Re: [PyMOL] APBS with ions

2021-11-03 Thread Thomas Holder
Hi Kamil,

The "Selection" field uses "polymer & ..." by default, which excludes
ions. You can use a selection which includes ions instead, for example
"all", "not solvent", or something like "(polymer | name CAL) & ...".

Here an example that works for me:

fetch 1rx1
alter elem Ca, resn="CAL"
alter elem Ca, name="CAL"

In the APBS Electrostatics panel, use "(polymer | name CAL) & 1rx1" as
the selection and "--ff=CHARMM" as pdb2pqr command line option.

Hope that helps.

Cheers,
  Thomas

On Mon, Nov 1, 2021 at 9:21 PM Kamil Steczkiewicz
 wrote:
>
> Hi,
> How to include Ca/Zn ions when using APBS built into Pymol? I'm switching to 
> CHARMM in command line options; CHARMM has CAL and ZN2 atoms already defined 
> in the DAT file. But there's still no difference in electrostatics maps with 
> and without ions in the structure. Also, the default 'prepared01' object 
> lacks the ions.
> Thanks for any clues,
> Kamil
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Re: [PyMOL] How to label on surface

2021-10-13 Thread Thomas Holder
Hi Yeping,

Try something like this, it moves the label 6 angstrom towards the front:

set label_position, [0,0,6]

See also
https://pymolwiki.org/index.php/label_position

Cheers,
  Thomas

> On Oct 11, 2021, at 05:52, sunyeping via PyMOL-users 
>  wrote:
> 
> Dear Pymol users,
> 
> I wish to label the one-letter residue names for a bunch of selected resides 
> on surface representation of a protein, but I found the labels cannot be seen 
> on the image. It seems that these labels can been seen on cartoon 
> representation when the surface is hide.
> Could you tell to how to show the labels on the surface?
> I will appreciate any help!
> 
> Best regards
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Re: [PyMOL] Capping of multiple pdb file using python script in pymol

2021-10-13 Thread Thomas Holder
Hi Shivani,

Your selection needs to be object-specific, e.g. like this:

for filename in glob("*.pdb"):
   cmd.load(filename)
   obj = filename[:-4]
   editor.attach_amino_acid(obj + " and resi 10 and name N", 'ace')

Hope that helps.

Cheers,
 Thomas


> On Oct 9, 2021, at 21:18, shivani sharma  wrote:
> 
> Hi everyone, 
> 
> I am trying to cap (with ace and nme) various *.pdbs. I made a folder, where 
> I have placed *.py file and *.pdb files. When I load the run following script:
> 
> from pymol import cmd, editor
> from glob import glob
> for filename in glob("*.pdb"):
>cmd.load(filename)
>editor.attach_amino_acid("resi 10 and name N", 'ace')
>editor.attach_amino_acid("resi 11 and name C", 'nme')
> 
> It is opening all files but capping only one of the files and giving me back 
> an error:
> Traceback (most recent call last):
>  File "pyformol.py", line 6, in 
>editor.attach_amino_acid("resi 10 and name N", 'ace')
>  File 
> "C:\Users\Shivani\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\pymol\editor.py",
>  line 129, in attach_amino_acid
>raise pymol.CmdException("invalid connection point: must be one atom, name 
> N or C.")
> pymol.CmdException:  Error: invalid connection point: must be one atom, name 
> N or C.
> 
> This seems like a looping error. I haven't been able to find much about 
> "glob". Could someone suggest an easy way out? I want to create a loop where 
> ace and nme should be added to all the dipeptides and save them as separate 
> pdb files.
> 
> Shivani
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[PyMOL] Farewell

2021-04-30 Thread Thomas Holder
Dear PyMOL community -

The time has come for me to hand over my PyMOL development
responsibilities at Schrödinger. It's been an incredible journey for
me to get involved with the PyMOL community, to become a PyMOL fellow
in 2011 and to start working full time for the project in 2012. I'm
extremely grateful to all the people at Schrödinger who made this
possible, and of course to all of you - the user community - who've
shown me every day that my work is meaningful.

PyMOL has a unique place within Schrödinger, and a highly motivated
and skilled team of developers and scientists stand behind it. They
have some great plans and I'm excited to watch how they will take
PyMOL to the next level.

I don't think that my PyMOL journey is over yet. But for the next
chapter in my career, I'll "just" be a user and a member of the
community. See you around.

Cheers,
  Thomas

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Running PyMOL on a headless machine

2021-04-30 Thread Thomas Holder
Hi Andras,

Thanks for reporting this issue and for posting your solution/workaround.
This issue will be fixed in PyMOL 2.5.

Cheers,
  Thomas

On Wed, Mar 24, 2021 at 10:25 AM András Ferenc WACHA
 wrote:
>
> Dear fellow PyMOL users,
>
> I have found a solution (at least a workaround):
>
> pymol -cpihq <
> import pymol.plugins
>
> pymol.plugins.initialize(-1)
>
> ...
>
> EOF
>
> This way all plug-ins are loaded in the same way as when graphics mode is 
> used, but the legacy Tk-based app part (which threw the exception) is not 
> initialized.
>
> Kind regards,
>
> Andras
>
> On 3/24/21 9:48 AM, András Ferenc WACHA wrote:
>
> Dear fellow PyMOL users,
>
> I'm trying to run open source PyMOL v2.4.0 on a Linux computer with no X11 
> available (as part of a script on a HPC cluster). I noticed that plug-ins are 
> not loaded automatically, therefore I force the required plug-in (pmlbeta) to 
> load as follows:
>
> pymol -cpihq <
> import pymol.plugins
>
> pymol.plugins.plugin_load('pmlbeta')  # or "apbs_tools" or 
> "lightingsettings_gui"
>
> EOF
>
> However, an exception is thrown by PyMOL:
>
> Exception in thread Thread-2:
> Traceback (most recent call last):
>   File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/threading.py", line 954, 
> in _bootstrap_inner
> self.run()
>   File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/threading.py", line 892, 
> in run
> self._target(*self._args, **self._kwargs)
>   File 
> "/opt/miniconda3/envs/gmxbatch/lib/python3.9/site-packages/pymol/plugins/legacysupport.py",
>  line 134, in starttk
> app.root = Tkinter.Tk()
>   File "/opt/miniconda3/envs/gmxbatch/lib/python3.9/tkinter/__init__.py", 
> line 2270, in __init__
> self.tk = _tkinter.create(screenName, baseName, className, interactive, 
> wantobjects, useTk, sync, use)
> _tkinter.TclError: no display name and no $DISPLAY environment variable
>
> I have ascertained that the exception occurs even before the __init__.py 
> module of my plugin starts running.
>
> In principle, my plug-in does not strictly need graphics, I would like to use 
> only the custom commands supplied by my plug-in (e.g. with cmd.extend()).
>
> Is this possible? Or do I do something wrong (e.g. the forced loading of the 
> plug-in)?
>
> Kind regards,
>
> Andras Wacha
>
>
>
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> --
> András Ferenc Wacha, PhD
> research fellow, CREDO instrument responsible
>
> Biological Nanochemistry Research Group (310)
>
> Institute of Materials and Environmental Chemistry
> Research Centre for Natural Sciences (RCNS)
> Magyar tudósok körútja 2.
> H-1117 Budapest, Hungary
> Phone: +36-1-382-6427
> Web: http://bionano.ttk.hu
> CREDO SAXS instrument: http://credo.ttk.hu
>
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Re: [PyMOL] Problem with Pymol following update to Mac Big Sur

2021-04-30 Thread Thomas Holder
Hi Marc,

The latest versions of PyMOL (e.g. 2.4) work fine on macOS Big Sur.
Old versions of MacPyMOL (until 1.8.6) are not compatible, unfortunately,
and we're not aware of any workarounds to make it work. Upgrading PyMOL is
your only option.

