Hi Noel,
>>> 
>>> No. I used --unique option to generate 2D coformations from smiles and got 
>>> ~7000 compounds.
>>> While generating 3D from the 2D I only used --gen3d
>>> 
>>> Thanks,
>>> Jubilant
>>> 
>>> On Fri, Oct 13, 2017 at 11:28 AM, Noel O'Boyle <baoille...@gmail.com 
>>> <mailto:baoille...@gmail.com>> wrote:
>>> Hi there,
>>> 
>>> The "--unique" option removes duplicates. My guess is that you have only 
>>> 800 unique compounds.
>>> 
>>> Regards,
>>> - Noel
>>> 
>>> On 13 October 2017 at 11:58, Sundar <jubilantsun...@gmail.com 
>>> <mailto:jubilantsun...@gmail.com>> wrote:
>>> Hi everyone,
>>> 
>>> I am pretty new to OB. I am trying to convert a database of compounds 
>>> (~7000) from smiles to 3D.
>>> I first converted them into 2D using -h -r --unique -b -c --partialcharge 
>>> mmff94
>>> followed by --gen3d. 
>>> It only converted ~800 compounds saying nothing about other conformers.
>>> Any idea it behaves this way?
>>> 
>>> -Jubilant
>>> 
>>> --
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>>> <https://lists.sourceforge.net/lists/listinfo/openbabel-discuss>
>>> 
>>> 
>>> 
>>> 
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> 

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

[David Hall]

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 --gen3d -O output3D.sdf
> 
> output2D.sdf contains 7581 compounds exactly as in input.smi but
> output3D.sdf only has 881 compounds.
> 
> Thanks,
> Sundar
> 
> 
>> On Fri, Oct 13, 2017 at 2:18 PM, Noel O'Boyle  wrote:
>> I'm a bit confused. Can you write out in full the commands you used?
>> 
>>> On 13 Oct 2017 6:53 p.m., "Sundar"  wrote:
>>> Hi Noel,
>>> 
>>> No. I used --unique option to generate 2D coformations from smiles and got 
>>> ~7000 compounds.
>>> While generating 3D from the 2D I only used --gen3d
>>> 
>>> Thanks,
>>> Jubilant
>>> 
 On Fri, Oct 13, 2017 at 11:28 AM, Noel O'Boyle  
 wrote:
 Hi there,
 
 The "--unique" option removes duplicates. My guess is that you have only 
 800 unique compounds.
 
 Regards,
 - Noel
 
> On 13 October 2017 at 11:58, Sundar  wrote:
> Hi everyone,
> 
> I am pretty new to OB. I am trying to convert a database of compounds 
> (~7000) from smiles to 3D.
> I first converted them into 2D using -h -r --unique -b -c --partialcharge 
> mmff94
> followed by --gen3d. 
> It only converted ~800 compounds saying nothing about other conformers.
> Any idea it behaves this way?
> 
> -Jubilant
> 
> --
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> 
 
>>> 
> 
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Re: [Rdkit-discuss] Using inchikey as entry

[David Hall]

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 number of molecules 
(e.g. NCI CADD resolver, PubChem).

-David


> On Aug 1, 2017, at 9:05 PM, Kazmierczak Stéphane  
> wrote:
> 
> Hello, I would like to draw molecules with rdkit, but only have inchikeys.
> I compiled rdkit with inchi support but it seems that I can only output 
> inchikeys but not import them. 
> 
> Are there any api function that I am missing ?
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Re: [PyMOL] (no subject)

[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 pymol will now crash randomly.

Here's how I got to the old version that worked

$ cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/
$ git checkout 46e1ef94247cd2fb9555b724c051e8907996 -- tcl-tk.rb
$ cd ../../homebrew-science/
Edit the pymol.rb file so that it depends on "tcl-tk" instead of
"homebrew/dupes/tcl-tk"

$ brew remove tcl-tk python pymol
$ brew install pymol
$ brew pin tcl-tk

Really, I uninstalled all my homebrew packages and then reinstalled
everything because some of their changes over the last 6 months had made
things oddly broken. If you want to do the same, you can try this:

$ brew list > installed
$  wrote:

> Hi,
> pymol external gui menus missing, I have compiled pymol in mac os by using
> brew.
>
> Anyone can provide some suggestions?
>
> Jacky
>
> --
> Lei Zhao, Ph.D. & M.D.
> Associate Professor
> National Clinical Research Center for Normal Aging and Geriatric
> National Engineering Research Center for Antibody Medicine
> The Key Lab of Normal Aging and Geriatric
> PLA General Hospital
> Beijing 100853
> P.R.China
> Tel:86-15210661966
>
>
> 
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Re: [Cdk-user] Computing the LogD

[David Hall via Cdk-user]

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 computes this property. Is there one? If 
> not, what would you recommend as a freely accessible library that computes 
> the LogD?
> 
> Thanks,
> Yannick
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Re: [PyMOL] Why does Pymol display the chain as disconnected?

[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 




> On Jun 20, 2017, at 6:09 AM, Ahmad Abdelzaher  wrote:
> 
> http://www.rcsb.org/pdb/explore.do?structureId=1ax8
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Re: [PyMOL] Error aroused when install pymol from source

[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, 2017, at 10:18 PM, sunyeping via PyMOL-users 
>  > wrote:
> 
> Dear pymol users,
> 
> I am trying to intall pymol on my centos 7 system from source using the 
> mothed discribed at pymolwiki (https://pymolwiki.org/index.php/Linux_Install 
> )
> Everything was ok until I run install script: 
> 
> #!/bin/bash -e
> 
> prefix=/opt/pymol-svn
> modules=$prefix/modules
> 
> # If you want to install as root, then split this line up in "build"
> # and "install" and run the "install" with "sudo"
> python2.7 setup.py build install \
> --home=$prefix \
> --install-lib=$modules \
> --install-scripts=$prefix
> 
> I got a error message and the installation process was terminated:
> 
> In file included from contrib/mmtf-c/mmtf_parser.cpp:31:0:
> contrib/mmtf-c/mmtf_parser_private.h:38:23: fatal error: msgpack.hpp: No such 
> file or directory
>  #include 
>^
> compilation terminated.
> 
> I then installed msgpack by yum command and tried to run the pymol install 
> script again, but the same error still occurred.
> 
> I googled this problem but cannot find a answer. Could anyone help me here?
> 
> Best regards.
> 
> Yeping Sun
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Re: [Open Babel] how to use CMAKE_PREFIX_PATH with openbabel

[David Hall]

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 4:22 AM, Davide Olianas  wrote:

Hello,

the openbabel version shipped with my distribution (ubuntu 16.04) is quite
old; I’d like to link my programs to the most recent one, which I installed
in ~/opt using the option CMAKE_INSTALL_PREFIX=~/opt.

Sadly, the environment variable CMAKE_PREFIX_PATH doesn’t appear to be used
by FindOpenBabel2.cmake. I copied this module because OpenBabel can’t be
found by default (is this a packaging problem of the distribution? If not,
could it be possible to add FindOpenBabel2.cmake to OpenBabel source such
that package maintainers can add the module?)

You can clone this repo  for a
minimal (not) working example. If you have vagrant installed, just run vagrant
up to set up a clean virtual machine. If you don’t use vagrant, you can
look bootstrap.sh for the commands to reproduce the problem.

Thanks for any help,
Davide
​

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

[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 structures of
> molecules?
> Then why not PyMol be capable of yielding such values for individual bonds?
> 
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Re: [PyMOL] show surface on pymol

[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 
> have a problem and maybe need your help. I want to show surface of a ligand 
> in which there is a methylated lysine. Other residues are OK except the 
> methylated lysine. Could you help me to deal with this problem? Should I 
> install any plugin that can recognize molecules like methylated lysine or 
> anything? Thanks a lot.
> 
> Yanchao Liu
> 
> Shanghai Institute of Biochemistry and Cell Biology.
> 
> Shanghai Institutes for Biological Sciences.
> 
> Chinese Academy of Sciences.
> 
> 320 Yueyang Road ,Shanghai 200031,China.
> 
> 
>  
> 
> 
> 
> 
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Re: [Open Babel] How to run readstring in pybel?

[David Hall]

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', 'from_json', 'from_cx_path', 'utils', 'parser',
> '__path__', 'manager', 'to_json', 'io', 'canonicalize', 'from_pickle',
> 'to_pickle', 'from_jsons', 'to_bytes', 'from_cx', '__all__',
> 'BELGraph', 'graph', 'from_cx_jsons', 'NDEX_SOURCE_FORMAT',
> '__package__', 'to_bel', 'from_lines', 'from_cx_json', '__doc__',
> 'to_neo4j', '__title__', 'to_cx_json', '__license__', 'to_jsons',
> '__builtins__', '__file__', 'to_cx_jsons', '__author__', 'to_csv',
> 'from_json_dict', 'from_path', '__name__', 'from_url', '__version__',
> 'constants', 'to_bel_lines', '__url__', '__copyright__',
> 'to_json_dict', '__description__', '__email__', 'to_cx',
> 'from_database', 'to_graphml', 'to_database', 'exceptions',
> 'database_io', 'from_bytes']
> 
> On Sun, May 7, 2017 at 9:20 PM, Hongbin Yang  wrote:
>> Hi, Peng,
>> 
>>I guess you installed pybel via `pip install pybel`, which is the
>> "wrong" pybel (https://pypi.python.org/pypi/PyBEL/0.5.4 ) You should install
>> openbabel and use it's pthon wrapper via `pip install openbabel`
>> (https://pypi.python.org/pypi/openbabel/2.4.1 ).
>> 
>> 
>> Hongbin Yang
>> 
>> 
>> From: Peng Yu
>> Date: 2017-05-08 09:07
>> To: openbabel-discuss
>> Subject: [Open Babel] How to run readstring in pybel?
>> Hi, I got the following error. Does anybody know what is wrong? Thanks.
>> 
>> $ cat main.py
>> #!/usr/bin/env python
>> 
>> import pybel
>> mymol = pybel.readstring("smi", "")
>> print mymol.molwt
>> $ ./main.py
>> Traceback (most recent call last):
>>  File "./main.py", line 5, in 
>>mymol = pybel.readstring("smi", "")
>> AttributeError: 'module' object has no attribute 'readstring'
>> 
>> --
>> Regards,
>> Peng
>> 
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> 
> 
> 
> -- 
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> Peng
> 
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[PyMOL] Packaging python3 version of pymol

[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
precedent for how to name the python3 version so they can be installed
beside each other. Another option is to use the alternatvies system so that
a user can choose which they want to use.

Other maintainers, let me know if you've added a python3 version and if you
made any decisions along these lines,

David

(P.S. to be clear, there are no issues building pymol for python3, this is
just about naming the /usr/bin/pymol file when installing a python3 version
so that users can also have the python2 version installed alongside it)
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Re: [PyMOL] Using API to select resi, and return some information within a certain distance

[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 selector with a residue number.

If you replace resn with resi , you should get nice pictures.

> 2) I still have no idea what the command cmd.get_pdbstr do

It returns a string in PDB format of the set of atoms in the selection. So,
the same string as would be in a file if you said save('xxx.pdb', 'sele')



On Tue, May 2, 2017 at 3:47 AM, Ahmad Abdelzaher 
wrote:

> Thank you. I made a few mistakes in my code. I wasn't paying attention
> to the commented code because I was only trying stuff there. I still
> get:
>
> 1) a bunch of 3 kb black png's
> 2) I still have no idea what the command cmd.get_pdbstr do
> 3) can you give me a line using iterate to get the residue names and
> numbers?
>
>
> import __main__
> __main__.pymol_argv = ['pymol','-qc']
> import pymol
> from pymol import cmd, stored, util
>
> pymol.finish_launching()
>
> residues = {'3s4m.pdb': {'102': 'THR',
>   '143': 'TYR',
>   '158': 'SER',
>   '166': 'TYR',
>   '173': 'TRP',
>   '181': 'SER',
>   '183': 'HIS',
>   '206': 'SER',
>   '95': 'TYR'}}
>
> for name, data in residues.items():
> for resnumber, resname in data.items():
> cmd.delete('all')
> bare_name = name.split('.')[0]
> cmd.load(name, bare_name)
> cmd.select('%s_%s%s' % (bare_name, resname, resnumber), 'byres
> resn %s around 10' % resnumber)
> cmd.dist('mysele_polar_conts','%s_%s%s' % (bare_name, resname,
> resnumber),'all within 5 of %s_%s%s' % (bare_name, resname,
> resnumber), quiet=1,mode=2,label=0,reset=1)
> cmd.show_as('sticks', '%s_%s%s' % (bare_name, resname, resnumber))
> util.cnc('%s_%s%s' % (bare_name, resname, resnumber))
> cmd.hide('everything', 'all and not %s_%s%s' % (bare_name,
> resname, resnumber))
> cmd.zoom('%s_%s%s' % (bare_name, resname, resnumber), 5)
> cmd.png('%s_%s%s.png' % (bare_name, resname, resnumber), ray=1)
>
>
>
> On Tue, May 2, 2017 at 7:14 AM, Jared Sampson
>  wrote:
> > Hi Ahmad - Please see below for some suggestions on getting your script
> to
> > do what I understand you would like to do.
> >
> > Cheers,
> > Jared
> >
> >
> > On May 1, 2017, at 4:54 PM, Ahmad Abdelzaher 
> wrote:
> >
> > OK I finally tried some of Jared suggestions, I'm not sure why
> > util.cnc doesn't work I get "NameError: name 'util' is not defined",
> >
> >
> > You will need to import the `util` namespace.  Try changing the pymol
> > submodule import line to:
> >
> > from pymol import cmd, stored, util
> >
> > Again, I want to color by element, second option from the gui. Also
> > the script outputs black screenshots, nothing is there, so there is a
> > bug somewhere! I attached the script and pdb below. I would appreciate
> > your help.
> >
> > import __main__
> > __main__.pymol_argv = ['pymol','-qc']
> > import pymol
> > from pymol import cmd, stored
> >
> > pymol.finish_launching()
> >
> > residues = {'3s4m.pdb': {'102': 'THR',
> >  '143': 'TYR',
> >  '158': 'SER',
> >  '166': 'TYR',
> >  '173': 'TRP',
> >  '181': 'SER',
> >  '183': 'HIS',
> >  '206': 'SER',
> >  '95': 'TYR'}}
> >
> > for name, data in residues.items():
> >for resnumber, resname in data.items():
> >cmd.delete('all')
> >cmd.load(name, name)
> >
> >
> > The load command here gives you an object called "3s4m.pdb" but you later
> > try to use a selection called only "3s4m" (`bare_name`).  If you leave
> the
> > second argument off from cmd.load(), the .pdb extension will be stripped
> > automatically.  Alternatively, you could assign `bare_name` first and
> give
> > that as the 2nd argument:
> >
> > bare_name = name.split('.')[0]
> > cmd.load(name, bare_name)
> >
> >
> >bare_name = name.split('.')[0]
> >cmd.select('%s_%s%s' % (bare_name, resname, resnumber), 'byres
> > resn %s around 3' % resnumber)
> >#selee = cmd.get_pdbstr('%s' % name.split('.')[0])
> >
> >
> > Since you've already assigned a variable for this, you can (and should!)
> use
> > `bare_name` instead of `name.split('.')[0]` wherever it occurs.  Also,
> you
> > don't need to do "%"-style string formatting if your variable is a string
> > and comprises the entire argument string.  Simply
> > `cmd.get_pdbstr(bare_name)`, for example, will work just fine.
> >
> >#print(selee)
> >cmd.dist('mysele_polar_conts','%s_%s%s' % (bare_name, resname,
> > resnumber),'all within 5 of %s_%s%s' % (name.split('.')[0], resname,
> > resnumber), quiet=1,mode=2,label=0,reset=1)
> >cmd.show_as('sticks', '%s_%s%s' % (bare_name, resname, resnumber))
> >#util.cnc('%s' % name.split('.')[0])
> >cmd.hide('everything', 