Cheers,
  Thomas


On Mon, Apr 19, 2021 at 8:16 AM Marc Graille 
wrote:

> Hello,
>
> I have recently updated the iOS of my MacBook Air to Big Sur (version
> 11.2.3) and since then, I cannot use Pymol anymore. This is very annoying
> as it is my favorite program to generate publication grade figures.
>
> Here is the error message I get :
> *This Executable Build integrates and extends Open-Source PyMOL 1.7.2.3.*
> * Detected OpenGL version 2.0 or greater. Shaders available.*
> * Detected GLSL version 1.20.*
> * Detected 8 CPU cores.  Enabled multithreaded rendering.*
> * OpenGL graphics engine:*
> *  GL_VENDOR:   Intel Inc.*
> *  GL_RENDERER: Intel(R) Iris(TM) Plus Graphics OpenGL Engine*
> *  GL_VERSION:  2.1 INTEL-16.1.12*
> *ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns
> err=1281*
>
> My graphics card is : Intel Iris Plus Graphics 1536 Mo.
>
> Any solution to solve this problem?
>
> Thanks a lot for your help,
>
> Yours,
>
> Marc
>
>
> —
> *Marc GRAILLE, PhD*
> DR1-CNRS
> Laboratoire de Biologie Structurale de la Cellule  (BIOC; Ex-Laboratoire
> de Biochimie)
> UMR7654 du CNRS
>
> Head of the team: “Translation and degradation of eukaryotic mRNAs”
>
> *ÉCOLE POLYTECHNIQUE*
> 91128 PALAISEAU CEDEX
> FRANCE
> : +33 (0)1 69 33 48 90
>
>  : marc.grai...@polytechnique.edu / : @GrailleLab
> 
>
> https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes
> —
>
>
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Re: [PyMOL] Problem with pymol

2021-03-23 Thread Thomas Holder
Hi Roger,

Looks like Open3dQSAR tries to use a pipe to communicate with PyMOL. That is 
possible with "PyMOLWin.exe +2", with "PyMOLWinWithConsole.bat" and with 
"Scripts\pymol.exe". I suggest that you try this:

env pymol="C:\Users...\PyMOLWinWithConsole.bat"

Hope that helps.

Cheers,
  Thomas

> On Mar 21, 2021, at 8:26 PM, Roger Vuong  wrote:
> 
> Hi,
> I am using Open3DQSAR and I am having trouble getting molecules to show in 
> pymol using an educational license. In Open3DQSAR I am able to change the 
> executable using the env pymol command, I then change the directory, then 
> import the sdf file, and pymol opens but pymol does not show the molecules. 
> The error points to a python script in pymol and states
> Traceback (most recent call last):
> File 
> "C:\Users\roger\Appdata\Local\Schrodinger\Pymol2\lib\site-packages\pymol\parser.py",
>  line 52, in stdin_reader
> 1 = sys.stdin.readline()
> AttributeError: 'NoneType' object has no attribute 'readline'
> Screenshots are attached below. Do you have a solution to fix this problem?
> Thanks,
> Roger 
> 
> 
> 
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Re: [PyMOL] How to read the alignment object

2021-02-23 Thread Thomas Holder
Hi Pedro,

Are you looking for cmd.get_raw_alignment()?

https://pymolwiki.org/index.php/Get_raw_alignment

Cheers,
  Thomas

On Tue, Feb 23, 2021 at 9:33 PM Pedro Lacerda  wrote:
>
> Hi,
>
> I aligned my structures with the align command and the object argument. So I 
> got an alignment object.
>
> But how can I read this data structure?
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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Re: [PyMOL] representation of residue sidechain within a beta strand?

2021-01-29 Thread Thomas Holder
Hi Yufeng,

The "Properties" panel can show you which settings got changed with the preset. 
The "pretty" preset indeed sets "cartoon_side_chain_helper" to "off" for the 
object. The easiest way to clear this setting is to use the "unset_deep" 
command.

unset_deep cartoon_side_chain_helper
set cartoon_side_chain_helper

https://pymolwiki.org/index.php/Unset_deep
https://pymolwiki.org/index.php/Properties_Inspector

Cheers,
  Thomas


> On Jan 29, 2021, at 6:26 AM, Yufeng Tong  wrote:
> 
> Hi Tomas,
> 
> I noticed this setting is not working when
> preset.pretty(selection='all') has been invoked, that is, whether
> cartoon_side_chain_helper is set to on or off, the side chain is
> disconnected. Do you know what is changed when preset.pretty() is
> called?
> 
> The reason I want to call preset.pretty() is that if this is not
> called, the sticks representation of an isopeptide cannot be properly
> displayed (no sticks shown for the isopeptide bond), a bit of a
> dilemma.
> 
> Thanks,
> 
> Yufeng
> 
> 
> On Mon, Jan 18, 2021 at 3:35 AM Tomas Malinauskas
>  wrote:
>> 
>> Hi Emilia,
>> 
>> You might try the following:
>> set cartoon_side_chain_helper, on
>> 
>> Hope that helps,
>> Tomas
>> 
>> On Mon, Jan 18, 2021 at 7:52 AM Emilia C. Arturo (Emily)
>>  wrote:
>>> 
>>> Hi All,
>>> 
>>> I'm wondering if anyone here knows how to represent an amino acid residue 
>>> side chain that resides within a beta strand in stick representation such 
>>> that the residue is linked in space with the backbone. This works fine when 
>>> representing as sticks a residue that is within a loop or helix, but not 
>>> within a strand; there it just sticks out into space, which looks awful if 
>>> the figure is not turned 'just so' so that the viewer cannot see the space. 
>>> I am using version 2.4.0 on my Mac.
>>> 
>>> Regards,
>>> Emilia.
>>> 
>>> --
>>> "Study as if you were going to live forever; live as if you were going to 
>>> die tomorrow." - Maria Mitchell
>>> 
>>> "I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May 
>>> Alcott
>>> 
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>> 
>> 
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Re: [PyMOL] Iterate over residue index

2021-01-27 Thread Thomas Holder
Hi Ioannis,

You could make a mapping of rank to residue selection and then sort that by 
rank. Something like this:

from pymol import cmd, stored
stored.mydict = {}
cmd.iterate("guide", "stored.mydict[rank] = f'///{chain}/{resi}'")
for rank, sele in sorted(stored.mydict.items()):
cmd.iterate(sele, "print(chain, resi, resn, name)")


Cheers,
  Thomas


> On Jan 13, 2021, at 10:38 AM, Ioannis G. Riziotis  wrote:
> 
> Hello,
> 
> Is there any way to iterate over residues by index in the PDB file (not resi, 
> but the absolute order of the residues in the pdb). Something like the 
> equivalent of ‘rank’ for atoms, but in residue level.
> 
> Best,
> Ioannis
> 
> 
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Re: [PyMOL] Mac Installation Question

2021-01-27 Thread Thomas Holder
Hi Justine,

Have you tried with the official schrodinger::pymol package? If the user who 
wants to use your plugin has a PyMOL license, that should be the best option 
for him.

conda create -n pymol -c conda-forge python=3.7 rdkit=2020.03.3.0 matplotlib 
seaborn pip numpy schrodinger::pymol schrodinger::tk scikit-learn git

You can also test this without a license, PyMOL will run in evaluation mode but 
your plugin should be fully functional.

Cheers,
  Thomas


> On Jan 27, 2021, at 1:46 AM, Justine Williams  
> wrote:
> 
> Dear users,
>  
> Could someone please help me with installing open source pymol on MacOS? I 
> created a plugin, but to allow it to be more easily available to users with 
> different OS, I need to include installation instructions for installing open 
> source pymol on each. I prepared some installation instructions for creating 
> a conda environment that works with Windows and Linux, but am having some 
> issues getting the installation to work consistently for the MacOS case. As a 
> note, I am not a Mac user myself, and have been trying to troubleshoot 
> remotely with the help of colleagues who own Macs.
>  
> I need to have the rdkit package usable to pymol, which is why I was creating 
> the conda environment. The general conda steps that worked for Windows/Linux 
> were to install and activate Anaconda3 
> (https://docs.anaconda.com/anaconda/install/mac-os/). Next, to open a 
> terminal in the Anaconda3 directory named "envs." Then to use the following 
> command to create an environment named pymol with the packages necessary:
>  
> conda create -n pymol python=3.7 rdkit=2020.03.3.0 matplotlib seaborn pip 
> numpy conda-forge::pmw tpeulen::pymol-open-source scikit-learn git
>  
> Finally, to activate the environment:
>  
> conda activate pymol 
>  
> The error that is generated for this approach is “ImportError: 
> dlopen(/Users/FarFar/anaconda3/envs/pymol/lib/python3.7/site-packages/pymol/_cmd.cpython-37m-darwin.so,
>  2): Symbol not found: _glAccum”
>  
> I would really appreciate any assistance with installation for Mac cases, or 
> if anyone knows of known issues with this. As of now, it seems like using 
> homebrew to install open source pymol and rdkit might be the best approach to 
> take, but I have not been able to get that working. If there are other 
> strategies for installing open source pymol and rdkit I would really 
> appreciate the help.
>  
> Thank you,
>  
> Justine   
>   
>
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Re: [PyMOL] how to pass an argument to python in pymol

2020-12-01 Thread Thomas Holder
Hi Michael,

You can use two dashes to separate your custom arguments.

pymol -c myscript.py -- argument1 argument2


Cheers,
  Thomas


> On Dec 1, 2020, at 8:45 AM, Michael Morgan  wrote:
> 
> I usually run "pymol -c myscript.py". Now I want to pass an argument to 
> myscript.py. 
>  
> Normally I can use "sys.argv" when run python script as "python myscript.py 
> argument1 argument2 ...". But when I tried "pymol -c myscript.py argument1 
> argument2 ..." it did not work. So what's the correct way to pass arguments?
>  
> Thank you vey much.
> Michael
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Re: [PyMOL] Suppressing text output message when writing a PNG image

2020-11-25 Thread Thomas Holder
vely for 
> the addressee. If your receive this message by mistake, you should not 
> disseminate, distribute or copy this e-mail. Please inform the sender and 
> delete the message and attachments from your system. No confidentiality or 
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> 
> No me imprimas si no es necesario.
> Don't print me unless it's necessary.
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Re: [PyMOL] VdW radii

2020-11-17 Thread Thomas Holder
Hi Timofey,

There is currently no way to automatically substitute the radii. But you can 
bind a keyboard shortcut to do the substitution, maybe that's convenient enough?

Put this in your pymolrc to bind the F1 key:

python

@cmd.set_key("F1")
def update_ionic_radii(selection="all"):
cmd.alter("elem Mg & ({})".format(selection), "vdw = 0.72")
cmd.alter("elem Na & ({})".format(selection), "vdw = 0.95")
# more elements here...
cmd.rebuild()

python end


Cheers,
  Thomas


> On Nov 12, 2020, at 5:50 AM, Timofey Tyugashev  
> wrote:
> 
> It look like PyMOL uses atomic VdW values to draw spheres even for species 
> that are better suited with ionic ones, like metal ions in solution.
> 
> A very old wiki page says they're harcoded, and putting a command like
> 
> alter (name Mg), vdw=0.72
> 
> in pymolrc is ineffective, since it's executed before loading any atoms.
> 
> Is there any way to substitute in proper values automatically?
> 
> 
> 
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Re: [PyMOL] Importing Pymol as library

2020-11-17 Thread Thomas Holder
Hi Yannis,

Here is a way to suppress it (not very elegant, sorry):

from pymol import cmd
if cmd._COb is None:
import pymol2
import pymol.invocation
pymol.invocation.parse_args(['pymol', '-q']) # optional, for quiet flag
pymol2.SingletonPyMOL().start()


Cheers,
  Thomas


> On Nov 15, 2020, at 3:05 PM, Ioannis Riziotis  wrote:
> 
> Good afternoon,
> 
> I am using pymol as a python library for a pipeline, in which I just use some 
> fitting functions (no GUI). Is there a way to suppress the warning ‘PyMOL not 
> running, entering library mode (experimental)’?
> 
> Thanks,
> Yannis
> 
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Re: [PyMOL] cannot read the character in the registraton for education page

2020-11-12 Thread Thomas Holder
Just enter your best guess. If it was wrong, you'll get a new chance
with a new code. The code is composed of upper case letters and
numbers.

Cheers,
  Thomas

On Fri, Nov 13, 2020 at 8:32 AM PLOYPLOEN PHIKULSOD
 wrote:
>
> Hello,
>
> I am registering for permission to use Pymol for educational purposes. At the 
> final process, where one needs to enter the character seen in the figure. I 
> cannot guess the character to match them. Is there any trick to read the code?
>
> Thanks.
>
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Re: [PyMOL] How to get the object name from chempy.Atom

2020-11-09 Thread Thomas Holder
Hi Pedro,

chempy.Atom doesn't store model and state. The only option I can think of right 
now is to use a custom property (Incentive PyMOL feature, won't work in 
Open-Source PyMOL):

cmd.alter('all', 'p.model = model')
print(cmd.get_model('all').atom[0].atom_properties['model'])

Or maybe you can do the same thing with cmd.iterate_state, consider the 
following two approaches to the same problem:

# using get_model
for state in range(1, cmd.count_states() + 1):
for at in cmd.get_model("all", state):
print(at.coord)
print(at.text_type)
print(at.atom_properties['model'])
print(state)

# using iterate or iterate_state
def callback(x, y, z, text_type, model, state):
print((x, y, z))
print(text_type)
print(model)
print(state)
cmd.iterate_state(0, "all", "callback(x,y,z,text_type,model,state)",
  space={"callback": callback})


Hope that helps.

Cheers,
  Thomas


> On Nov 6, 2020, at 6:29 PM, Pedro Lacerda  wrote:
> 
> Hi,
> 
> I got an `chempy.Atom` instance via `cmd.get_model().atom`.
> 
> How to get the state and object name.
> 
> 
> Thank you!
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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Re: [PyMOL] How to edit a volume field?

2020-11-09 Thread Thomas Holder
Hi Pedro,

Try these two changes:

# shape - 1
xinc, yinc, zinc = (
abs(xmax - xmin) / (field.shape[0] - 1),
abs(ymax - ymin) / (field.shape[1] - 1),
abs(zmax - zmin) / (field.shape[2] - 1),
)

# position rounding by +0.5
idx = (
int((at.coord[0] - xmin) / xinc + 0.5),
int((at.coord[1] - ymin) / yinc + 0.5),
int((at.coord[2] - zmin) / zinc + 0.5),
)


Cheers,
  Thomas


> On Nov 8, 2020, at 11:20 AM, Pedro Lacerda  wrote:
> 
> Hi,
> 
> I'm using `cmd.get_volume_field(copy=0)` to edit maps. Each grid cell must 
> increase by 1 each time the condition `atom.text_type in atomtypes` is met.
> 
> But something went wrong and the map mesh didn't align with the atoms.
> 
> `ensemble.selection` and `obj` spawns atoms in the exact same positions.
> 
> 
> 
> map_obj = prefix + "." + title
> pm.map_new(map_obj, type="vdw", selection=ensemble.selection)
> field = pm.get_volume_field(map_obj, copy=0)
> if -1 is field:
> colorprinting.error("Unable to get volume field.")
> continue
> xinc, yinc, zinc = (
> abs(xmax - xmin) / field.shape[0],
> abs(ymax - ymin) / field.shape[1],
> abs(zmax - zmin) / field.shape[2],
> )
> field[:] = 0
> for at in pm.get_model(obj).atom:
> if at.text_type in atomtypes:
> idx = (
> int((at.coord[0] - xmin) / xinc)-1,
> int((at.coord[1] - ymin) / yinc)-1,
> int((at.coord[2] - zmin) / zinc)-1,
> )
> field[idx] += 1
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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[PyMOL] Fwd: Join us: Augmenting PyMOL’s World-Class Visualisation with Cutting Edge Science Webinar on November 12th and 19th

2020-11-05 Thread Thomas Holder
Greetings,

Schrödinger is hosting some free webinars which could be relevant for PyMOL 
users.
If you are interested, please follow the registration links below.