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

[David Hall]

> how to calculate the center of mass of an entire structure

Let's say I want the center of mas of the structure from the PDB 1vdd

cmd.fetch('1vdd', async=0)

cmd.centerofmass('1vdd')

Now, I see 1vdd has a bunch of water molecules that I don't want in in my
calculation

cmd.centerofmass('1vdd and not solvent')

Now maybe I only care about chain A.

cmd.centerofmass('1vdd and not solvent and chain A')

I suggest reading more about selections in the pymolwiki. That is actually
a topic where I feel the wiki could be better organized, but almost every
command in pymol operates on selections, so it is a fundamental concept you
should spend time to understand if you are planning to use pymol.

https://pymolwiki.org/index.php/Category:Selecting


On Thu, Apr 6, 2017 at 1:13 AM, Ahmad Abdelzaher <underoath...@gmail.com>
wrote:

> Hi Tsjerk,
>
> What you said makes perfect sense. Since an atom could be considered as a
> point with uniform density, it's center of mass is indeed its position.
>
> Which, begs the question, what is the purpose of cmd.centerofmass() and
> how to calculate the center of mass of an entire structure (the only
> calculation that would make sense with regards to the center of mass).
>
> Cheers.
>
>
> On Thu, Apr 6, 2017 at 6:49 AM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
>
>> Hi Ahmad,
>>
>> The center of mass of an atom is its position. A function like
>> cmd.centerofmass in the context of pymol only makes sense with a selection.
>> E.g.:
>>
>> x,y,z = cmd.centerofmass('byres n. ca')
>> print "COM of protein:", x, y, z
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Thu, Apr 6, 2017 at 6:30 AM, 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?
>>>
>>> On Thu, Apr 6, 2017 at 4:48 AM, David Hall <li...@cowsandmilk.net>
>>> wrote:
>>>
>>>> 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 <underoath...@gmail.com>
>>>> wrote:
>>>>
>>>> I find the documentation about the python api here to be a bit lacking.
>>>>
>>>> https://pymolwiki.org/index.php/Centerofmass
>>>>
>>>> I would appreciate more info on how to use this: cmd.centerofmass()
>>>> returns a list of 3 floats.
>>>>
>>>> 
>>>> --
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>>>>
>>>>
>>>
>>> 
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>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>
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Re: [PyMOL] Calculating center of mass for the entire protein

[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  wrote:
> 
> I find the documentation about the python api here to be a bit lacking. 
> 
> https://pymolwiki.org/index.php/Centerofmass
> 
> I would appreciate more info on how to use this: cmd.centerofmass() returns a 
> list of 3 floats.
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Re: [PyMOL] problems creating object using align method

[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 coordinates, you use the existing objects.

-David

> On Mar 13, 2017, at 1:31 AM, Sanaa Syed  wrote:
> 
> Hello,
> Can somebody please help me with creating aligned object using pymol API? i 
> want   to split chains from my protein and superimpose first chain on the 
> rest. the chains get loaded. and superimposed as well but i am unable to save 
> superimposed coordinates in a new file because no object is created.  this is 
> my script:
> list1=["chain_A","chain_B","chain_C","chain_D"]
> for every in list1:
> cmd.load("/home/sanaa/pymol/"+every+".pdb")
> object_list=cmd.get_object_list()
> aligned=[ ]
> list2=[ ]
> #object=string(alignedA_B)
> for j in range(len(object_list)):
>try:
> 
> aligned=cmd.align(object_list[0],object_list[j+1],object=AlnAB)
> list2.append(aligned)
> except IndexError:
> pass
> 
> this is giving me name error like:
> NameError: name 'AlnAB' is not defined
> 
> the object is not being created after calling the align command. it creates 
> an object if i give the command directly on  pymol command line but not 
> through the script. i have tried everything. please help!
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[ccp4bb] MX Support Scientist Positions at Diamond Light Source

[David Hall]

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

http://www.diamond.ac.uk/Careers/Vacancies/All/009_17_CH.html

Best wishes

Dave Hall
MX Village Coordinator
Diamond Light Source
www.diamond.ac.uk/mx




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

[David Hall]

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 intention is to use "Pybel" to 
> calculate structural similarity. 
> 
> First, I have installed Pybel for Python 3 this way:
> 
> $> pip3 install pybel
> 
> However, I cannot use the function "readstring":
> 
> $> python3
> >>> import pybel
> >>> smiles = ['', 'CCCN']
> >>> mols = [pybel.readstring("smi", x) for x in smiles] # Create a list of 
> >>> two molecules
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "", line 1, in 
> AttributeError: module 'pybel' has no attribute 'readstring'
> 
> Do you know why is this happening?
> 
> The other problem is that I am interested in using Pybel in Python 2.7. 
> However, I cannot successfully run it. I install it properly this way:
> 
> $> pip install pybel
> 
> But then, when importing it, I get the following error:
> 
> $> python
> >>> import pybel
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/Library/Python/2.7/site-packages/pybel/__init__.py", line 54, in 
> 
> from . import io
>   File "/Library/Python/2.7/site-packages/pybel/io.py", line 31, in 
> from .canonicalize import decanonicalize_node
>   File "/Library/Python/2.7/site-packages/pybel/canonicalize.py", line 9, in 
> 
> from .parser.language import rev_abundance_labels
>   File "/Library/Python/2.7/site-packages/pybel/parser/__init__.py", line 8, 
> in 
> from .parse_bel import BelParser
>   File "/Library/Python/2.7/site-packages/pybel/parser/parse_bel.py", line 
> 15, in 
> from .baseparser import BaseParser, WCW, nest, one_of_tags, triple
>   File "/Library/Python/2.7/site-packages/pybel/parser/baseparser.py", line 
> 22, in 
> quote = dblQuotedString().setParseAction(removeQuotes)
> TypeError: __call__() takes exactly 2 arguments (1 given)
> 
> Do you know what could be the reason of these errors? It would be very 
> interesting for me to be able to use this package.
> 
> Thank you very much,
> 
> Quim
> 
> -- 
> Joaquim Aguirre Plans
> Researcher in the Structural Bioinformatics Laboratory (DCEXS-UPF)
> Student of the MSc Bioinformatics for Health Sciences (UPF/UB)
> Graduate in Biotechnology (UAB), specialization in Biotechnology of Processes
> [Tel.] +34 692 352 112
> quim.agui...@gmail.com
> joaquim.agui...@upf.edu
> 
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Re: [OpenBabel-Devel] Proposal to overhaul/replace OBElementTable

[David Hall]

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 enough - does it make sense to hand-write the switch statements,
> though?
>
>
My suggestion would be to use gperf

https://www.gnu.org/software/gperf/

I have cmake run gperf for me as part of my builds. It has been at least a
year since I did a build on Windows though, so I don't recall whether it
was annoying to get it working there.
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Re: [Open Babel] OpenBabel for Python 3?

[David Hall]

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 means that FindPythonInterp could not determine the
version of python, so it is assuming it is 1.4 (see
https://github.com/Kitware/CMake/blob/master/Modules/FindPythonInterp.cmake
).



On Sun, Feb 19, 2017 at 5:26 PM, i4hashmi  wrote:

> Hi David,
>
> Can you please suggest me a solution? I am trying it for the last two weeks
> but could not find a solution. I even posted a thread at this forum but
> could not solve the problem.
> Now as your directions, I downloaded the openbabel from git:
> https://github.com/openbabel/openbabel
>
> And then used the command:
> *cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON
> -DRUN_SWIG=ON*
>
> but the installation gave error at the end. I am appending the whole output
> below. Please help me here.
>
> c02j2e0bdhjf:build hashmimu$ cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/
> python3
> -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
> -- The C compiler identification is AppleClang 8.0.0.842
> -- The CXX compiler identification is AppleClang 8.0.0.842
> -- Check for working C compiler:
> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/cc
> -- Check for working C compiler:
> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/cc
> -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler:
> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/c++
> -- Check for working CXX compiler:
> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/c++
> -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Using included inchi library.
> -- Found LibXml2: /usr/lib/libxml2.dylib (found version "2.9.4")
> -- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.8")
> -- Found wxWidgets: -L/usr/local/lib;;;-framework IOKit;-framework
> Carbon;-framework Cocoa;-framework AudioToolbox;-framework
> System;-framework
> OpenGL;-lwx_baseu-3.0;-lwx_osx_cocoau_core-3.0;-lwx_osx_cocoau_adv-3.0
> (found version "3.0.2")
> -- Looking for conio.h
> -- Looking for conio.h - not found
> -- Looking for sys/time.h
> -- Looking for sys/time.h - found
> -- Looking for time.h
> -- Looking for time.h - found
> -- Looking for strings.h
> -- Looking for strings.h - found
> -- Looking for rpc/xdr.h
> -- Looking for rpc/xdr.h - not found
> -- Looking for regex.h
> -- Looking for regex.h - found
> -- Looking for C++ include sstream
> -- Looking for C++ include sstream - found
> -- Looking for rint
> -- Looking for rint - found
> -- Looking for snprintf
> -- Looking for snprintf - found
> -- Looking for sranddev
> -- Looking for sranddev - found
> -- Looking for strcasecmp
> -- Looking for strcasecmp - found
> -- Looking for strncasecmp
> -- Looking for strncasecmp - found
> -- Looking for dlopen in dl
> -- Looking for dlopen in dl - found
> -- Looking for sys/types.h
> -- Looking for sys/types.h - found
> -- Looking for stdint.h
> -- Looking for stdint.h - found
> -- Looking for stddef.h
> -- Looking for stddef.h - found
> -- Check size of clock_t
> -- Check size of clock_t - done
> -- Performing Test SCANDIR_NEEDS_CONST
> -- Performing Test SCANDIR_NEEDS_CONST - Failed
> -- Checking available shared pointer...
> -- Performing Test HAVE_STD_SHARED_PTR
> -- Performing Test HAVE_STD_SHARED_PTR - Success
> -- Performing Test HAVE_STD_TR1_SHARED_PTR
> -- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed
> -- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER
> -- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Failed
> -- Use std::shared_ptr in memory
> -- Found Eigen3: /usr/local/include/eigen3 (Required is at least version
> "2.91.0")
> -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.1")
> -- Checking for module 'cairo'
> --   Found cairo, version 1.14.8
> -- Found Cairo: /usr/local/Cellar/cairo/1.14.8/lib/libcairo.dylib
> -- Cairo found. PNG output will be supported.
> -- Looking for getopt
> -- Looking for getopt - found
> -- GUI will not be built
> -- Found PythonInterp: /usr/bin/python3 (found version "1.4")
> -- Found SWIG: /usr/local/bin/swig (found version "3.0.12")
> -- Found SWIG: /usr/local/bin/swig (found suitable version "3.0.12",
> minimum
> required is "2.0")
> -- Found PythonLibs:
> /usr/local/Frameworks/Python.framework/Versions/3.6/lib/
> libpython3.6m.dylib
> (found version "3.6.0")
> -- Python bindings will be compiled
> CMake Error at 

Re: [Open Babel] Batch minimization of ligands

[David Hall]

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 prepared ligands in chemsketch, now I have to do energy minimization
> of the molecules before docking. I want this to be done in batch mode as
> there are hundreds of ligands. I have used obminimize -ff MMFF94 -sd
> input.mol > output.mol which does only for one molecule.
> Is it possible to do batch energy minimization in openbabel? Can anybody
> suggest me the correct command to do batch minimization?
>
> Thanks and Regards
> Ishan
>
>
>
> --
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> Batch-minimization-of-ligands-tp4659635.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> 
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Re: [Open Babel] Build a pdb molecule. problem to provide the atoms name

[David Hall]

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 c++.
> I only have a problem to define the name of the atoms. I need to choice 
> myself there names.
> 
> For this I use SetType of OBAtom :
> 
> OBAtom *Atom;
> Atom→SetType(NewName[i]); // NewName[i] is a string
> 
> The command Atom→GetType() works well and return the good name but nothing is 
> written in the pdb file at the place of atom name ( column 3 ). Thus I think 
> that SetType is not the attribute used to put the name of the atom in the pdb 
> format.
> How does work the attribution of the atom name in the pdb format? What should 
> I do to provide the name of the atom and write well the column 3 of the pdb 
> file ?
> 
> Greetings, Ivan
> 
> OBMol mol;
> OBFormat *format;
> OBConversion conv;
> conv.SetOutFormat("pdb");
> mol.BeginModify()
> for (int i=0;i {
> item=i;
> if ( std::find(atom.begin(), atom.end(), item) != atom.end() )
> {
> }
> else
> {
> OBAtom *Atom;
> OBResidue *Residu;
> Residu=mol.NewResidue();
> Atom=mol.NewAtom();
> atom.push_back(i);
> countAtom++;
> countResidu++;
> Atom->SetResidue(Residu);
> Atom->SetType(NewName[i]);
> Residu->SetName(AtomInResidu[i]);
> Residu->SetNum(countResidu);
> Atom->SetVector(coord[stepInitial][i][0],coord[stepInitial][i][1],coord[stepInitial][i][2]);
> cout << Atom->GetIdx() << " " << Atom->GetType() << " " << Residu->GetName() 
> << " " << Residu->GetIdx() << " " << Atom->GetVector() << endl ;
> }
> mol.EndModify();
> conv.Write(,);
> --
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Re: [PyMOL] Atom Order when Saving