Cheers,
  Thomas


> Begin forwarded message:
> 
> From: Schrödinger 
> Subject: Join us: Augmenting PyMOL’s World-Class Visualisation with Cutting 
> Edge Science Webinar on November 12th and 19th
> 
> 
>  
> Join us online!
> We hope you'll join us on November 12th and 19th for webinar presentations 
> focusing on the topic of Augmenting PyMOL’s World-Class Visualisation with 
> Cutting Edge Science <https://go.schrodinger.com/Q0OU07O0EJ3aU0j3P00L2r0>. In 
> these presentations, we will explore some of the limitations of relying 
> solely on PyMOL, showing how Schrödinger’s more chemistry/biology-aware 
> modelling platform, Maestro, yields quantitatively superior insights and 
> conclusions.  
> 
> These presentations will conclude the "Schrödinger Autumn of Design Webinar 
> Series" but there is still time to register. Please click on the buttons 
> below to register or visit the event website 
> <https://go.schrodinger.com/Q0OU07O0EJ3aU0j3P00L2r0> for more information. 
>  
>  
> Augmenting PyMOL’s World-Class Visualisation with Cutting Edge Science: 
> Working towards Small Molecule Design for Chemists 
> featuring Tatjana Braun at Schrödinger 
> Time: 11.00 CET 
> Date: Thursday, Nov. 12 
> REGISTER  <https://go.schrodinger.com/wO7Uj2PEar3M00U3K0O>
>  
>  
> Augmenting PyMOL’s World-Class Visualisation with Cutting Edge Science: 
> Working towards Detailed Structural Analysis for Biologists 
> featuring Jas Bhachoo at Schrödinger 
> Time: 11.00 CET 
> Date: Thursday, Nov. 19  
> REGISTER  <https://go.schrodinger.com/har3L2O00E000UPOj030UN7>
>  
>  <https://go.schrodinger.com/a0300a03UE0700OUMOjO2rP>  
> <https://go.schrodinger.com/R00a273OUP0030r0ENUOPj0>
> Copyright © 2020 Schrödinger, Inc.
> Our address is 120 West 45th Street, 17th Floor, New York, NY 10036, USA
> 

--
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Schrödinger, Inc.

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Re: [PyMOL] pref_get() on library mode

2020-10-26 Thread Thomas Holder
Hi Pedro,

If you call `plugin_load` that will trigger initialization.

pymol.plugins.plugin_load('yourplugin')
value = pymol.plugins.pref_get('YOUPLUGIN_SOME_KEY')


I feel like this plugin API is due for an overhaul, there are no great answers 
to your various questions :-/

Cheers,
  Thomas


> On Oct 26, 2020, at 5:40 AM, Pedro Lacerda  wrote:
> 
> Hi,
> 
> How to use pref_get() on library mode.
> 
> Or even better, how to use pref_get() even before library mode?
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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Re: [PyMOL] Formatted output

2020-10-26 Thread Thomas Holder
Hi Pedro,

The Incentive PyMOL Qt GUI is able to handle a small subset of ANSI color codes.

pymol.colorprinting.error("Text in red")
pymol.colorprinting.warning("Text in magenta")
print("\033[31mRed \033[32mGreen \033[33mYellow\033[m Default")

https://en.wikipedia.org/wiki/ANSI_escape_code

Open-Source PyMOL will simply strip the color codes.

Cheers,
  Thomas


> On Oct 26, 2020, at 3:10 AM, Pedro Lacerda  wrote:
> 
> I see that probably you are using HTML for this.
> https://github.com/schrodinger/pymol-open-source/blob/69b1f0b53b4109c34604adcea3983e4d3886069e/modules/pymol/colorprinting.py
> 
> But printing HTML directly into the console didn't worked.
> 
> Em dom., 25 de out. de 2020 às 23:06, Pedro Lacerda  
> escreveu:
> Hi,
> 
> How can I print formatted output into the PyMOL console?
> 
> I see that on the incentive version the output is coloured (eg errors are 
> red).
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

2020-10-20 Thread Thomas Holder
See last question here ("Ray tracing does not work"):
https://pymol.org/edu/faq.php

Cheers,
  Thomas

On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC)
 wrote:
>
> Hi Jeff,
>
> I have the incentive version of PyMOL.
> It too is saving draw images with ray tracing when using the batch mode and 
> also when using the pymol api in Jupyter.
> As you report, saving a draw image from inside PyMOL works.
>
> This is a very annoying bug.
> You should report it as an issue on the PyMOL github site.
>
> Perhaps this is not an issue with an order version of PyMOL.
> Try one from before the switch from lines to cartoon as the default molecular 
> representation (say version 2.1).
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> 
> From: Jeff Saxon [jmsstarli...@gmail.com]
> Sent: Tuesday, October 20, 2020 5:48 AM
> To: Mooers, Blaine H.M.  (HSC); pymol-users
> Subject: Re: [EXTERNAL] [PyMOL] png command in Educational Pymol
>
> Hi Blaine,
> I've just checked on trial 26 day version of Pymol it use always RAY=1
> while I run pymol from script regardless of ray flag (tested with
> ray=1, ray=0, without ray as in you case etc :-)
> I am going to try open source pymol!
> Cheers,
> J
>
> вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
> :
> >
> > Hi Jeff,
> >
> > I do not know the answer to your question. This is a work around.
> > Try dropping ray=0 and adding the draw command with the dimensions in 
> > pixels (width, height).
> >
> > cmd.draw(1600,1600);cmd.png('test1600.png')
> >
> > I would not use the Educational PyMOL for the kind of serious work that you 
> > are trying to do.
> > The PyMOL Wiki has several pages about open source versions of PyMOL.
> > Use one of those instead.
> >
> > Best regards,
> >
> > Blaine
> >
> > Blaine Mooers, Ph.D.
> > Associate Professor
> > Department of Biochemistry and Molecular Biology
> > College of Medicine
> > University of Oklahoma Health Sciences Center
> > S.L. Young Biomedical Research Center (BRC) Rm. 466
> > 975 NE 10th Street, BRC 466
> > Oklahoma City, OK 73104-5419
> >
> > 
> > From: Jeff Saxon [jmsstarli...@gmail.com]
> > Sent: Tuesday, October 20, 2020 5:24 AM
> > To: pymol-users
> > Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
> >
> > hello,
> > I am using educational version of Pymol to generate png image of
> > protein-ligand complex
> >
> > First, there are no problems in the case of PNG command from pymol's
> > GUI. However if I run the same from script from terminal:
> >
> >   MacPyMOL -c -d "
> >   from pymol import cmd
> >   cmd.load('${pdb}')
> >   cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
> >   "
> > it  does not produce an image with the following message:
> >
> >  ! Ray tracing is not supported in Educational-Use-Only PyMOL. This version
> >
> >  ! has a reduced set of features compared to the full Incentive PyMOL 
> > version.
> >
> >  ! Please visit 
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_edu=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0=wc9BhPQsimg9JTvkDK5bNL1mUeSQplkvyIKIvNtXP5A=
> >   for details. If you want to generate
> >
> >  ! figures for publication, then please obtain an academic license,
> >
> >  ! see 
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_academic=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0=AyyjBPHDzcks30uu67ZXdfPu0lx4oJroZwNpS2_J1Yc=
> >
> > note that ray is disabled in my command (since I do not need a HQ
> > image) and as I've mentioned there were no problems to create an image
> > from gui session using the same command. Could it be fixed for my case
> > or I need another version of Pymol ?
> >
> > Thank you !
> >
> >
> > ___
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> > Archives: 
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net=DwICAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0=-1_AqsLVgFJuceEfbluv4cGyYN2K2-202Lt95lZ68pE=
> > Unsubscribe: 
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>
>
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Re: [PyMOL] Pymol install on CentoOS7

2020-10-08 Thread Thomas Holder
Hi Yanni,

What's your Python version? You need at least Python 3.6.