[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 an old post on this 
> [https://sourceforge.net/p/pymol/mailman/message/7561093/ 
> ] and not sure if 
> there is a direct way now to do this.
> 
> Thanks and Best Regards,
> Subha
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Re: [PyMOL] loading StringIO

[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 
> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could 
> handle an open file instead of a file?
> 
> Thanks,
> Albert
> 
> 
> -- 
> -
>   Dr Albert Solernou
>   EPSRC Research Fellow,
>   Department of Physics and Astronomy,
>   University of Leeds
>   Tel: +44 (0)1133 431451
> 
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Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

[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 why you are only 
processing the first file, probably doing so 100 times.

you probably want something like

with open(“out") as f:
for line in f:
  in_pdb_file = line.strip()
  // code for processing in_pdb_file here

or

for X in range(1,101):
in_pdb_file = “dockout/F"+ str(X).zfill(2)
   // code for processing in_pdb_file here


Generally, I would recommend strongly against using os.system for performing 
file operations. You should look into shutil.copy , shutil.move , and os.remove 


> On Oct 12, 2016, at 2:16 PM, Subha K  wrote:
> 
> Hi There,
> 
> I am looking to automate the calculation of centre of mass and placing a 
> pseudo atom on the COM and save it as a pdb file . Going through the forum 
> [https://sourceforge.net/p/pymol/mailman/message/34458943/ 
> ] , I found some 
> useful scripts for this, but, I am having trouble getting it done for all 
> files in a directory. My script does what I need for the first file alone. 
> Some looping or other is not correct. Or there could be an easy and better 
> way to do it. I couldn't figure that out.  So, could some one please help me 
> solve this?
> 
> I have 100 files F01, F02, F100 ... in the directory dockout. I would like to 
> calculate the COM and place a pseudo atom on the COM and save it as a pdb for 
> all the 100 files. 
> 'out' in the script corresponds to the list of all the 100 files.
> 
> import pymol
> from pymol import cmd
> pymol.finish_launching()
> import numpy as np
> import glob
> import fileinput
> def center(selection, com=True):
> model = cmd.get_model(selection)
> xyz = np.array(model.get_coord_list())
> mass = [i.get_mass() for i in model.atom]
> xyz_m = xyz * np.array([mass]).T
> if com:
> return tuple(np.sum(xyz_m, 0)/model.get_mass())
> else:
> return tuple(np.average(xyz, 0))
> 
> def GetListOfFiles (filename):
> l = []
> for line in fileinput.input( filename ):
> tokens = line.split( )
> l.append(tokens)
> return l
> 
> def Calculate_COM (list):
> for i in range (len(list)):
> print list[i][0]
> X=1
> if (X<101):
> os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")
> for pdb in glob.glob("lig.pdb"):
> cmd.load(pdb)
> COM = center('resn UNK')
> cmd.pseudoatom('ligCOM', pos=COM)
> cmd.save("complex_dummy.pdb", "all")
> os.system("mv complex_dummy.pdb complex_" + str(X).zfill(2) + 
> "_dummy.pdb")
> os.system("rm lig.pdb")
> X=X+1
> else:
> break
> listofFiles = GetListOfFiles ("./out")
> print listofFiles
> Calculate_COM(listofFiles)
> 
> 
> Thanks,
> Subha 
> 
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Re: [Open Babel] Java bindings for openbabel 2.4.0

[David Hall]

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 ports,
> downloaded source and compiled using the following flags: 
> -DCMAKE_INSTALL_PREFIX=~/Applications/openbabel -DJAVA_BINDINGS=ON 
> -DBUILD_GUI=OFF
> 
> I am running MacOS Sierra.  No special configs or anything.  The java 
> bindings are never generated in the openbabel-openbabel-2.4.0/scripts/java/ 
> folder or anywhere in the installation location.
> 
> When I do the "cmake ./ -DCMAKE_INSTALL_PREFIX=~/Applications/openbabel 
> -DJAVA_BINDINGS=ON -DBUILD_GUI=OFF" I  get the following output:
> -- Using included inchi library.
> -- Could NOT find wxWidgets (missing:  wxWidgets_LIBRARIES 
> wxWidgets_INCLUDE_DIRS)
> -- Checking available shared pointer...
> -- Use std::shared_ptr in memory
> -- Cairo found. PNG output will be supported.
> -- GUI will not be built
> -- Could NOT find SWIG (missing:  SWIG_EXECUTABLE SWIG_DIR)
> -- Could NOT find SWIG (missing:  SWIG_EXECUTABLE SWIG_DIR) (Required is at 
> least version "2.0")
> -- SWIG 2.0 NOT found
> -- Configuring done
> -- Generating done
> -- Build files have been written to: 
> /Users/jason/Desktop/openbabel-openbabel-2-4-0
> 
> So that tells me that that java AND python bindings should exist *somewhere* 
> but they don't. 
> 
> Thanks,
> 
> Jason
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Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

[David Hall]

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 Adler  wrote:

> Dear All,
>
> I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04 as per
> the instructions at http://www.rdkit.org/docs/Install.html For reasons
> which I don't really want to get into we would prefer to avoid anaconda for
> the time being.
>
> That being said, when I try to test the build, I get a number of errors
> and failed tests (the build does not work when called from Python, which is
> unsurprising).
>
> For reference, the cmake command I issued was:
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -D PYTHON_LIBRARY=/usr/lib/python
> 3.4/config-3.4m-x86_64-linux-gnu/libpython3.4.so -D
> PYTHON_INCLUDE_DIR=/usr/include/python3.4/ -D
> PYTHON_EXECUTABLE=/usr/bin/python3.4 -DBOOST_ROOT=/usr/lib/x86_64-linux-gnu/
> ..
>
> The tests which fail are as follows:
>
> The following tests FAILED:
>   5 - pyBV (SEGFAULT)
>   6 - pyDiscreteValueVect (SEGFAULT)
>   7 - pySparseIntVect (SEGFAULT)
>   8 - pyFPB (SEGFAULT)
>  11 - testPyGeometry (SEGFAULT)
>  14 - pyAlignment (Failed)
>  18 - pyForceFieldConstraints (SEGFAULT)
>  20 - pyDistGeom (Failed)
>  33 - pyDepictor (SEGFAULT)
>  45 - pyChemReactions (SEGFAULT)
>  50 - pyFilterCatalog (SEGFAULT)
>  52 - pyFragCatalog (SEGFAULT)
>  54 - pyMolDescriptors (SEGFAULT)
>  57 - pyPartialCharges (SEGFAULT)
>  59 - pyMolTransforms (SEGFAULT)
>  63 - pyForceFieldHelpers (SEGFAULT)
>  65 - pyDistGeom (SEGFAULT)
>  67 - pyMolAlign (SEGFAULT)
>  69 - pyChemicalFeatures (SEGFAULT)
>  71 - pyShapeHelpers (SEGFAULT)
>  73 - pyMolCatalog (SEGFAULT)
>  75 - pyMolDraw2D (SEGFAULT)
>  77 - pyFMCS (SEGFAULT)
>  80 - pyMolHash (SEGFAULT)
>  82 - pyMMPA (SEGFAULT)
>  84 - pyReducedGraphs (SEGFAULT)
>  86 - pySLNParse (SEGFAULT)
>  87 - pyGraphMolWrap (SEGFAULT)
>  88 - pyTestConformerWrap (SEGFAULT)
>  89 - pyTestThreads (SEGFAULT)
>  92 - pyMatCalc (SEGFAULT)
>  93 - pySimDivPickers (SEGFAULT)
>  94 - pyRanker (Failed)
>  96 - pyFeatures (SEGFAULT)
>  97 - pythonTestDbCLI (Failed)
>  98 - pythonTestDirML (Failed)
>  99 - pythonTestDirDataStructs (Failed)
> 101 - pythonTestDirSimDivFilters (Failed)
> 102 - pythonTestDirVLib (Failed)
> 103 - pythonTestDirChem (SEGFAULT)
>
> I must confess I'm a little out of my depth right now, so I don't even
> know where to begin debugging this. Any advice would be greatly appreciated,
>
> Best,
>
> Phil
>
> 
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Re: [Rdkit-discuss] The RDKit and modern C++

[David Hall]

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 variables whenever I log in. That includes some code built on
top of RDKit, so it seems like it should work on the technical side,
although obviously there is a barrier in getting it installed and set up
correctly.

-David


On Sat, Sep 24, 2016 at 2:25 AM, Greg Landrum 
wrote:

> Dear all,
>
> I just did a blog post describing a proposal for some upcoming changes to
> the RDKit code base:
> https://medium.com/@greg.landrum_t5/the-rdkit-and-
> modern-c-48206b966218?source=linkShare-d698b3fa9f7-1474698147
>
> This is a big and important change and I'd love to hear whatever feedback
> members of the community may have. Please comment either on the blog post
> or here.
>
> Best Regards,
> -greg
>
>
>
>
> 
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Re: [Open Babel] Converting PDB to SMILES and matching atom orders

[David Hall]

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 time, it does the right thing.

For the system you are discussing, here's an example using the attached
script:

$ ./isomorph.py 1PE_model.sdf 1kf6_1pe.pdb
[{0: 0,
  1: 1,
  2: 2,
  3: 3,
  4: 4,
  5: 5,
  6: 6,
  7: 7,
  8: 8,
  9: 9,
  10: 10,
  11: 11,
  12: 12,
  13: 13,
  14: 14,
  15: 15},
 {0: 15,
  1: 13,
  2: 14,
  3: 12,
  4: 11,
  5: 10,
  6: 9,
  7: 8,
  8: 7,
  9: 6,
  10: 5,
  11: 4,
  12: 3,
  13: 1,
  14: 2,
  15: 0}]

Since 1PE is symmetric, it outputs the forward ordering of the 1st -> 1st,
2nd -> 2nd, etc. and reverse ordering of 1st->16th, 2nd  -> 15th.

Hopefully the attached script gives an idea of how to incorporate this idea
into your code.


On Wed, Aug 31, 2016 at 4:51 PM, Sam Tonddast-Navaei 
wrote:

> I am trying to read a small molecule from PDB file and match its atom
> numbers to the same molecule in a SDF file. I have tried both matching
> SMART patterns and using OBIsomorphismMapper, both work for 70% of cases.
> However there are cases for which OpenBabel can not simply get the right
> SMILES from just the PDB file (e.g.  adds extra double bonds or miss ones). 
> For
> example in PDB ID 1KF6 and ligand name IPE, if you generate SMILES from PDB
> you will get OCCO/C=C/OCCO/C=C/O/C=C/O while the correct one should be
> OCCOCCOCCOCCOCCO. I would appreciate if someone can give me some advise on
> this.
>
> Thanks,
> Sam
>
> 
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#!/usr/bin/env python
# Copyright 2016 Acpharis Inc, All Rights Reserved
import pprint
import networkx
from networkx.algorithms import isomorphism
import argparse
import pybel
import openbabel

parser = argparse.ArgumentParser()
parser.add_argument('sdf')
parser.add_argument('pdb')
args = parser.parse_args()


mol1 = pybel.readfile('sdf', args.sdf).next()
mol2 = pybel.readfile('pdb', args.pdb).next()


G1 = networkx.Graph()
G2 = networkx.Graph()

for index, atom in enumerate(mol1):
G1.add_node(index, type=atom.atomicnum)

for bond in openbabel.OBMolBondIter(mol1.OBMol):
G1.add_edge(bond.GetBeginAtomIdx()-1, bond.GetEndAtomIdx()-1)

for index, atom in enumerate(mol2):
G2.add_node(index, type=atom.atomicnum)

for bond in openbabel.OBMolBondIter(mol2.OBMol):
G2.add_edge(bond.GetBeginAtomIdx()-1, bond.GetEndAtomIdx()-1)

class GraphMatcherLocal(isomorphism.GraphMatcher):
def semantic_feasibility(self, G1_node, G2_node):
return self.G1.node[G1_node]['type'] == self.G2.node[G2_node]['type']

GM = GraphMatcherLocal(G1, G2)
gen_isms = GM.subgraph_isomorphisms_iter()

# networkx gives us a generator, we need a list that we can iterate over
# multiple times
isms = []
for ism in gen_isms:
isms.append(ism)

pprint.pprint(isms)
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Re: [PyMOL] Modeling protein-dna complex

[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 the complex
(2) an object that has just your DNA that you want in the complex

In the bottom right, where it typically says “Selecting Residues”, click where 
it says Residues until that it says “Objects”

Click on your protein

Click on your dna

Click on File->Save Molecule and save “sele” as a PDB file.

> On Aug 13, 2016, at 8:22 AM, soumi  wrote:
> 
> Hi,
> I carry on my research work on protein-dna complex system.I have one dna 
> pdb and one protein-dna complex pdb.I want to make new protein-dna complex 
> pdb taking  dna from single pdb and protein from protein-dna complex.Protein 
> possess similar DNA-binding specificities.I superimpose two pdb file and 
> remove dna from protein-dna complex pdb .But I can not save new protein-dna 
> complex.Please let me know by pymol how I would be able to model of the 
> referred paper was done.
> Thanks
> soumi
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Re: [Open Babel] OpenBabel for Python 3?

[David Hall]

do you have python3-dev installed?


> On Aug 9, 2016, at 12:57 PM, John  wrote:
> 
> PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7

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Re: [Open Babel] OpenBabel for Python 3?

[David Hall]

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
$ cmake .. -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON
-DRUN_SWIG=ON
...
-- Found PythonInterp: /usr/bin/python3 (found version "3.5.1")
-- Found PythonLibs: /usr/lib64/libpython3.5m.so (found version "3.5.1")
...
$ grep '^PYTHON' CMakeCache.txt
...
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3
PYTHON_INCLUDE_DIR:PATH=/usr/include/python3.5m
PYTHON_LIBRARY:FILEPATH=/usr/lib64/libpython3.5m.so
...