If you don't have Python 3.6 available, you can try the legacy Python 2 branch:
https://github.com/schrodinger/pymol-open-source/tree/py2

Cheers,
  Thomas

> On Oct 6, 2020, at 2:53 PM, Yanni G  wrote:
> 
> Hello everyone
> 
> I'm having difficulty installing pymol on my Centos7 machine. I have followed 
> the instructions on the Pymol wiki page but when I try to build+install, I 
> get this error:
> 
> python3 setup.py build install --home=/opt/pymol-osbuild
>   File "setup.py", line 227
> out.write(f'set PYMOL_PATH={pymol_path}' + os.linesep)
>^
> SyntaxError: invalid syntax
> 
> Has anyone seen this before? If you have any suggestions please let me know. 
> I'm stuck at the moment.
> 
> Many thanks
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Re: [PyMOL] Rendering Unit Cell in API

2020-10-08 Thread Thomas Holder
Hi Shay,

I think the unit cell is simply clipped off with how you set up the camera 
view. Try calling "clip" after every "zoom" call, like this:

cmd.zoom(complete=1)
cmd.clip("slab", 100)


Cheers,
  Thomas


> On Sep 30, 2020, at 4:42 PM, CHAUDHURI, SHAY (PGR) 
>  wrote:
> 
> Hi all,
> 
> I'm trying to generate a series of rendered images using the API. The script 
> itself works fine but the only thing that isn't being rendered is the unit 
> cell. I have been using the cmd.show(representation='cell') command to try 
> and get the unit cell to show but it doesn't appear to be working and there 
> is no documentation on how to show the unit cell using the API.
> 
> This is one of the structures I have been trying to render (called 
> "structure.pdb"):
> CRYST1 2.526 3.572 40.104 90.00 90.00 90.00 P 1
> MODEL 1
> ATOM 0 C MOL 1 -0.018 2.808 5.068 1.00 0.00 C
> ATOM 1 C MOL 1 1.245 1.012 6.314 1.00 0.00 C
> ATOM 2 C MOL 1 1.245 1.920 5.067 1.00 0.00 C
> ATOM 3 C MOL 1 -0.018 0.143 6.315 1.00 0.00 C
> ATOM 4 C MOL 1 -0.017 2.833 7.563 1.00 0.00 C
> ATOM 5 C MOL 1 1.245 1.895 7.564 1.00 0.00 C
> ATOM 6 O MOL 1 -0.017 -0.218 8.794 1.00 0.00 O
> ATOM 7 O MOL 1 1.245 1.373 8.794 1.00 0.00 O
> ATOM 8 C MOL 1 -0.018 6.380 5.068 1.00 0.00 C
> ATOM 9 C MOL 1 1.245 4.584 6.314 1.00 0.00 C
> ATOM 10 C MOL 1 1.245 5.492 5.067 1.00 0.00 C
> ATOM 11 C MOL 1 -0.018 3.715 6.315 1.00 0.00 C
> ATOM 12 C MOL 1 -0.017 6.405 7.563 1.00 0.00 C
> ATOM 13 C MOL 1 1.245 5.467 7.564 1.00 0.00 C
> ATOM 14 O MOL 1 -0.017 3.354 8.794 1.00 0.00 O
> ATOM 15 O MOL 1 1.245 4.945 8.794 1.00 0.00 O
> ATOM 16 C MOL 1 2.508 2.808 5.068 1.00 0.00 C
> ATOM 17 C MOL 1 3.771 1.012 6.314 1.00 0.00 C
> ATOM 18 C MOL 1 3.771 1.920 5.067 1.00 0.00 C
> ATOM 19 C MOL 1 2.508 0.143 6.315 1.00 0.00 C
> ATOM 20 C MOL 1 2.509 2.833 7.563 1.00 0.00 C
> ATOM 21 C MOL 1 3.771 1.895 7.564 1.00 0.00 C
> ATOM 22 O MOL 1 2.509 -0.218 8.794 1.00 0.00 O
> ATOM 23 O MOL 1 3.771 1.373 8.794 1.00 0.00 O
> ATOM 24 C MOL 1 2.508 6.380 5.068 1.00 0.00 C
> ATOM 25 C MOL 1 3.771 4.584 6.314 1.00 0.00 C
> ATOM 26 C MOL 1 3.771 5.492 5.067 1.00 0.00 C
> ATOM 27 C MOL 1 2.508 3.715 6.315 1.00 0.00 C
> ATOM 28 C MOL 1 2.509 6.405 7.563 1.00 0.00 C
> ATOM 29 C MOL 1 3.771 5.467 7.564 1.00 0.00 C
> ATOM 30 O MOL 1 2.509 3.354 8.794 1.00 0.00 O
> ATOM 31 O MOL 1 3.771 4.945 8.794 1.00 0.00 O
> ENDMDL
> 
> This is my rendering script:
> 
> from pymol import cmd
> 
> #Viewing settings
> cmd.load("structure.pdb")
> cmd.set('orthoscopic', 1)
> cmd.show(representation='cell')
> 
> #Ball-and-stick model
> cmd.show('spheres')
> cmd.set('sphere_scale', 0.33)
> cmd.show('sticks')
> cmd.set('stick_radius', 0.2)
> 
> #Colours
> cmd.color('grey', 'name C*')
> cmd.set('stick_transparency', 0.05)
> cmd.bg_color('white')
> cmd.set('ray_opaque_background', 0)
> cmd.set('ray_shadow', 0)
> 
> #Render image
> basename = 'Structure'
> cmd.zoom(complete=1)
> cmd.ray(1024, 1024)
> cmd.png(basename+'_Z'+'.png', dpi=600)
> 
> cmd.rotate('y',-90)
> cmd.rotate('z',-90)
> cmd.ray(1024, 1024)
> cmd.zoom(complete=1)
> cmd.png(basename+'_X'+'.png', dpi=600)
> 
> cmd.rotate('z',-90)
> cmd.rotate('x',-90)
> cmd.rotate('z', 90)
> cmd.ray(1024)
> cmd.zoom(complete=1)
> cmd.png(basename+'_Y'+'.png', dpi=600)
> 
> cmd.quit()
> 
> Many thanks,
> 
> Shay Chaudhuri
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Re: [PyMOL] Edu-PyMOL Bachelor Thesis

2020-09-24 Thread Thomas Holder
Hi Vivian,

Yes you can use Edu-PyMOL for your bachelor thesis.

Best,
  Thomas

> On Sep 13, 2020, at 8:14 PM, Vivian Espig Palacios  
> wrote:
> 
> Dear PyMOL users 
>  
> I want to ask if I can use Edu-PyMOL for my bachelor thesis?
> Thank you for taking the time to answer my question. I look forward to your 
> response.
> Vivian
>  
>  
>  
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Re: [PyMOL] Command varargs

2020-07-30 Thread Thomas Holder
Hi Pedro,

Add `_self=pymol.cmd` as a keyword argument, then it should work
properly as a command.

@pm.extend
def func(*args, kw1=1, kw2=True, _self=pm):
  pass

Cheers,
  Thomas

On Thu, Jul 30, 2020 at 11:52 AM Pedro Lacerda  wrote:
>
> Hi,
>
> How can I accept variable arguments in my command? My first attempt was:
>
> @pm.extend
> def func(*args, kw1=1, kw2=True):
>   pass
>
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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Re: [PyMOL] Reading Cell Dimensions from GROMACS XTC file

2020-07-14 Thread Thomas Holder
Hi Dan,

Showing different cells for each state is currently not implemented, but I 
think it would not be too difficult to add support for that.