-David


On Tue, Aug 9, 2016 at 10:00 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:

> Please don't reply to me directly. Many other people on the mailing list
> can answer your question.
>
> Your problem is clear from the WARNING. You want something like
> -DPYTHON_LIBRARY=/usr/lib/python3.4/libpython.so
>
> You need to link to a *file* not a directory where the file is found.
>
> Hope that helps,
> -Geoff
>
> > On Aug 9, 2016, at 9:51 AM, John  wrote:
> >
> > Geoff,
> >
> >
> > I downloaded the source and installed all the prerequisites. I can't
> figure out how to get it to link to the Python 3 bindings, however.
> >
> > $ cmake ../openbabel-2.3.2 -DPYTHON_BINDINGS=ON
> -DPYTHON_LIBRARY=/usr/lib/python3.4 -DEIGEN3_INCLUDE_DIR=/home/
> john/eigen/eigen-eigen-dc6cfdf9bcec
> >
> > 
> >
> > -- Found PythonInterp: /usr/bin/python (found version "2.7.6")
> > -- Found PythonLibs: /usr/lib/python3.4 (found version "2.7.6")
> > -- Python bindings will be compiled
> > -- Configuring done
> > WARNING: Target "bindings_python" requests linking to directory
> "/usr/lib/python3.4".  Targets may link only to libraries.  CMake is
> dropping the item.
> > -- Generating done
> > -- Build files have been written to: /home/john/openbabel/build
> >
> > As you can see, the configuration has linked to the Python 2
> installation, not Python 3. What is the correct setting to get it to link
> to Python 3 instead?
> >
> >
> > Thanks,
> >
> > John Todd
> >
> >
> > P.S. A few of the tests seem to have failed, but several Google pages
> make it sound like it's no big deal. Should I worry about:
> >
> > -- Looking for conio.h - not found
> >
> > -- Performing Test SCANDIR_NEEDS_CONST - Failed
> > CMake Warning (dev) at test/CMakeLists.txt:171 (include):
> >  Syntax Warning in cmake code at
> >
> > /home/john/openbabel/openbabel-2.3.2/cmake/modules/
> UsePythonTest.cmake:54:14
> >
> >  Argument not separated from preceding token by whitespace.
> > This warning is for project developers.  Use -Wno-dev to suppress it.
> >
> > CMake Warning (dev) at test/CMakeLists.txt:171 (include):
> >  Syntax Warning in cmake code at
> >
> > /home/john/openbabel/openbabel-2.3.2/cmake/modules/
> UsePythonTest.cmake:54:31
> >
> >  Argument not separated from preceding token by whitespace.
> > This warning is for project developers.  Use -Wno-dev to suppress it.
> >
> > CMake Warning (dev) at test/CMakeLists.txt:171 (include):
> >  Syntax Warning in cmake code at
> >
> > /home/john/openbabel/openbabel-2.3.2/cmake/modules/
> UsePythonTest.cmake:57:25
> >
> >  Argument not separated from preceding token by whitespace.
> > This warning is for project developers.  Use -Wno-dev to suppress it.
> >
> > CMake Warning (dev) at test/CMakeLists.txt:171 (include):
> >  Syntax Warning in cmake code at
> >
> > /home/john/openbabel/openbabel-2.3.2/cmake/modules/
> UsePythonTest.cmake:57:39
> >
> >  Argument not separated from preceding token by whitespace.
> > This warning is for project developers.  Use -Wno-dev to suppress it.
> >
> >
> > On 08/08/2016 01:27 PM, Geoffrey Hutchison wrote:
> >>> I am fairly new at Python, and am trying to stick to the latest
> version.
> >>> Is it possible to install the Open Babel bindings for Python 3?
> >> Yes. I don't know about the pip packages (or Mint ones) but you can do
> this from source, e.g.:
> >> https://open-babel.readthedocs.io/en/latest/Installation/install.html#
> compile-bindings
> >>
> >> Hope that helps,
> >> -Geoff
> >
>
>
> 
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Re: [Rdkit-discuss] Problems after installing rdkit release 2016_03_1

[David Hall]

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 the new 
> release 2016.
> It works in terminal and Ipython Notebook but shows error in IDLE and 
> Spyder.
> 
> In Terminal:
> 
> Python 2.7.12 (default, Jul  1 2016, 15:12:24)
> [GCC 5.4.0 20160609] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
 from rdkit import rdBase
 print rdBase.rdkitVersion
> 2016.03.1
 import os
 os.environ["PYTHONPATH"]
> '/opt/rdkit-Release_2016_03_1:'
 
> 
> In IDLE/Spyder:
> 
> Python 2.7.12 (default, Jul  1 2016, 15:12:24)
> [GCC 5.4.0 20160609] on linux2
> Type "copyright", "credits" or "license()" for more information.
 from rdkit import rdBase
> 
> Traceback (most recent call last):
>   File "", line 1, in 
> from rdkit import rdBase
> ImportError: No module named rdkit
 
> 
> 
> Can somebody help me with this!
> 
> 
> Thanks & Regards,
> 
> Jessica
> 
> 
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Re: [Open Babel] GAFF2 in babel?

[David Hall]

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 we implement it to openBabel?
>
> Than you very much
>
> Albert
>
>
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Re: [Open Babel] GAFF2 in babel?

[David Hall]

poking around, it appears there are some new atom types in
dat/antechamber/ATOMTYPE_GFF2.DEF . Since AmberTools is GPLv3, I'll leave
it to others to decide what that means for the ability to implement gaff2 .
I'll note that gaff2.dat is public domain though, so that part should be
clean.

On Thu, 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> wrote:
>
>> Hello:
>>
>> I noticed that GAFF2 is released in recent Amber 16. I am just wondering
>> how can we implement it to openBabel?
>>
>> Than you very much
>>
>> Albert
>>
>>
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Re: [Open Babel] Unable to import pybel in Python

[David Hall]

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.

-David

> On Jul 8, 2016, at 11:14 AM, Dan Smith  
> 
> Importing pybel and openbabel works now. I tried to work through some of the 
> examples on the web 
> (http://openbabel.org/docs/current/UseTheLibrary/Python_Pybel.html).  The 
> examples do not work exactly as written.  For instance, I cannot use the 
> command “read string”, but I can use “pybel.readstring”.
> 
> >>> mymol = readstring("smi", "")
> Traceback (most recent call last):
>   File "", line 1, in 
> NameError: name 'readstring' is not defined
> >>> mymol = pybel.readstring("smi", "")
> >>> print mymol.molwt
> 58.1222
> 
> Is this normal or is there something wrong with my installation?
> 
> Thanks,
> 
> Dan
> 
> 
>> On Jul 7, 2016, at 6:01 PM, Leonardo Lazzaro  wrote:
>> 
>> Hello,
>> 
>> try to use the options DPYTHON_INCLUDE_DIR, DCMAKE_INSTALL_PREFIX.
>> for example for anaconda2 I used the following command:
>> 
>> cmake .. -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON 
>> -DCMAKE_INSTALL_PREFIX=~/anaconda2 
>> -DPYTHON_INCLUDE_DIR=~/anaconda2/include/python2.7 
>> -DCMAKE_LIBRARY_PATH=~/anaconda2/lib 
>> -DSWIG_DIR=~/anaconda2/share/swig/3.0.2/ 
>> -DSWIG_EXECUTABLE=~/anaconda2/bin/swig 
>> -DPYTHON_LIBRARY=~/anaconda2/lib/libpython2.7.so 
>> -DCMAKE_BUILD_TYPE=DEBUG
>> 
>> hope it helps,
>> Leonardo
>> 
>>> On 2016-07-07 17:23, Dan Smith wrote:
>>> Hello,
>>> 
>>> I am using openbabel on a Mac - El Capitan OS X 10.11.5 operating
>>> system.
>>> 
>>> I have installed eigen2. I have python version 2.7.10.
>>> 
>>> I have successfully compiled version 2.3.90 using the following
>>> commands in terminal.
>>> 
>>> cmake ../openbabel -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
>>> make
>>> sudo make install
>>> export PYTHONPATH=/usr/local/lib:$PYTHONPATH
>>> 
>>> When I attempt to import pybel or openbabel in Python I get the
>>> following messages.
>>> 
>> import pybel
>>> Traceback (most recent call last):
>>> File "", line 1, in 
>>> ImportError: No module named pybel
>>> 
>> import openbabel
>>> Traceback (most recent call last):
>>> File "", line 1, in 
>>> ImportError: No module named openbabel
>>> 
>>> I have tried to search previous posts but have not found an answer
>>> that will solve my problem. At this point I’m not sure what to do to
>>> diagnose the problem.
>>> 
>>> Any help in solving my problem would be appreciated.
>>> 
>>> Thanks,
>>> 
>>> Dan
>>> --
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Re: [PyMOL] Video in Ubuntu Linux

[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 users,
>>> 
>>> I use Kubuntu 14.04. I compiled PyMOL, following some instructions on the
>>> web. This produced the directory:
>>> 
>>> /opt/pymol-svn/
>>> 
>>> and a symbolic link to pymol executable:
>>> 
>>> /usr/bin/pymol -> /opt/pymol-svn/pymol*
>>> 
>>> PyMOL works fine. Nevertheless, when I try:
>>> 
>>> File > Save Movie As > MPEG...
>>> 
>>> I get the following error message:
>>> 
>>> MPEG encoder missing.
>>> The FreeMOL add-ons may not be installed
>>> 
>>> I downloaded the source code for mpeg_encode (freemol-mpeg_encode.tar.gz)
>>> from:
>>> 
>>> http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_en
>>> code/?view=tar
>>> 
>>> and I did the following:
>>> 
>>> tar zxvf freemol-mpeg_encode.tar.gz
>>> cd mpeg_encode
>>> ./configure
>>> make
>>> sudo make install
>>> 
>>> This created the following file:
>>> 
>>> /bin/mpeg_encode.exe
>>> 
>>> That means that mpeg_encode.exe is in the PATH (it runs from any
>>> directory). mpeg_encode.exe seems to work. Unfortunately, when I try to
>>> produce a movie in pymol, I get the same error message. What have I done
>>> wrong?
>> 
>> I hope it is very simple.
>> You need to include an environment variable $FREEEMOL pointing at the
>> directory where
>> freemol is installed
>> 
>> If you are using bash that would be
>> export FREEMOL=/your/bath/to/freemol/
>> where the mpeg_encode.exe file is in
>> /your/bath/to/freemol/bin/mpeg_encode.exe
>> 
>> Hope this helps!
> 
> I created a directory:
> 
> /opt/freemol
> 
> with two subdirectories:
> 
> /opt/freemol/bin
> /opt/freemol/licenses
> 
> which contain the files:
> 
> /opt/freemol/bin/mpeg_encode.exe
> /opt/freemol/licenses/mpeg_encode.txt
> 
> I created the file:
> 
> pymol.sh
> 
> with this content:
> 
> #!/bin/bash
> FREEMOL=/opt/freemol
> export FREEMOL
> pymol
> 
> I ran pymol.sh, but the problem remained the same. Any idea?
> 
> Ioannis
> 
>> Folmer
>> 
>>> Thank you in advance.
>>> 
>>> Best Regards,
>>> 
>>> Ioannis
> 
> -- 
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> Staff Research Scientist - Associate Professor Level
> Centre of Systems Biology
> 
> Tel: +30 210 6597 127
> Fax: +30 210 6597 545
> Email: imicha...@bioacademy.gr
> _
> Biomedical Research Foundation, Academy of Athens
> Soranou tou Efessiou 4, 115 27 Athens, Greece
> 
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Re: [PyMOL] ABPS Tools 2.1 plugin error

[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
> 
> When I launch the ABPS Tools 2.1, I get these errors:
> 
> Could not find default location for file: psize.py
> Could not find default location for file: apbs.exe
> Could not find default location for file: apbs-mpi.exe
> Could not find default location for file: apbs-mpi-openmpi.exe
> Could not find default location for file: apbs-mpi-lammpi.exe
> Could not find default location for file: pdb2pqr.py
> 
> I run a "find / -name psize.py " command but it can not locate the file.
> 
> Can somebody please help me? Where can I get 'psize.py' and the APBS 
> binary so I can
> specify them in the APBS plugin under "Program locations"?
> 
> Many thanks
> 
> 
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Re: [PyMOL] High Resolution Ray Tracing

[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 am unable to do so as I always run out of 
> memory at the end of the ray tracing process, with the following error:
> 
> python2.7(972,0x7fff7397f300) malloc: *** 
> mach_vm_map(size=18446744068907188224) failed (error code=3)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> 
> This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor and 
> 32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than twice 
> this reserved for virtual memory, but no swap is actually used.
> 
> Decreasing hash_max just increases the ray tracing time until the error at 
> the end. Sometimes PyMOL will be terminated with this error, whilst at other 
> times a transparent PNG is all that is produced.
> 
> Is there a way to force PyMOL to use virtual memory to avoid these 
> errors/crashes at the expense of processing time?
> 
> If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB 
> or more RAM, who would be able to render this ray traced image if I send the, 
> the .pse file and .pml script off list? Takes about 10 mins to process.
> 
> Cheers,
> 
> Stephen
> 
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Re: [PyMOL] Bash scripting and pymol

[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
> 
> 
> # A simple FETCHER via PYMOL: download pdbs to the folder and pre-process 
> them!
> mkdir ${pdb_array_store}
> for i in ${pdb_array[@]}; do
> pdb_tit=$(basename "$i")
> pymol -d "fetch $i; save ${pdb_array_store}/${pdb_tit}_proc.pdb,
> ${pdb_tit}" -c ;
> rm ${pdb_array_store}/*.log
> done
> 
> 
> while executing it sends error
> 
> PyMOL>fetch 5A2H; save
> /projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb,
> 5A2H
> please wait ...
> Selector-Error: Invalid selection name "5A2H".
> ( 5A2H )<--
> Save: wrote 
> "/projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb".
> PyMOL: normal program termination.
> 
> if I change save selection just to 'polymer' it saved empty pdbs-
> where might be an error here?
> 
> Thanks!
> 
> 2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar :
>> Hi,
>> 
>> You need
>> 
>> for i in ${pdb_array[@]}
>> do
>> ...
>> done
>> 
>> Cheers,
>> 
>> Tsjerk
>> 
>> On Apr 27, 2016 4:44 PM, "James Starlight"  wrote:
>>> 
>>> so As I tried to do it but it was not worked :-O)
>>> 
>>> #pdbs list
>>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>>> #where to save
>>> pdb_array_store=$template/pymol/
>>> 
>>> 
>>> # A simple FETCHER: download pdbs to the folder and pre-process them!
>>> #mkdir ${pdb_array_store}
>>> for i in `cat ${pdb_array}` ; do wget
>>> http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
>>> done
>>> 
>>> result
>>> cat: 1UBI: No such file or directory
>>> 
>>> 2016-04-27 12:29 GMT+02:00 James Starlight :
 Please give me an example of the list of 3 pdbs instead of just cat $1
 :)
 as well as proper syntax of how to save each pdb after fetching in
 pymol using same command line
 Forgot to mention important points:
 1) that list should be physically in my script like in python
 2) I use pymol because I will need to process each of the pdb- e,g to
 remove from them ligands or water etc
 
 Thanks!
 