I've opened a feature request ticket:
https://github.com/schrodinger/pymol-open-source/issues/114

Cheers,
  Thomas


> On Jul 13, 2020, at 4:20 PM, Daniel Kozuch  wrote:
> 
> Hello,
> 
> I would like to load a GROMACS xtc trajectory and visualize the (changing) 
> cell size.
> 
> My current workflow is:
> 
> load sim.pdb
> load_traj sim.xtc, sim
> show cell
> 
> This shows a cell/box but it is the wrong size and does not update every 
> frame. Is there some way to load the proper cell dimensions?
> 
> Best regards,
> Dan Kozuch
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Re: [PyMOL] choice of color in util.cbc

2020-07-14 Thread Thomas Holder
Hi Charles,

The `first_color` argument is only active with `legacy=1`.

  util.cbc 6uwz, first_color=1, legacy=1

Other options for coloring by chain:

  spectrum chain, rainbow, 6uwz

  spectrum chain, blue green red yellow, 6uwz


Hope that helps.

Cheers,
  Thomas


> On Jul 14, 2020, at 7:18 PM, Chen, Qiang  wrote:
> 
> Hi, Pymol Users
> 
> Is it possible to choose different color pattern when using util.cbc?
> 
> Wiki says I could use the following to choose the first_color
> 
> util.cbc 6uwz, first_color=1, quiet=0
> 
> 6uwz is just an example of a pentameric protein.
> 
> However, there is no change when specify any other number for first_color. It 
> always starts with cyan on the first chain.
> 
> I know I can color the chain individually. I am just puzzled that util.cbc 
> behaves this way.
> 
> I am using open-source pymol2.5.0a0 running on windows 10.
> 
> Thanks!
> 
> Charles 
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Re: [PyMOL] How to count the number of molecules in a selection?

2020-07-09 Thread Thomas Holder
@cmd.extend
def count_molecules(selection="all", quiet=0):
tmpsele = cmd.get_unused_name("_tmp")
count = 0
if cmd.select(tmpsele, selection):
count += 1
while cmd.select(tmpsele, f'{tmpsele} &! bm. first {tmpsele}'):
count += 1
cmd.delete(tmpsele)
if not int(quiet):
print(f' Number of molecules: {count}')
return count

Cheers,
  Thomas


> On Jul 9, 2020, at 9:52 PM, Pedro Lacerda  wrote:
> 
> ... via programming
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

2020-07-07 Thread Thomas Holder
Hi Vaheh,

As far as I know, any Nvidia Quadro card with a 3-pin mini-DIN connector should 
work. For example the Quadro P4000 or P5000.

See also:
https://nvidia.custhelp.com/app/answers/detail/a_id/4845
https://www.schrodinger.com/kb/1745

Cheers,
  Thomas

> On Jul 7, 2020, at 4:16 PM, Oganesyan, Vaheh 
>  wrote:
> 
> Hi Thomas,
>  
> Can you also mention appropriate graphics cards that pair well with the 
> Volfoni hardware?
>  
> Thank you.
>  
> From: Thomas Holder  
> Sent: Tuesday, July 7, 2020 10:03 AM
> To: David Krause 
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision 
> is discontinued)
>  
> Hi David,
> 
> I won't be able to really give a future proof recommendation, but at least I 
> can say that we have emitters and glasses from Volfoni which work so far as a 
> suitable replacement for Nvidia's 3D vision.
> 
> emitter: Volfoni ActivHub RF one (VPES-07000)
> glasses: Volfoni EDGE RF 3D (VPEG-03210)
> 
> A new technology that we at Schrödinger are pretty excited about is the 
> Looking Glass display. We think this has much more potential than VR to be a 
> useful tool for drug discovery and research.
> https://lookingglassfactory.com/schrodinger
> 
> Cheers,
> Thomas
> 
> 
> > On Jul 2, 2020, at 3:48 PM, David Krause  
> > wrote:
> > 
> > Dear List,
> > 
> > 
> > one of our research groups needs a new 3D PyMol setup.
> > Looking through the wiki 
> > (https://pymolwiki.org/index.php/Stereo_3D_Display_Options) the most 
> > prominent way to do 3D seemed through Nvidia's 3D Vision,
> > but since 3D Vision is discontinued, i struggle a bit to find a good and 
> > future proof 3D solution.
> > 
> > Can you recommend a 3D Setup?
> > Should we go VR?
> > 
> > We're planning to use the Commercial PyMol version, not the open source one.
> > 
> > 
> > -- 
> > Mit freundlichen Grüßen / With kind regards
> > 
> > David Krause
> > IT
> > Institute of Biochemistry II
> > 
> > Gustav Embden-Zentrum der Biochemie
> > Goethe University Frankfurt - Medical Faculty
> > 
> > University Hospital - Building 75
> > Theodor-Stern-Kai 7
> > 60590 Frankfurt am Main
> > Germany
> > 
> > +49 (0)69 6301 84971 (Phone)
> > +49 (0)69 6301 84975 (Fax)
> > kra...@biochem2.uni-frankfurt.de
> > 
> > 
> > 
> > ___
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> > Unsubscribe: 
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> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> 
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Re: [PyMOL] cmd.get_fastastr()

2020-07-07 Thread Thomas Holder
Hi Pedro,

I would probably just count CA atoms. Something like this:

# Check nearby peptides
tmpsele = pm.get_unused_name("_tmp")
pm.select(tmpsele, f"({sim_pdb} and polymer) within 5 of "
f"({entry.pdb_id} and (bysegi resid {entry.ligand_resid} "
f"and chain {entry.ligand_chain}))")
for chain in pm.get_chains(tmpsele):
if pm.count_atoms(f"guide & bs. ({tmpsele} & chain {chain})") <= 25:
pm.delete(sim_pdb)
is_apo = False
break
pm.delete(tmpsele)


Cheers,
  Thomas


> On Jul 6, 2020, at 10:59 PM, Pedro Lacerda  wrote:
> 
> I used the function to check if the fasta is smaller than 25 characters. If 
> it is then it is a peptide:
> https://github.com/pslacerda/pymol-labimm/blob/master/scripts/peptbase/create.py#L186
> 
> There is another way to check for peptides using only selection?
> 
> Em seg., 6 de jul. de 2020 às 02:47, Thomas Holder 
>  escreveu:
> Hi Pedro,
> 
> cmd.get_fastastr() always returned a FASTA formatted string. What changed in 
> PyMOL 2.2 is that it now creates a record for every chain, not just for every 
> object. There is a new "key" argument, you get the old behavior with 
> key="model".
> 
> print(cmd.get_fastastr(key="model"))
> 
> If you actually want the plain sequence and not the fasta formatted string, 
> then I suggest you use a function like this:
> 
> def get_sequence(selection='all'):
> return ''.join(L.strip() for L in cmd.get_fastastr(selection).splitlines()
>if not L.startswith('>'))
> 
> 
> Cheers,
>   Thomas
> 
> 
> > On Jul 4, 2020, at 5:17 PM, Pedro Lacerda  wrote:
> > 
> > Hi,
> > 
> > The get_fastastr function changed. Before it returned the aminoacid 
> > sequence. Now it returns a FASTA  formatted string.
> > 
> > How can I get the old behaviour (ie. get the aminoacid sequence)?
> > 
> > -- 
> > Pedro Sousa Lacerda
> > 
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> > 
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
> > ___
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> > Unsubscribe: 
> > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907

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Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

2020-07-07 Thread Thomas Holder
Hi David,

I won't be able to really give a future proof recommendation, but at least I 
can say that we have emitters and glasses from Volfoni which work so far as a 
suitable replacement for Nvidia's 3D vision.

emitter: Volfoni ActivHub RF one (VPES-07000)
glasses: Volfoni EDGE RF 3D (VPEG-03210)

A new technology that we at Schrödinger are pretty excited about is the Looking 
Glass display. We think this has much more potential than VR to be a useful 
tool for drug discovery and research.
https://lookingglassfactory.com/schrodinger

Cheers,
  Thomas


> On Jul 2, 2020, at 3:48 PM, David Krause  
> wrote:
> 
> Dear List,
> 
> 
> one of our research groups needs a new 3D PyMol setup.
> Looking through the wiki 
> (https://pymolwiki.org/index.php/Stereo_3D_Display_Options) the most 
> prominent way to do 3D seemed through Nvidia's 3D Vision,
> but since 3D Vision is discontinued, i struggle a bit to find a good and 
> future proof 3D solution.
> 
> Can you recommend a 3D Setup?
> Should we go VR?
> 
> We're planning to use the Commercial PyMol version, not the open source one.
> 
> 
> -- 
> Mit freundlichen Grüßen / With kind regards
> 
> David Krause
> IT
> Institute of Biochemistry II
> 
> Gustav Embden-Zentrum der Biochemie
> Goethe University Frankfurt - Medical Faculty
> 
> University Hospital - Building 75
> Theodor-Stern-Kai 7
> 60590 Frankfurt am Main
> Germany
> 
> +49 (0)69 6301 84971 (Phone)
> +49 (0)69 6301 84975 (Fax)
> kra...@biochem2.uni-frankfurt.de
> 
> 
> 
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Re: [PyMOL] cmd.get_fastastr()

2020-07-05 Thread Thomas Holder
Hi Pedro,

cmd.get_fastastr() always returned a FASTA formatted string. What changed in 
PyMOL 2.2 is that it now creates a record for every chain, not just for every 
object. There is a new "key" argument, you get the old behavior with 
key="model".

print(cmd.get_fastastr(key="model"))

If you actually want the plain sequence and not the fasta formatted string, 
then I suggest you use a function like this:

def get_sequence(selection='all'):
return ''.join(L.strip() for L in cmd.get_fastastr(selection).splitlines()
   if not L.startswith('>'))


Cheers,
  Thomas


> On Jul 4, 2020, at 5:17 PM, Pedro Lacerda  wrote:
> 
> Hi,
> 
> The get_fastastr function changed. Before it returned the aminoacid sequence. 
> Now it returns a FASTA  formatted string.
> 
> How can I get the old behaviour (ie. get the aminoacid sequence)?
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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Re: [PyMOL] transparent electron density silhouette

2020-06-23 Thread Thomas Holder
Hi Dan,

I think in PyMOL you can only do this in two steps and compose the two images, 
e.g. with ImageMagick.

# white background
bg white

# step 1
as surface
set ray_trace_mode, 2
png surface.png, ray=1

# step 2
hide surface
show cartoon
set cartoon_cylindrical_helices
set ray_trace_mode, 1
png cartoon.png, ray=1

# If you have ImageMagick installed
system composite surface.png cartoon.png combined.png
load combined.png

Cheers,
  Thomas


> On Jun 19, 2020, at 4:04 AM, Daniel P Farrell  wrote:
> 
> Hello,
> I'm working with some cryo-EM density and I'm trying to get my isosurface or 
> volume (whichever's easier) to display transparent except for the curves and 
> turns of the density.
> similar to this (done in chimeraX) https://imgur.com/a/lZuG8gD
> 
> Does anyone know if this is possible?
> 
> thanks
> ~Dan
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Re: [PyMOL] Python script with iterate_state and selection command

2020-06-23 Thread Thomas Holder
Hi Stéphane,

Pedro is correct, you should change the selection like he suggested.

You also need to:
- Make a state specific selection with cmd.select(..., state=i)
- Adjust the loop to start at 1 and not at 0
- Use "stored.resid.append(resv)" as the expression

This should work:

###
from pymol import cmd, stored

objname = "mytraj"

cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb",
 objname)
cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc",
 objname)

nb_states = cmd.count_states(objname)

for i in range(1, nb_states + 1):
stored.resid = []
cmd.select("water_channel", "resn SOL within 3.5 of resn CHO", state=i)
cmd.iterate("water_channel", 'stored.resid.append(resv)')
print("frame " + str(i) + ":" + str(stored.residues))
###


Hope that helps.

Cheers,
  Thomas


> On Jun 22, 2020, at 4:52 PM, ABEL Stephane  wrote:
> 
> Hi Pedro 
> 
> It does not work, the pymol crashes if I use this selection
> 
> Stéphane
> 
> --
> Stéphane Abel, Ph.D.
> CEA Centre de Saclay
> DRF/JOLIOT/I2BC-S/SB2SM/LBMS
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> 
> De : Pedro Lacerda [pslace...@gmail.com]
> Envoyé : lundi 22 juin 2020 16:26
> À : ABEL Stephane
> Cc : pymol-users
> Objet : Re: [PyMOL] Python script with iterate_state and selection command
> 
> Hi,
> 
> Not sure if I understood your code but maybe you want change Myselection to:
> 
> Myselection="resname SOL within 3.5 of resname CHO"
> 
> -- Pedro Lacerda
> 
> Em seg, 22 de jun de 2020 10:44, ABEL Stephane 
> mailto:stephane.a...@cea.fr>> escreveu:
> Hello all,
> 
> I would like to write a basic python script to select residues for each state 
> using the iterate_state and output the results first in pymol console window 
> with the following format
> 
> frame 1 : resid ...
> frame 2 : resid ...
> ...
> 
> ### my script ##
> 
> from pymol import cmd, stored
> 
> mytraj=""
> mytraj2=""
> 
> ## Load PDB
> cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb"),
>  mytraj
> 
> ## Load XTC
> cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc"),
>  mytraj2
> 
> stored.resid = []
> 
> Myselection="select water_channel, resname SOL within 3.5 of resname CHO"
> 
> nb_states=cmd.count_states(mytraj2)---> Contains 102 states
> print(mytraj2, nb_states)
> 
> state=1
> for i in range (nb_states) :
>print(i)
>cmd.iterate_state (i, (Myselection), 'resid.append(resv)')   > 
> Should to ireate for all the states
>print("frame " + str(i) + ":" + str(stored.residues))   ---> Print the 
> results of the Myselection command in the console
> 
> ###
> 
> But the first problem I have is the syntax of the iterate_state. I obtain the 
>  following error
> "Selector-Error: Invalid selection name "select".
> ( select water_channel, resname SOL within 3.5 of resname CHO )<--"
> 
> When I put this selection command directly in Pymol, it works and i can 
> obtain the desired waters that was near 3.5 A of the CHO over all the states 
> . So What is the correct syntax for the selection with "iterate_state" ? And 
> how to output the results again for each state in the screen .
> 
> Thanks in advance for your help
> 
> Stéphane
> 
> 
> _______
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Re: [PyMOL] Install license file from CLI

2020-06-22 Thread Thomas Holder
Hi Antonio,

Thanks for the diagnostics data.

> I'm working with a virtual environment.

Ah, that's the crux. I assume you've used something like `python3 -m venv 
--system-site-packages`. That happens to be not compatible with how PyMOL finds 
$PYMOL_PATH, it uses `sys.prefix` for that which now points to your virtual 
environment.

Here some options which should all solve the issue:

1) Place the license file at $HOME/.pymol/license.lic

2) Export PYMOL_PATH=/home/my_user/pymol/share/pymol before importing the 
`pymol` module (can be done with `os.environ['PYMOL_PATH'] = ...` from your 
Python script). This option I would avoid if possible, better not to hard-code 
any paths in your script.

3) Use conda environments instead of venv. That's my preferred solution.

. $HOME/pymol/bin/activate
conda create -p $HOME/envs/dqn_pymol2 schrodinger::pymol
conda activate $HOME/envs/dqn_pymol2


Cheers,
  Thomas

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Re: [PyMOL] Install license file from CLI

2020-06-19 Thread Thomas Holder
That's unexpected. Can you send the output of the following command?

pymol -cd diagnostics

This will report the exact installation location, and also if a license file 
was found.