 2016-04-27 12:18 GMT+02:00 James Starlight :
> Please give me an example of the list of 3 pdbs instead of cat $1  as
> well as how to save syntax of how to save each pdb
> 
> 
> Thanks!
> 
> J
> 
> 2016-04-27 12:09 GMT+02:00 Jordan Willis :
>> If you really want to use pymol, this works
>> 
>> #!/bin/bash
>> #myscript.bash
>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
>> 
>> 
>> Then on the command line
>>> chmod +x myscript.bash; ./myscript.bash mylist.txt
>> 
>> 
>> On Apr 27, 2016, at 2:55 AM, Jordan Willis 
>> wrote:
>> 
>> Must you use pymol?
>> 
>> 
>> Try directly from the PDB
>> 
>> #!/bin/bash
>> #myscript.bash
>> 
>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ;
>> done
>> 
>> 
>> 
>> 
>> Then on the command line
>>> chmod +x myscript.bash; ./myscript.bash mylist.txt
>> 
>> 
>> J
>> 
>> On Apr 27, 2016, at 2:41 AM, James Starlight 
>> wrote:
>> 
>> Dear Pymol users!
>> 
>> I need to add a few strings to my simple bash script which will creat
>> a list of pdb files and than will call pymol without GUI from the
>> terminal to fetch all the pdbs and save it to the desired location.
>> For one pdb it should be smth like
>> 
>> pdbs="1f88"
>> 
>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
>> ${tmp}/pymol_${pdbs}.log
>> 
>> will be thankful for the correction of this string as well as example
>> how it can be adapted for a list of pdbs in bash.
>> 
>> Thanks!
>> 
>> J
>> 
>> 
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>> 
>> 
>> 
>>> 
>>> 
>>> 

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

[David Hall]

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:

https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Wrap/MolOps.cpp#L483

There is a nice if-else that shows you how to get the behaviors of asMols = 
False, then asMols=True. There is obviously a little bit of manipulation to get 
the output into python, but hopefully it is clear how one might make a similar 
pure C++ function.

-David


> On Apr 11, 2016, at 8:24 AM, Yingfeng Wang  wrote:
> 
> lgor,
> 
> Yes, this version looks good. But, I am wondering whether I can specify 
> asMols. I specify asMols in the python version of my tool, so I want to do 
> the same thing for getting the same result in my C++ code. Or could you help 
> me to confirm that the version you mentioned actually has the same effect as 
> asMols = true?
> 
> Thanks.
> Yingfeng
> 
> On Sun, Apr 10, 2016 at 11:35 PM, Igor Filippov  > wrote:
> Did you want
> std::vector> > 
> RDKit::MolOps::getMolFrags ( const ROMol 
>  &  mol, bool  
> sanitizeFrags = true, 
> by any chance? This will return a vector of ROMol's which correspond to the 
> contiguous fragments.
> 
> Igor
> 
> 
> On Sun, Apr 10, 2016 at 11:04 PM, Yingfeng Wang  > wrote:
> Greg,
> 
> Thanks. In python, I am using GetMolFrags by the following way,
> 
> Chem.GetMolFrags(current_modified_mol, asMols=True, sanitizeFrags=False)
> 
> However, there is not a version at the link you mentioned allows me to 
> specify asMols. Could you please give me more hints?
> 
> Thanks.
> Yingfeng
> 
> On Sun, Apr 10, 2016 at 10:49 PM, Greg Landrum  > wrote:
> 
> 
> On Mon, Apr 11, 2016 at 1:35 AM, Yingfeng Wang  > wrote:
> 
> Thanks. Say, the current RWMol object has 10 bonds, so ids of these bonds 
> should be from 1-10. Now, I remove one bond. How do I reset all nine bonds 
> with ids from 1-9 (if one or two atoms are gone with this bond, I also want 
> to reset the ids of these atoms).
> 
> You don't need to do that, it happens automatically
>  
> In addition, say, there are two fragments after one bond is removed. How do I 
> get these two fragments as mols. In python, I can use Chem.GetMolFrags. But 
> how do I get my job done in C++?
> 
> There are a number of different versions of MolOps::getMolFrags(), pick the 
> on that does what you like:
> http://rdkit.org/docs/cppapi/namespaceRDKit_1_1MolOps.html#ad8100d785d32fb3c173b83949766b87b
>  
> 
> 
> Since the Python and C++ function/method names are often similar to each 
> other, a good way to find answers like this is to google for the name of the 
> Python function you are looking for and look for the link to the C++ 
> documentation in the results. 
> 
> Best,
> -greg
> 
> 
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Re: [PyMOL] pymolrc location

[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 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
> 
> 
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Re: [PyMOL] running python scripts from within python loops in a pymol scripts

[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 in which two 
> protein domains are joined by a shared helix
> and highlights backbone steric clashes
> 
> python 
> for i in range(1, 25):
> cmd.fit('/DARPin2//C/15-22/CA','/helix1//B/%d-%d/CA'%(i, i+7),matchmaker 
> = -1) 
> cmd.save('model_%d.pdb'%i,'/DARPin1//A/1-160 or /helix1//B/1-%d or 
> /DARPin2//C/23-169'%(i+7))
> cmd.color('white','DARPin1')
> cmd.color('paleyellow','/DARPin1//A/37-135')
> cmd.hide('spheres')
> cmd.select('clash','/DARPin1//A/1-157/N+CA+C+A within 2.5 of 
> /DARPin2//C/26-169/N+CA+C+N')
> cmd.show('spheres','clash')
> cmd.color('red','clash')
> cmd.ray(2048, 1536)
> cmd.png('model_%dA.png'%i)
> cmd.turn('x', -90)
> cmd.ray(2048, 1536)
> cmd.png('model_%dB.png'%i)
> cmd.turn('x', 90)
> cmd.hide('spheres','clash')   
> python end 
> 
> 
> Now, to visualize and quantitate the relative domain orientations in the 
> models by a pseudo-torsion angle 
> between the centers of gravity of the two domains around the axis of the 
> shared helix.
> 
> #this needs to be done only once: 
> 
> run py_scripts/center_of_mass.py
> run py_scripts/anglebetweenhelices.py
> 
> ...
> 
> com /DARPin1//A/37-135/CA, object=com1
> color black, name PS1
> helix_orientation_hbond /helix1//B/159-193
> 
> ...
> 
> # this would define the center of gravity of the mobile domain and should be 
> within the loop:
> 
> com /DARPin2//A/37-135/CA, object=com2
> 
> however, since “com” is not a standard pymol command, but added by script 
> center_of_mass.py,
> I do not know how to use it from within the loop. If I try to use it 
> analogous to normal commands, I get the error message:
> 
> Traceback (most recent call last):
>   File 
> "/Users/ahonegger/Desktop/MacPyMOL1.8.0.2.app/Contents/pymol/modules/pymol/parser.py",
>  line 157, in parse
> exec(py_block,self.pymol_names,self.pymol_names)
>   File "", line 4, in 
> AttributeError: 'module' object has no attribute 'com'
> 
> Can somebody please help me?
> 
>   Thanks
>   Annemarie
> ___
> 
> Dr. Annemarie Honegger PhD
> Department 
> of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
> 
> e-Mail: honeg...@bioc.uzh.ch 
> 
> websites
> http://www.bioc.uzh.ch/plueckthun 
> http://www.bioc.uzh.ch/plueckthun/antibody 
> 
> http://www.bioc.uzh.ch/plueckthun/nanowelt 
> 
> 
> 
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Re: [Open Babel] SMARTS query

[David Hall]

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:
> 
> Good day,
>  
> I wonder if somebody could please help me with the construction of a SMARTS 
> query.
>  
> I am trying to search for compounds that have a five-membered ring attached 
> to the para- position of an unsubstituted pyridine ring.
>  
> I have tried the following SMARTS expression: 
>  
> [c1ccncc1]-!:-!:[r5]
> However when I ran this SMARTS pattern it doesn’t appear to be bringing back 
> the expected structures.
> I was also not sure how to specify explicit hydrogen atoms on the pyridine 
> ring in the SMARTS expression.
> I wonder if you could please help me with this query?  What is the best way 
> to construct the necessary SMARTS?
>  
> Best regards,
> David
> __
> David Gravestock, Ph.D.
> 
> Chemical Indexing Unit, Syngenta, Jealott's Hill International Research 
> Centre, Bracknell, Berkshire, RG42 6EY, United Kingdom
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> 
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>  
> 
>  
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> Park, Guildford, Surrey, GU2 7YH, United Kingdom
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Re: [Open Babel] - problem with PHP script

[David Hall]

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 
each change.

-David

> On Mar 17, 2016, at 6:21 AM, Muriel Keribin  wrote:
> 
> Hello,
> 
> I have a problem with the PHP script of Openbabel (I must use it for a 
> project).
> 
> I downloaded it from the git repository and I compile with php binding
> ($ cmake -DBUILD_GUI=FALSE -DCMAKE_INSTALL_PREFIX=/usr/local/openbabel 
> -DRUN_SWIG=ON -DPHP_BINDINGS=ON .. )
> The installation seems to work (two test of the 155 failed, without php all 
> tests works but I do not think it is a big issue). But I cannot launch the 
> php script.
> I am obtaining the following error :
> 
> PHP Warning:  dl(): Dynamically loaded extensions aren't enabled in 
> /usr/local/openbabel/lib/openbabel.php on line 22
> PHP Fatal error:  Call to undefined function new_OBMol() in 
> /usr/local/openbabel/lib/openbabel.php on line 7466
> 
> I tried to preload the libray, (LD_PRELOAD=...) but then it tells me it 
> cannot read the library file.
> I changed the new_OBMol() in new OBMol() in the openbabel.php, and then I 
> obtain a error of memory allocation.
> 
> So I am wondering what I am doing wrong, and if I should change some options 
> in the "swig"
> 
> I am using a virtual machine linux (x86_64-linux-gnu), gcc version 4.8.4, php 
> 5.5.9 and swig 2.0.11
> 
> Thank you and kinds regards,
> Muriel
> 
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Re: [PyMOL] why lib/python folder is missing?

[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 PYmol:
> 
> setenv prefix /home/albert/install/pymol/open-1.8
> setenv modules $prefix/modules
> python setup.py build install --home=$prefix --install-lib=$modules 
> --install-scripts=$prefix
> 
> However, I noticed that there is no the "lib/python2.7" folder in the 
> installation directory..
> 
> normally this should be placed in :
> 
> /home/albert/install/pymol/open-1.8/ext/lib/python2.7
> 
> I am just wondering how can we fix this problem?
> 
> thanks a lot
> 
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Re: [PyMOL] Filled rings on stick mode

[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 have the rings filled for the 
> nucleobases (or nucleobases + riboses) while being simply in the mode "stick" 
> and not in the "cartoon" mode.
> 
> Many thanks for your answers,
> 
> 
> Maria,
> 
> I2BC - CNRS
> France
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Re: [Talk-se] Operator på postlådor

[David Hall]

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 Sat, Jan 23, 2016 at 1:37 PM Kristoffer Malmström 
wrote:

> Bara en liten rättelse.. Posten har inte köpts upp av PostNord. Posten är
> PostNord under nytt namn efter att man 2009 slog ihop svenska Posten och
> Post Danmark där bolaget till en början hette Posten Norden och sedan
> (2015) bytte namn i Sverige på den svenska postoperatören Posten AB till
> PostNord Group AB och använder sig nu av varumärket PostNord.
>
> Det är bara Bring som konkurrerar med PostNord med brevutdelning, men de
> har inga postlådor och har bara företagskunder.
>
> *Med vänliga hälsningar*
> *Kristoffer Malmström*
> Tel: 0733690161
>
> Den 23 januari 2016 10:56 skrev Mikael Nordfeldth :
>
>> "Andreas Vilén"  skrev: (23 januari 2016
>> 10:45:25 CET)
>> >Finns det andra än Posten/Postnord
>> >som
>> >har den här typen av postlådor i Sverige?
>>
>> Själv har jag vid kartläggning av brevlådor inte angett operator= för att
>> jag tänker att det är implicit Posten/postnord som är det om det inte t.ex.
>> är någon slags lokal/intern/privatägd brevlåda (varpå jag skulle märka ut
>> det).
>>
>> Har inget erfaret svar på ditt förslag utan mer en fundering om ändringen
>> då istället skulle kunna vara att lämna operator tom?
>>
>>
>> --
>> Mikael Nordfeldth
>> XMPP/mail: m...@hethane.se
>>
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Re: [PyMOL] pdb edition

[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 mode 
http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#move

And then save http://pymolwiki.org/index.php/Save


But honestly, the description sounds like something that would be infinitely 
easier to do using some plain python code rather than in pymol.

-David


> On Jan 19, 2016, at 4:59 PM, Edward A. Berry  wrote:
> 
> 
> 
> On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote:
>> Hi Pascual,
>> 
>> The PDB file does not really have information on bonds. If atoms are closer 
>> than some cutoff a bond is drawn. Unbonding and saving will not change the 
>> distance, so the bond will be drawn again when loaded again. What is your 
>> aim?
>> 
>> Cheers,
> 
> (Actually of course the PDB file format does (or did) have a way to specify
> bonds, but i guess no programs ever used it)
> But the poster did specify moving atoms (to) break bonds and separate atoms,
> so maybe that is where the help is needed- how do you move atoms in Pymol?
> Or since this is probably a RTFM-type question, perhaps a pointer
> to chapter and verse in the wiki would be more appropriate?
> And then to save the modified pdb: I suppose file:save:molecule, and
> it will be obvious which molecule to save?
>> 
>> Tsjerk
>> 
>> On Tue, Jan 19, 2016 at 12:15 PM, Pascual Lahuerta >  > >> wrote:
>> 
>>I am new user of Pymol and I would like to use this program for a very 
>> simple task that I describe here in three steps:
>> 
>>1. Start with a simple structure (structure 1.pdb1) either loaded or 
>> created with the editor.
>>2. The second task will be to change the position of the atoms in 
>> structure 1, breaking bonds and separating atoms.
>>3. The third step will be to save the resulting structure as 
>> structure2.pdb file.
>> 
>>I wonder if  pymol allows me to perform this task.  iI hope someone can 
>> guide me in this task.
>> 
>>Thanks in advance
>> 
>>Pascual
>>=
>> 
>> 
>>Pascual Lahuerta
>>Universitat de Valencia
>>Dep. Q. Inorganica
>>Edificio Investigación 3.36
>>Dr. Moliner 50
>>46100 Burjassot-Valencia
>>Despacho 96 354 3147
>>Movil 617 188 331
>>lahue...@uv.es  > >
>> 
>> 
>> 
>>
>> --
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>> > >)
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>> 
>> 
>> 
>> 
>> --
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>> 
>> 
>> 
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Re: Eigenvalue solver

[David Hall]

(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
implicitly/distributed, whatever) by a breeze.linalg.DenseVector.

This is the Breeze implementation for sparse SVD (which is fully generic
and might be hard to follow if you're not used to Breeze/typeclass-heavy
Scala...)

https://github.com/dlwh/breeze/blob/aa958688c428db581d853fd92eb35e82f80d8b5c/math/src/main/scala/breeze/linalg/functions/svd.scala#L205-L205

The difference between SVD and EVD in arpack (to a first approximation) is
that you need to multiple by A.t * A * x for SVD, and just A * x for EVD.

The basic idea is to implement a Breeze UFunc eig.Impl2 implicit following
the svd code (or you could just copy out the body of the function and
specialize it.) The signature you're looking to implement is:

implicit def Eig_Sparse_Impl[Mat](implicit mul: OpMulMatrix.Impl2[Mat,
DenseVector[Double], DenseVector[Double]],
  dimImpl: dim.Impl[Mat, (Int, Int)])
  : eig.Impl3[Mat, Int, Double, EigenvalueResult] = {

The type parameters of Impl3 are: the matrix type, the number of
eigenvalues you want, and a tolerance, and a result type. If you implement
this signature, then you can call eig on anything that can be multiplied by
a dense vector and that implements dim (to get the number of outputs).

(You'll need to define the class eigenvalue result to be what you want. I
don't immediately know how to unpack ARPACK's answers, but you might look
at this scipy thing:
https://github.com/thomasnat1/cdcNewsRanker/blob/71b0ff3989d5191dc6a78c40c4a7a9967cbb0e49/venv/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py#L1049
)

I'm happy to help more if you decide to go this route, here, or on the
scala-breeze google group, or on github.

-- David


On Tue, Jan 12, 2016 at 10:28 AM, Lydia Ickler 
wrote:

> Hi,
>
> I wanted to know if there are any implementations yet within the Machine
> Learning Library or generally that can efficiently solve eigenvalue
> problems?
> Or if not do you have suggestions on how to approach a parallel execution
> maybe with BLAS or Breeze?
>
> Thanks in advance!
> Lydia
>
>
> Von meinem iPhone gesendet
> -
> To unsubscribe, e-mail: dev-unsubscr...@spark.apache.org
> For additional commands, e-mail: dev-h...@spark.apache.org
>
>

Re: [PyMOL] optimize and open babel troubles

[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:
> 
> Hello all,
> 
> I am trying to utilize the optimize plugin within pymol. I have installed 
> open babel per their instructions on their website. All of the "test to see 
> if it is working" tests seem to work (eg,using import openbabel in the cmd 
> window).
> 
> For what it is worth, I am running 64 bit windows, but am using the 32 bit 
> windows pymol since there doesn't seem to be a 64 bit version of open babel 
> for windows.
> 
> When I load pymol, I still get the following:
> "Optimize plug-in needs openbabel to be installed in your system, please 
> follow the instructions at
> http://openbabel.org/wiki/Get_Open_Babel 
> "
> 
> Several other plugins also fail to load properly, due to the inability to 
> import scimath.
> 
> I have also tried this on ubuntu 12.04, but that is a 32 bit operating system 
> and it seems there is no 32 bit linux version of pymol readily available.
> 
> Thanks for your time,
> Joe
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Re: [PyMOL] Pymol issues for coloring ball and stick representation

[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 all
> 
> I am a user of PyMol using an academic version (free). 
> I am trying to develop a 3D model for my protein-protein interactions. I have 
> chosen a ball and stick preset representations.
> The problem is that I cannot get a single color for the stick and the ball 
> for representing my molecule. While the ball color is easily changed, the 
> stick color remains grey. I have tried most of the options for color change 
> but am not getting the desired results. Any suggestions for this?
> 
> Anurag
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Re: [PyMOL] Pymol under El Capitan

[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 (
> http://www.macinchem.org/blog/files/c92b0faf48c1bb7dee5eeba1260cff43-1657.php)
> and I tried a pre installed version of Pymol and it worked without issue.
> However I have had a few readers email me saying they are having problems
> so I took a new machine running El Capitan and tried to instal a variety of
> cheminformatics tools including Pymol using Homebrew and PIP as described
> here (http://www.macinchem.org/reviews/cheminfo/cheminfoMac.php). All
> worked fine except Pymol which opened but crashed with the following error.
>
> Username:~ prompt$ pymol
>  PyMOL(TM) Molecular Graphics System, Version 1.7.6.0.
>  Copyright (c) Schrodinger, LLC.
>  All Rights Reserved.
>
>
> Created by Warren L. DeLano, Ph.D.
>
>
> PyMOL is user-supported open-source software.  Although some versions
> are freely available, PyMOL is not in the public domain.
>
>
> If PyMOL is helpful in your work or study, then please volunteer
> support for our ongoing efforts to create open and affordable
> scientific
> software by purchasing a PyMOL Maintenance and/or Support subscription.
>
> More information can be found at "http://www.pymol.org;.
>
>
> Enter "help" for a list of commands.
> Enter "help " for information on a specific command.
>
>  Hit ESC anytime to toggle between text and graphics.
>
>  Detected OpenGL version 2.0 or greater. Shaders available.
>  Detected GLSL version 1.20.
>  OpenGL graphics engine:
>   GL_VENDOR:   NVIDIA Corporation
>   GL_RENDERER: NVIDIA GeForce 8600M GT OpenGL Engine
>   GL_VERSION:  2.1 NVIDIA-10.0.40 310.90.10.05b12
>  Detected 2 CPU cores.  Enabled multithreaded rendering.
> libpng warning: Application built with libpng-1.6.19 but running with
> 1.5.23
> /usr/local/bin/pymol: line 4:  3628 Segmentation fault: 11
> "/usr/local/opt/python/bin/python2.7" "/usr/local/Cellar/pymol/
> 1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__init__.py" "$@“
>
> Any suggestions?
>
> Cheers
> Chris
>
>
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Re: [PyMOL] on PDB

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

[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  wrote:

> Dear All,
>
> Is any way we can colour the molecule by pymol based on the y values in
> the z y z coordinates, so that we can view easily the residues (or atoms)
> with equivalent position in the primary sequence but has a y-axis shift in
> the 3-D structure?
>
> Smith
>
>
>
>
>
> --
>
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Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

[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 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 <smith_liu...@163.com> wrote:
>
>> Dear All,
>>
>> Is any way we can colour the molecule by pymol based on the y values in
>> the z y z coordinates, so that we can view easily the residues (or atoms)
>> with equivalent position in the primary sequence but has a y-axis shift in
>> the 3-D structure?
>>
>> Smith
>>
>>
>>
>>
>>
>> --
>>
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Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

[David Hall]

clearly shouldn’t write e-mails before having my morning coffee. Those %
symbols should have been pounds, I was aiming to make comments


As an example:

fetch 1acb, prot,  async=0
stored.y=[]
iterate_state 1, prot, stored.y.append(y)
alter prot, b=stored.y.pop(0)
spectrum b



On Nov 18, 2015, at 9:12 AM, Smith Liu <smith_liu...@163.com> wrote:

Dear David,

I am unfamiliar with the pymol scripts so I do not understands where your
scripts end at each line. Can we write this way,

stored.y=[]
iterate_state 1, prot, stored.y.append(y)
alter prot, b=stored.y.pop(0)

which means those from % in your scripts will be not used in each line for
pymol reading?

Can you introduce a website to introduce the pymol scripts? For stored.y=，
following y= is it the file name of file stores y for each coordinates? Can
you introduce to me a server or software which can extract y coordinates
from the 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.net> wrote:

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 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 <smith_liu...@163.com> wrote:
>
>> Dear All,
>>
>> Is any way we can colour the molecule by pymol based on the y values in
>> the z y z coordinates, so that we can view easily the residues (or atoms)
>> with equivalent position in the primary sequence but has a y-axis shift in
>> the 3-D structure?
>>
>> Smith
>>
>>
>>
>>
>>
>> --
>>
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Re: [PyMOL] placing protein into lipid bilayer

[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 top of the atoms of the membrane.

For this, they likely:
1) Open protein and equilibrated membrane in pymol
2) From the menu: Choose Mouse-> 3 button editing
3) Shift+Middle click to move the protein on top of the membrane
4) Shift+Left click to rotate the protein into the desired orientation.
5) save the protein in its new location

Then, they run the program they wrote, which uses grimaces to insert the
protein into the membrane at roughly the position and orientation where
they have dragged it.

If you don't have any experimental evidence for how the protein sits in the
membrane, http://opm.phar.umich.edu/server.php can give you a start.




On Sat, Nov 14, 2015 at 11:35 AM, samira poulakchi 
wrote:

> there is an article''g membed: Efficient insertion of a membrane protein
> into an equilibrated lipid bilayer with minimal perturbation.'' which use
> pymol to insert protein into bilayer membrane. How can they do it?
>
>
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Re: [PyMOL] Pymol Morph movie error

[David Hall]

Are you using “Incentive Pymol” (that based on a license from Schrodinger) or 
“Open Source Pymol” (that built from source code)?

For anyone looking for mpeg_encode source code on freemol.org , there is source 
code in the svn repository

http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_encode/

-David

> On Oct 20, 2015, at 4:46 AM, <h.c.van_leeu...@lumc.nl> 
> <h.c.van_leeu...@lumc.nl> wrote:
> 
> Dear Thomas, David,
>  
> I appreciate your help.
> First I'm using windows 7.
>  
> The link from:
> http://freemol.org <http://freemol.org/>
> leading to 
> http://bmrc.berkeley.edu/frame/research/mpeg/mpeg_encode.html 
> <http://bmrc.berkeley.edu/frame/research/mpeg/mpeg_encode.html>
>  
> is empty.(?)
>  
> David your link is for Linux correct?
> http://software.opensuse.org/download.html?project=home%3Acowsandmilk=mpeg_encode
>  
> <http://software.opensuse.org/download.html?project=home%3Acowsandmilk=mpeg_encode>
>  
> I attached my Pymol file maybe you can see whether you get the same error. 
> (The movie is mout)
>  
> Thanks again,
>  
> Hans
>  
>  
>  
> -Original Message-
> From: Thomas Holder [mailto:thomas.hol...@schrodinger.com 
> <mailto:thomas.hol...@schrodinger.com>] 
> 
>  
> David, Incentive PyMOL does bundle mpeg_encode.exe and uses it for movie 
> export. It is also available 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...@cowsandmilk.net>> wrote:
>  
> > 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) 
> > athttps://build.opensuse.org/package/show/home:cowsandmilk/mpeg_encode 
> > <https://build.opensuse.org/package/show/home:cowsandmilk/mpeg_encode> , 
> > you can download by clicking the files with the up arrow (I know, those 
> > symbols make no sense).
> > 
> > It uses an old version of libjpeg with apis that have been long abandoned.
> > 
> > Basically, you don't have a binary for what I think is a long abandoned 
> > program that depends on old versions of libraries.
> > 
> > Hopefully someone else will tell me there's some magical updated version 
> > floating around out there, but I doubt it. Otherwise, no new features in 20 
> > years and no bug/compatibility fixes in 13.
> > 
> > -David
> > 
> -Original Message-
>  
> > On Mon, Oct 19, 2015 at 8:36 AM, <h.c.van_leeu...@lumc.nl 
> > <mailto:h.c.van_leeu...@lumc.nl>> wrote:
> > Dear Pymol community,
> > 
> >  
> > 
> > Im using Pymol 1.7.6 and created a morph movie. Looks nice on screen!
> > 
> > However when I tried to save the movie, I get an error:
> > 
> > --
> > 
> > produce: creating 'C:/Users/hcvanleeuwen/Desktop/test2.mpg' (in 
> > background)...
> > 
> > please wait ...
> > 
> > Error: mpeg_encode did not run
> > 
> > Traceback (most recent call last):
> > 
> >   File "C:\Program Files\PyMOL\\PyMOL/modules\freemol\mpeg_encode.py", line 
> > 35, in run
> > 
> > mpeg_encode_in, mpeg_encode_out, mpeg_encode_err = 
> > os.popen3(_mpeg_encode_exe)
> > 
> > WindowsError: [Error 2] The system cannot find the file specified: 'Ex: 
> > C\\Temp /c "C:\\Program  
> > Files\\PyMOLPyMOL\\ext\\bin\\mpeg_encode.exe"'
> > 
> > produce: compression failed
> > 
> > -
> > 
> > Anyone suggestions how to solve this?
> > 
> > Thanks in advance,
> > 
> > Hans van Leeuwen
>  
> 

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Re: [PyMOL] Pymol Morph movie error

[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 arrow (I know, those symbols
make no sense).

It uses an old version of libjpeg with apis that have been long abandoned.

Basically, you don't have a binary for what I think is a long abandoned
program that depends on old versions of libraries.

Hopefully someone else will tell me there's some magical updated version
floating around out there, but I doubt it. Otherwise, no new features in 20
years and no bug/compatibility fixes in 13.

-David


On Mon, Oct 19, 2015 at 8:36 AM,  wrote:

> Dear Pymol community,
>
>
>
> Im using Pymol 1.7.6 and created a morph movie. Looks nice on screen!
>
> However when I tried to save the movie, I get an *error*:
>
> --
>
> *produce**: creating 'C:/Users/hcvanleeuwen/Desktop/test2.mpg' (in
> background)...*
>
> *please wait ...*
>
> *Error**: mpeg_encode did not run*
>
> *Traceback (most recent call last):*
>
> *  File "C:\Program Files\PyMOL\\PyMOL/modules\freemol\mpeg_encode.py",
> line 35, in run*
>
> *mpeg_encode_in, mpeg_encode_out, mpeg_encode_err =
> os.popen3(_mpeg_encode_exe)*
>
> *WindowsError**: [Error 2] The system cannot find the file specified:
> 'Ex: C\\Temp /c "C:\\Program
> Files\\PyMOLPyMOL\\ext\\bin\\mpeg_encode.exe"'*
>
> *produce: compression failed*
>
> -
>
>
>
> Anyone suggestions how to solve this?
>
>
>
> Thanks in advance,
>
>
>
> Hans van Leeuwen
>
>
>
>
>
>
>
>
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Re: [PyMOL] pymol to webGL?

[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 cmd.get_session) has changed in recent upgrades.
> I have to rewrite the program.
> 
> Does anyone know if there is a setting to export in the 'old' format?
> 
> Best regards,
> 
> Takanori Nakane
> 
> On 2015/10/18 1:47, Osvaldo Martin wrote:
>> That really weird! the script is expecting a list but is getting an
>> integer. Could you send me the "my" molecule or a pse file with that
>> molecule? or at least other molecule that give you the same error?
>> 
>> Cheers,
>> Osvaldo.
>> 
>> 
>> 
>> On Sat, Oct 17, 2015 at 5:49 PM, Albert  wrote:
>> 
>>> Thanks a lot for further advice.
>>> 
>>> Here is what I got:
>>> 
>>> PyMOL> run exportToWeb.py
>>> PyMOL>exportToWeb my
>>> Traceback (most recent call last):
>>>   File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line
>>> 256, in parse
>>> self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>>>   File "exportToWeb.py", line 118, in dump_rep
>>> ret += parseObjMol(obj)
>>>   File "exportToWeb.py", line 50, in parseObjMol
>>> if (rep[5] == 1):
>>> TypeError: 'int' object has no attribute '__getitem__'
>>> 
>>> 
>>> If possible, would you please give me some suggestions?
>>> 
>>> Thanks a lot
>>> 
>>> Albert
>>> 
>>> 
>>> 
>>> 
>>> On 10/17/2015 04:36 PM, Osvaldo Martin wrote:
>>> 
>>> Hi Albert,
>>> 
>>> I do the following steps and I get a .html file as expected.
>>> 
>>>1. I download and unpack this
>>>
>>> 
>>>file. The script there seems to be similar to the one you attached.
>>>2. Lauch PyMOL and do some stuff
>>>3. cd to the folder creating during unpacking
>>>4. run the script by doing
>>> 
>>> run exportToWeb.py
>>> 
>>>5. then run the commnand
>>> 
>>> exportToWeb PymolObjectName
>>> 
>>>where PymolObjectName is the name of the pymol object you want to
>>>export
>>>6. check the unpacked folder for a file with the name
>>>PymolObjectName.html
>>> 
>>> Could you try to follow these steps and tell us what you get?
>>> 
>>> Cheers,
>>> 
>>> Osvaldo.
>>> 
>>> 
>>> 
>> 
>> 
>> 
>> --
>> 
>> 
>> 
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> 
> 
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Re: [Rdkit-discuss] cis/trans directional bond and smiles strings in python

[David Hall]

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:
> 
> Hi all,
> 
> I just found an unexpected behaviour in the current RDKit. My input is a 
> perfectly valid smiles with explicitly specified double bond configuration. 
> Actually, similar smiles were obtained using the RDKit.
> 
> The problem is, when submitting the smiles string containing an \n to 
> MolFromSmiles only the part before the \n is used and the rest is 
> disregarded. The \ needs to be quoted to a \\ in order to work correct. 
> 
> Is this a desired / expected behaviour?
> 
> Best,
> Michael
> 
> 
> --
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Re: [ccp4bb] Advice for Structure Determination

[David Hall]

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: [ccp4bb] Advice for Structure Determination

Xe at longish wavelength (> 1.5Å), if you can find a pressure device (LURE 
maybe?)

Phil

> On 5 Oct 2015, at 09:08, Marc Graille  wrote:
> 
> Dear Monica,
> 
> I had solved couple of structures using anomalous signal for tungsten. I have 
> incubated the proteins with 25-50mM NaWO3 and set-up the crystallization 
> trays. 
> If you are lucky, WO3 might interact with your protein as SO4 ions do 
> sometimes and you might be able to get anomalous signals.
> This works fine for nucleic acid binding proteins.
> 
> Otherwise, I have also solved a structure of a protein expressed in Pichia 
> using anomalous signal from SeMet. It might be time-consuming and complicated 
> to get labeled protein in Pichia but could be faster than heavy atoms 
> derivatives.
> Here is a link to the publication describing the SeMet labeling procedure.
> http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed/26082394
> 
> Hope it helps,
> 
> Good luck,
> 
> Marc
> 
>> Le 5 oct. 2015 à 09:38, Monica Mittal  a écrit :
>> 
>> Dear all,
>> 
>> I need a general advice. I don't have a suitable Model (Lets say only with a 
>> similarity of 15%) and no other model to solve the structure by MR. Then i 
>> think of anomalous experiments, but soaking with heavy metals is not good 
>> for the crystals. Since the protein is being expressed in Pichia cells, 
>> growth in Seleno-media is cumbersome. There are no ligands or ions that i 
>> can use for anomalous scattering of protein crystals. I am trying to express 
>> it in bacteria but have some issues. What is the option that i can choose to 
>> solve the structure of such a protein ? Your suggestions are highly 
>> recommended.
>> 
>> Thanks in advance.
>> Monica
> 
> Marc GRAILLE, PhD
> Directeur de recherche CNRS
> 
> Laboratoire de Biochimie
> ECOLE POLYTECHNIQUE - UMR7654 CNRS
> 91128 PALAISEAU CEDEX
> 
> 
> 
> Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09
> 
> Email: marc.grai...@polytechnique.edu
> 
> Team: Translation and degradation of eukaryotic mRNAs
> http://bioc.polytechnique.fr/spip.php?rubrique117
> Team supported by the ATIP-Avenir CNRS program
> 
> 
> 

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Re: [PyMOL] Using cartoon putty-like command

[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 a pdb files with b-factors that i
> would like to represent as the *cartoon putty* command is doing.(ie pdb
> file)
> The main problem is that I don't precisely know what *cartoon putty* is
> doing.
>
> So I would like to know where the code of cartoon putty is hidden in pymol
> and how the code could be modify in order to work on all atoms rather than
> CA.
>
> Many thanks,
>
>
> --
> *Damien CLAVEL*
> Cellphone +33 7 81 66 61 70
> Landline   +33 4 57 42 87 35
> PhD student at Laboratoire Chimie Physique (UP Sud)
> and Institut de Biologie Structurale (EPN Campus)
> --
> Laboratoire de Chimie Physique
> Institut de
> Biologie Structurale 
> Bul. 350 Campus Orsay EPN Campus
> 15, Av. Jean Perrin 6, rue Jules Horowitz
> F-91405 ORSAY Cedex F-38000 GRENOBLE
>
>[image: Image and video hosting by TinyPic]
> 
>
>
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[kde-doc-english] Documentation

[David Hall]

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 menu item 'File-> 'New Wallet'  

what menu?? where?  In this window there is a File item in the menu with just 
'Print' and 'Quit'

Use the 'New' button.

what new button where???

On the first attempt to store login information in a wallet when you did not 
create a wallet so far, ..

have someone correct your English =

If you have not created a wallet yet, then ..

Blowfish encryption

 KWallet saves this sensitive data for you in a strongly encrypted file.

 (finally a definition of what has been up to now a vague concept)

farther down

Launch KWallet Manager - how do I do that?

and select your old wallet - old wallet, new wallet, 
  I have no wallets at all at this point
  

It's all quite frustrating.

D. Hall
rapidr...@yahoo.de





 


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

[David Hall]

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:

> Dear Nicholas,
>
> We need to have access rawData in javascript directly from gz files but
> the python pickle.load function has no equivalent in javascript as far as
> I know.
>
> So I need to find a way either to read the file in JS or to extract those
> data into json format or binary json.
>
> Best regards,
>
> *Dr. Guillaume GODIN*
>
> Project Manager
>
> Innovation
>
> CORPORATE R DIVISION
>
> DIRECT LINE +41 (0)22 780 3645
>
> MOBILE   +41 (0)79 536 1039
>
> *Firmenich SA*
>
> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
> --
> *De :* Nicholas Firth [nicholas.fi...@icr.ac.uk]
> *Envoyé :* dimanche, 6. septembre 2015 15:59
> *À :* Guillaume GODIN
> *Cc :* rdkit-discuss@lists.sourceforge.net
> *Objet :* Re: [Rdkit-discuss] NP-score and SA-score datas
>
> Dear Guillaume,
>
> This is a one liner in Python, the model is saved as a Python dictionary
> in the case of the NP model and I believe the SA score is a Python list.
> Probably best you work out what you want to do with it rather than have
> multiple versions of such large files packaged with the source.
>
> >>> import gzip, pickle
> >>> rawData = pickle.load(gzip.open('publicnp.model.gz', 'rb'))
>
> Best,
> Nick
>
> *Nicholas C. Firth* | PhD Student | Cancer Therapeutics
> The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton |
> Surrey | SM2 5NG
>
> *T* 020 8722 4033 | *E* nicholas.fi...@icr.ac.uk | *W* www.icr.ac.uk |
> *Twitter* @ICRnews 
>
> *Facebook* www.facebook.com/theinstituteofcancerresearch
>
> *Making the discoveries that defeat cancer*
>
>
> On 6 Sep 2015, at 14:52, Guillaume GODIN 
> wrote:
>
> Dear all,
>
> I need the original unpickle data for javascript to implement those two
> descriptor in RDKitjs.
>
> Can you provide publicnp.model.gz fpscores.pkl.gz uncompressed files
> please ?
>
> thanks in advance
>
> Best regards,
>
> *Dr. Guillaume GODIN*
>
> Project Manager
>
> Innovation
>
> CORPORATE R DIVISION
>
> DIRECT LINE +41 (0)22 780 3645
>
> MOBILE   +41 (0)79 536 1039
>
> *Firmenich SA*
>
> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
>
> **
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Re: [PyMOL] creation of a sphere

[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 
 message instead of the pseudoatom:
  
 Traceback (most recent call last):
   File C:\Program Files (x86)\DeLano 
 Scientific\PyMOL/modules\pymol\parser.py, line 370, in parse
 exec(com2[nest]+\n,pymol_names,pymol_names)
   File string, line 1
  pseudoatom name
   ^
 SyntaxError: invalid syntax
  
 What is the error? What do I have to change?
  
 Thanks for your help,
 Christian
  
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Re: [PyMOL] Python from PyMOL or PyMOL from Python?

[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

Other options at: http://www.pymolwiki.org/index.php/Command_Line_Options 
http://www.pymolwiki.org/index.php/Command_Line_Options


Why is this my preferred method?
Running python from pymol doesn’t require you to do any of these arcane things 
like call “finish_launching”, etc. You just write a python script and run it.



 On Aug 14, 2015, at 5:27 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote:
 
 Dear PyMOLers,
 
 I want to modify atomic coordinates in a python program and make 
 pictures with PyMOL for making a movie.
 
 In your experience, is it better to call the python program from PyMOL 
 or to call PyMOL from the python program?
 
 And could you please give me any good pointer for your preferred method 
 (other than the simple scripting tutorial)?
 
 Best regards,
 
 Dirk.
 
 -- 
 
 ***
 Dirk Kostrewa
 Gene Center Munich, A5.07
 Department of Biochemistry
 Ludwig-Maximilians-Universität München
 Feodor-Lynen-Str. 25
 D-81377 Munich
 Germany
 Phone:  +49-89-2180-76845
 Fax:+49-89-2180-76999
 E-mail: kostr...@genzentrum.lmu.de
 WWW:www.genzentrum.lmu.de
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Re: [Open Babel] pybel.write() produces truncated pdbqt? (R. K. Belew)

[David Hall]

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
 Segmentation fault: 11
 obabel file1.pdbqt -O file2.pdb
 1 molecule converted
 
 and has nothing particular to do with pybel;  pybel is
 silently eating this fault and generating only partial
 output before it dies.
 
   Rik
 
 
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Re: [ccp4bb] Off-topic: Transfering data from Diamond

[David Hall]

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: 31 July 2015 11:20
To: ccp4bb
Subject: Re: [ccp4bb] Off-topic: Transfering data from Diamond

You can SSH to diamond using the host: nx.diamond.ac.uk

Jonathan

On 30/07/15 23:00, Mohamed Noor wrote:
 Dear all
 
 I have about 70 folders of data collected at Diamond. As I only want to keep 
 about 50 of them, is there a script that can read in the folder names from a 
 text file and download those?
 
 Normally, I use FileZilla but it gets tedious to click so many times after a 
 while
 
 Secondly, some folders have one sweep of data, some others with two or even 
 three, is it possible to run a command from terminal that will filter 
 different sweeps and output the number of frames?
 
 For example, in a folder with files:
 
 _sweep1_0001.cbf - _sweep1_1800.cbf _sweep2_0001.cbf - 
 _sweep2_0900.cbf
 
 I want to get a text file output containing a line saying:
 /folder/name/sweep1 - 1800
 /folder/name/sweep2 - 900
 
 The idea is so that I can feed those lines into XDS.INP without checking how 
 many sweeps there are in each folder and how many frames.
 
 I'm pretty sure someone on the BB has a trick for this.
 
 Thanks.
 

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

[David Hall]

I assume you are referring to 
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/fitting.py 
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/fitting.py

That is a script that creates a function. To turn it into a program, you need 
to set up what you read in and what you output.

In python, this is often done by command line arguments that can read from 
sys.argv 

import sys

arg1 = sys.argv[1]
arg2 = sys.argv[2]

cmd.load(arg1, “protein1”)
cmd.load(arg2, “protein2”)

You can have the definition of fitting in your script, then call

fitting(“protein1”, , “protein2”, )

I left in questions for the select1 and select2 arguments of the function since 
it is not at all clear what you would like to put in as arguments there.

Beyond that, I would recommend reading up on python assuming you are not 
familiar with the language.

-David


 On Jul 11, 2015, at 10:00 AM, Gazal gazal...@gmail.com wrote:
 
 Thank you for your help, Osvaldo and David.
 
 I tried using the command but did not get the RMS as expected.. Following are 
 the results:
 
 1.
 pymol -cqr fitting.py 1A6M.pdb 4OE9.txt
 PyMOLrun fitting.py,main
 HEADEROXYGEN TRANSPORT26-FEB-98   1A6M
 TITLE OXY-MYOGLOBIN, ATOMIC RESOLUTION
 COMPNDMOL_ID: 1;
 COMPND   2 MOLECULE: MYOGLOBIN;
 COMPND   3 CHAIN: A
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 2 symmetry operators.
  CmdLoad: 1A6M.pdb loaded as 1A6M.
 HEADERPROTEIN BINDING 12-JAN-14   4OE9
 TITLE THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF COMMD9
 COMPNDMOL_ID: 1;
 COMPND   2 MOLECULE: COMM DOMAIN-CONTAINING PROTEIN 9;
 COMPND   3 CHAIN: A, B;
 COMPND   4 FRAGMENT: COMMD9, UNP RESIDUES  1-117;
 COMPND   5 ENGINEERED: YES;
 COMPND   6 MUTATION: YES
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  Symmetry: Found 1 symmetry operators.
  CmdLoad: 4OE9.txt loaded as 4OE9.txt.
 
 2.
 pymol -cqr fitting.py --1A6M.pdb 4OE9.txt
 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://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 
 mailto:gazal...@gmail.com wrote:
 
 Hi,
 
 I'm trying to find the RMSD values for batch purposes. The command which I 
 found works for the Pymol-command line. 
 I was hoping if I could get an idea about using the python script fitting.py 
 in my shell script without triggering the Pymol GUI.
 
 Thanks in advance.
 
 Gazal 
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Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

[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 values for batch purposes. The command which I 
 found works for the Pymol-command line. 
 I was hoping if I could get an idea about using the python script fitting.py 
 in my shell script without triggering the Pymol GUI.
 
 Thanks in advance.
 
 Gazal 
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Re: [PyMOL] Problem with loadBfact.py on windows

[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'

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Re: [Open Babel] Partial charge on OSX system

[David Hall]

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 guoy...@asu.edu wrote:
 
 Hi,
 
 I installed the recommend 'ilabel' on my OSX system. I would like to use 
 openbabel to generate the partial charge of my molecules. I could use the 
 mmff partial charge method. But I still need to use qeq method. But it shows 
 system could not find qeq. 
 
 My workmate uses openbabel on his windows system and it works for him. I am 
 wondering that could you please show me a way to implement qeq partial charge 
 on my Macbook.
 
 Thanks,
 
 
 -- 
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 Graduate Research Associate
 Email: guoy...@asu.edu mailto:guoy...@asu.edu
 School for Engineering of Matter, Transport and Energy
 Adaptive Intelligent Materials  Systems (AIMS) Center
 http://aims.engineering.asu.edu/ http://aims.engineering.asu.edu/
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Re: [PyMOL] how can we rotate torsion angle of a molecule?

[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 about how to rotate a torsion angle of a molecule.

http://www.pymolwiki.org/index.php/Set_dihedral 
http://www.pymolwiki.org/index.php/Set_dihedral
http://stackoverflow.com/questions/19958043/change-dihedral-angles-using-the-mouse-in-pymol/25355318#25355318
 
http://stackoverflow.com/questions/19958043/change-dihedral-angles-using-the-mouse-in-pymol/25355318#25355318

 Meanwhile, I am just wondering is it possible for pymol give alternative 
 rotamer conformation of a protein residue?

http://pymolwiki.org/index.php/Mutagenesis 
http://pymolwiki.org/index.php/Mutagenesis (using without mutating gives you 
rotamers for a residue)
http://www.pymolwiki.org/index.php/Rotamer_Toggle 
http://www.pymolwiki.org/index.php/Rotamer_Toggle

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Re: [PyMOL] opensource for commercial use?

[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 of a lawyer's time to understand what you should do to comply with
the license.

-David


On Fri, Jul 3, 2015 at 10:39 AM, Albert mailmd2...@gmail.com wrote:

 Hello:

 I just got a question: can we use the open source version of pymol for
 commercial usage? Or can we develop some commercial tool based on Pymol?

 thank you very much.

 Albert


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

[David Hall]

 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 read (jobs=[]), no ?
 
 No. It's a feature of garbage collection: your memory may come back 
 anytime between then and program exit.

One could always trigger garbage collection manually.

https://docs.python.org/2/library/gc.html#gc.collect 
https://docs.python.org/2/library/gc.html#gc.collect

And use gc.get_count() to make sure the count of objects went down with the 
collection.

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

[David Hall]

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 cont...@hjhimmler.de wrote:
 
 From: Contact [mailto:cont...@hjhimmler.de mailto:cont...@hjhimmler.de] 
 Sent: Wednesday, May 20, 2015 10:16 AM
 To: 'Greg Landrum'
 Subject: RE: [Rdkit-discuss] rdkit can not read sodium hexaflourophosphate 
 molfile
  
 HI Greg,
  
 thanks for the answer.
 Since I am not very familiar with the internals of rdkit-
 What exactly do you mean with ‘.. adding the extra allowed valence for P..’ ?
 Does that mean there exists some kind of ‘ptable’ and I can add an extra 
 valence there ? If yes, where is that ptable located ?
 If not, how do I add the extra valence otherwise ?
  
 Would appreciate you let me know.
 Best regards
 Hans-Juergen
  
 From: Greg Landrum [mailto:greg.land...@gmail.com 
 mailto:greg.land...@gmail.com] 
 Sent: Wednesday, May 20, 2015 4:53 AM
 To: Contact
 Cc: RDKit Discuss
 Subject: Re: [Rdkit-discuss] rdkit can not read sodium hexaflourophosphate 
 molfile
  
 Hi,
  
 Properly handing the hypervalent PF6- species has been on the RDKit todo list 
 for a while. There is a quick solution (adding the extra allowed valence for 
 P) and there's a right solution (revisiting the valence model). Every time 
 I start to do the first I think I should be doing the second, but I don't 
 have the time to dedicate to that, so it just sits.
  
 Rather than continuing this, I'll just go ahead and add the extra valence. :-)
 Here's the github item:
 https://github.com/rdkit/rdkit/issues/510 
 https://github.com/rdkit/rdkit/issues/510
  
 -greg
  
  
 On Tue, May 19, 2015 at 3:25 PM, Contact cont...@hjhimmler.de 
 mailto:cont...@hjhimmler.de wrote:
 HI,
  
 I did draw sodium hexaflourophosphate (using marvin) and saved the structure 
 as molfile.
 I have a very simple knime workflow. The workflow consist of a molfile 
 reader node and a rdkit ‘RDKit From Molecule’ node.
 The readmolfile node has no problems to read the molfile. 
 The rdkit ‚RDKit From Molecule’ node can not read the molfile (i.e. the 
 structure ends up in the  ‘Erroneous input data’ output port.
 The structure is drawn correct i.e. positive charge on sodium, negative 
 charge on the phosphor atom.
 The molfile is attached to the mail.
  
 Any idea why rdkit has problems with reading this molfile ?
  
 Any feedback or clarification is appreciated.
 Best
 Hans-Juergen
 
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Re: [PyMOL] PyMOL ball stick representation of imatinib in 2HYY

[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 
 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13248.html)
  to another users' query on this list so I went to the PyMOL Wiki page 
 hyperlinked in the answer and found this piece of code:
 
 preset.ball_and_stick(selection='all', mode=1)
 set_bond stick_color, white, selection, selection
 set_bond stick_radius, 0.14, selection, selection
 set sphere_scale, 0.25, selection
 show sticks, selection
 show spheres, selection
 
 I want to customize it such that the selection that is changed in 
 representation from the cartoon style (which is the present style for the 
 macromolecule  I'd like it to stay the representation style for the 
 macromolecule) to ball-and-stick style, is just het ID STI (i.e., the 
 imatinib ligand) in 2HYY. Any ideas of how I might achieve this? 
 
 Thanks for your time,
 Brenton
 
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Re: [PyMOL] APBS plugin not working on both Ubuntu Windows 7

[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 ./configure appears to do, I suggest following the steps in
the INSTALL file.

-David


On Tue, Apr 14, 2015 at 2:39 AM, Brenton Horne brentonho...@ymail.com
wrote:

 Hi,

 pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or
 1.8 versions; in a previous question I was advised to use the 1.8
 version) and consequently APBS tools doesn't work. I have tried turning
 the pdb2pqr.py.in into pdb2pqr.py by removing the in extension, but
 the APBS failed to set up the grid after I did this. Is there any way
 around this?

 Thanks for your time,
 Brenton


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Re: [Open Babel] Protonation issues in 2.3.2 version

[David Hall]

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 protonate molecules from sdf file.

 Using obabel version 2.3.2, several molecules cannot be protonated.
 Using the python binders pybel/openbabel, I noticed that the the problem is
 related to the output of the structure as a new sdf file.
  I.e.
  1: load molecule
   cpd = pybel.readfile(sdf, moli).next()
  2: protonation
   cpd.OBMol.AddHydrogens(False, pHcorr, pH)
  3: save output
   pybel.Outputfile(sdf,fname,overwrite=True)

 The problem is never related to the step 1 or 2 (even changing the
 protonation options) but at step 3, the code gets stuck.
 The same problem happens when running openbabel from terminal
 i.e.
   obabel -isdf am03.sdf -osdf -p 7.4
  or  obabel -isdf am03.sdf -osdf -p

 The issue takes place ONLY with some compounds and it is reproducible among
 them (in attachment you can find an example), even if I couldn't find a
 regular pattern. Associated to this problem, an analogue problem takes
 place
 when 3d coordinates generation is performed for the same molecules (obabel
 --gen3D or obgen or through python bindings).

 The same compounds are correctly protonated using older versions of
 openbabel (both 2.3.0 and 2.3.1, install from rpm packages available within
 debian, ubuntu and centos). The version that gives problem is the 2.3.2,
 both when compiled from source (without no apparent errors) and from the
 precompiled version (ubuntu 14.04) on different systems.

 I was wondering if anyone experienced similar problems with 2.3.2 version
 and what are the major warnings in downgrading to 2.3.1 version (that seems
 to not show this issue).

 In attachment you can find two compounds showing this very problem.

 Thank you in advance,
 Luigi

 am03.sdf
 http://forums.openbabel.org/file/n4658239/am03.sdf
 CHEMBL194749.sdf
 http://forums.openbabel.org/file/n4658239/CHEMBL194749.sdf





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

[David Hall]

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:
 http://openbabel.org/wiki/Install_(source_code)
 Ans as i used this command: 'cmake ../ob-src 21 | tee cmake.out’ i get
 the following error in the terminal:

 Allassanes-MacBook-Pro:ob-build acamara$ cmake ../ob-src 21 | tee
 cmake.out
 CMake Error: The source directory /Users/acamara/Downloads/ob-src does
 not appear to contain CMakeLists.txt.
 Specify --help for usage, or press the help button on the CMake GUI.



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

[David Hall]

sure.

On Wed, Mar 18, 2015 at 12:19 AM, Debasish Das debasish.da...@gmail.com
wrote:

 Hi David,

 We are stress testing breeze.optimize.proximal and nnls...if you are
 cutting a release now, we will need another release soon once we get the
 runtime optimizations in place and merged to breeze.

 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. So, I made a
  jira
  ticket about this issue. We need to upgrade breeze from 0.11.1 to
 0.11.2 or
  later in order to fix the bug, when the new version of breeze will be
  released.
 
  [SPARK-6341] Upgrade breeze from 0.11.1 to 0.11.2 or later - ASF JIRA
  https://issues.apache.org/jira/browse/SPARK-6341
 
  Thanks,
  Yu Ishikawa
 
 
 
  -
  -- Yu Ishikawa
  --
  View this message in context:
 
 http://apache-spark-developers-list.1001551.n3.nabble.com/mllib-Is-there-any-bugs-to-divide-a-Breeze-sparse-vectors-at-Spark-v1-3-0-rc3-tp11056p11058.html
  Sent from the Apache Spark Developers List mailing list archive at
  Nabble.com.
 
  -
  To unsubscribe, e-mail: dev-unsubscr...@spark.apache.org
  For additional commands, e-mail: dev-h...@spark.apache.org
 
 

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

[David Hall]

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. So, I made a
 jira
 ticket about this issue. We need to upgrade breeze from 0.11.1 to 0.11.2
 or
 later in order to fix the bug, when the new version of breeze will be
 released.

 [SPARK-6341] Upgrade breeze from 0.11.1 to 0.11.2 or later - ASF JIRA
 https://issues.apache.org/jira/browse/SPARK-6341

 Thanks,
 Yu Ishikawa



 -
 -- Yu Ishikawa
 --
 View this message in context:
 http://apache-spark-developers-list.1001551.n3.nabble.com/mllib-Is-there-any-bugs-to-divide-a-Breeze-sparse-vectors-at-Spark-v1-3-0-rc3-tp11056p11058.html
 Sent from the Apache Spark Developers List mailing list archive at
 Nabble.com.

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 To unsubscribe, e-mail: dev-unsubscr...@spark.apache.org
 For additional commands, e-mail: dev-h...@spark.apache.org

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

[David Hall]

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 to 0.11.2 or
 later in order to fix the bug, when the new version of breeze will be
 released.

 [SPARK-6341] Upgrade breeze from 0.11.1 to 0.11.2 or later - ASF JIRA
 https://issues.apache.org/jira/browse/SPARK-6341

 Thanks,
 Yu Ishikawa



 -
 -- Yu Ishikawa
 --
 View this message in context:
 http://apache-spark-developers-list.1001551.n3.nabble.com/mllib-Is-there-any-bugs-to-divide-a-Breeze-sparse-vectors-at-Spark-v1-3-0-rc3-tp11056p11058.html
 Sent from the Apache Spark Developers List mailing list archive at
 Nabble.com.

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

[David Hall]

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 ). 

You appear to have a version of python you installed yourself (2.7.9), but 
openbabel is linking to the system python that comes with OS X (2.7.5 on 
Mavericks).

running /usr/bin/python should allow you to use the system python and importing 
pybel should work.

-David


 On Mar 13, 2015, at 10:53 PM, Yujie Tian yujie...@buffalo.edu wrote:
 
 Hey,
 
 I am so sorry I asked such an unprofessional question. But I just started to 
 learn about computational chemistry from this month and I don’t have any 
 programming background before. Hope you can understand.
 
 I tried your suggestion and the output is like the following:
 
 dhcp037-051-095:openbabel YujieTian$ otool -L 
 /usr/local/Download/openbabel/lib/python2.7/site-packages/_openbabel.so
 /usr/local/Download/openbabel/lib/python2.7/site-packages/_openbabel.so:
   /System/Library/Frameworks/Python.framework/Versions/2.7/Python 
 (compatibility version 2.7.0, current version 2.7.5)
   /usr/local/Download/openbabel/lib/libopenbabel.4.dylib (compatibility 
 version 4.0.0, current version 4.0.0)
   /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
 version 1197.1.1)
   /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 
 1.2.5)
   /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
 120.0.0)
 
 
 In former process of compiling, python was disabled suddenly so I installed 
 it again. I think this may lead to different versions of python.
 Please teach me how to solve this problem. And please give me some details. I 
 cannot express to you how grateful I am.
 
 Thanks again! 
 
 Yujie
 
 On Mar 13, 2015, at 6:01 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com 
 mailto:geoff.hutchi...@gmail.com wrote:
 
 Hey, I add the path correctly, but it turns out to be an error.
 
 As I commented multiple times on the list, this error indicates you're 
 compiling and linking against different versions of Python.
 
 In your case, I can guarantee that otool -L 
 /usr/local/Download/openbabel/lib/python2.7/site-packages/_openbabel.so 
 does not link to whatever version of Python you're using.
 
 -Geoff
 
 

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

[David Hall]

What version of CMake are you using?

-David

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