> On Jun 19, 2020, at 10:33 AM, Antonio Serrano  wrote:
> 
> I changed the name of the license file as you said, but the warning message 
> keeps popping:
> 
> 
> 
> 
> 
> 
> 
> 
> El jue., 18 jun. 2020 a las 20:16, Thomas Holder 
> () escribió:
> Hi Antonio,
> 
> Rename the file to "license.lic".
> 
> Cheers,
>   Thomas
> 
> > On Jun 18, 2020, at 6:08 PM, Antonio Serrano  wrote:
> > 
> > Hi Thomas. Thanks for your quick response. I installed Miniconda, so I put 
> > the license file (pymol-edu-license.lic) in the following path:  
> > $HOME/miniconda3/share/pymol/ . But a warning text stating "No License File 
> > - For evaluation Only (0 days remaining)" still appears when rendering PNG 
> > files with PyMol. Any suggestions?
> > 
> > El jue., 18 jun. 2020 a las 12:44, Thomas Holder 
> > () escribió:
> > Hi Antonio,
> > 
> > Did you install PyMOL into $HOME/anaconda3 ? If you installed into a 
> > different location, then that path to the license file will differ of 
> > course. Basically, path-to-pymol-dir/share/pymol/license.lic is the path.
> > 
> > Cheers,
> >   Thomas
> > 
> > > On Jun 17, 2020, at 2:15 PM, Antonio Serrano  wrote:
> > > 
> > > Hi:
> > > 
> > > I'm working with PyMol installed on a remote server, so I don't have 
> > > access to the GUI. I already have an educational license. According to 
> > > your FAQ at https://pymol.org/2/support.html?, the license file should be 
> > > placed in $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I 
> > > already did it but PyMol isn't still activated. Any idea on how to 
> > > completely install the license file using only the Command Line 
> > > Interface? Many thx.
> > > 
> > > BR,
> > > Antonio Serrano
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> 
> -- 
> Antonio Serrano 
> Predoctoral researcher - Contratado predoctoral
> 
> UCAM Universidad Católica de Murcia
> Phone:  +34 968 278 821
> Email:aserra...@ucam.edu

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Re: [PyMOL] Install license file from CLI

2020-06-18 Thread Thomas Holder
Hi Antonio,

Rename the file to "license.lic".

Cheers,
  Thomas

> On Jun 18, 2020, at 6:08 PM, Antonio Serrano  wrote:
> 
> Hi Thomas. Thanks for your quick response. I installed Miniconda, so I put 
> the license file (pymol-edu-license.lic) in the following path:  
> $HOME/miniconda3/share/pymol/ . But a warning text stating "No License File - 
> For evaluation Only (0 days remaining)" still appears when rendering PNG 
> files with PyMol. Any suggestions?
> 
> El jue., 18 jun. 2020 a las 12:44, Thomas Holder 
> () escribió:
> Hi Antonio,
> 
> Did you install PyMOL into $HOME/anaconda3 ? If you installed into a 
> different location, then that path to the license file will differ of course. 
> Basically, path-to-pymol-dir/share/pymol/license.lic is the path.
> 
> Cheers,
>   Thomas
> 
> > On Jun 17, 2020, at 2:15 PM, Antonio Serrano  wrote:
> > 
> > Hi:
> > 
> > I'm working with PyMol installed on a remote server, so I don't have access 
> > to the GUI. I already have an educational license. According to your FAQ at 
> > https://pymol.org/2/support.html?, the license file should be placed in 
> > $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I already did 
> > it but PyMol isn't still activated. Any idea on how to completely install 
> > the license file using only the Command Line Interface? Many thx.
> > 
> > BR,
> > Antonio Serrano

--
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Re: [PyMOL] Install license file from CLI

2020-06-18 Thread Thomas Holder
Hi Antonio,

Did you install PyMOL into $HOME/anaconda3 ? If you installed into a different 
location, then that path to the license file will differ of course. Basically, 
path-to-pymol-dir/share/pymol/license.lic is the path.

Cheers,
  Thomas

> On Jun 17, 2020, at 2:15 PM, Antonio Serrano  wrote:
> 
> Hi:
> 
> I'm working with PyMol installed on a remote server, so I don't have access 
> to the GUI. I already have an educational license. According to your FAQ at 
> https://pymol.org/2/support.html?, the license file should be placed in 
> $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I already did it 
> but PyMol isn't still activated. Any idea on how to completely install the 
> license file using only the Command Line Interface? Many thx.
> 
> BR,
> Antonio Serrano
> 
> 
> "Este mensaje es privado y confidencial y se dirige exclusivamente a su 
> destinatario. Si usted recibe este mensaje por error, no debe revelar, 
> distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y borre 
> el mensaje y los archivos adjuntos de su sistema. No hay renuncia a la 
> confidencialidad ni a ningún privilegio a causa de una transmisión errónea o 
> por mal funcionamiento". 
> 
> "This message is private and confidential and it is intended exclusively for 
> the addressee. If your receive this message by mistake, you should not 
> disseminate, distribute or copy this e-mail. Please inform the sender and 
> delete the message and attachments from your system. No confidentiality or 
> any privilege regarding the information is waived or lost by any 
> mistransmission or malfunction".
> 
> No me imprimas si no es necesario.
> Don't print me unless it's necessary.
> 
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Re: [PyMOL] User data

2020-06-15 Thread Thomas Holder
Hi Pedro,

There is no designated infrastructure for this. Other plugins typically create 
their own directory in the user's home folder, like "~/.myplugindata". You 
could also create it inside the "~/.pymol" directory (like 
"~/.pymol/myplugindata").

This works on all platforms:
os.path.expanduser("~/.pymol/myplugindata")

On Windows, you could also put it inside the %APPDATA% directory:
os.path.join(os.environ['APPDATA'], 'pymol', 'myplugindata')


Let me know how you decide or if you have other ideas!

Cheers,
  Thomas


> On Jun 9, 2020, at 10:20 PM, Pedro Lacerda  wrote:
> 
> Hi PyMOL users and developers,
> 
> I have a plugin that needs to download data periodically. Where should I 
> download to?
> 
> By the way, I managed to get a plugin into a python package.
> 
> https://github.com/pslacerda/pymol-labimm/blob/master/scripts/pymol_labimm.py
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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Re: [PyMOL] APBS plugin for Sugars

2020-06-15 Thread Thomas Holder
Hi Mario,

Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to 
manually edit the files there as well. For example with PyMOL 2.4.0 on Linux, 
the AMBER force field data files can be found like this:

$ find . -name "AMBER.*"
./lib/python3.7/site-packages/src/dat/AMBER.names
./lib/python3.7/site-packages/src/dat/AMBER.DAT


Hope that helps.

Cheers,
  Thomas


> On Jun 14, 2020, at 6:35 PM, Mario Garcia Urena  wrote:
> 
> Hi all,
>  
> I was trying to generate dipole moments with pymol using the APBS plugin. For 
> proteins I adapted a code and the dipole moments are correct and work just 
> fine, but for sugars it does not. I am well aware that the problem is that 
> many of the residues are not present in the AMBER force field data (or the 
> force field I want to use.) In APBS it is relatively easy to adapt and 
> introduce the sugars’ information manually, however in the APBS plugin for 
> pymol gets a little bit thorny. I cannot seem to find the files where I 
> should store the sugar information. Has anybody done this before? Any 
> alternatives with other programs or approaches are also welcome.
>  
> Thank you in advance,
>  
> Mario
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[PyMOL] Python 2 support removed from master branch

2020-06-06 Thread Thomas Holder
To those who compile Open-Source PyMOL from the github repo:

We've removed Python 2 support from the master branch, the master branch now 
requires Python 3.6 or later.

There is a new "py2" branch which marks the last Python 2 compatible state. We 
have no plans to actively maintain this legacy branch, but we will accept pull 
requests with bug fixes.

Cheers,
  Thomas

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Re: [PyMOL] [EXTERNAL] protecting a group during subsequent aligment

2020-06-04 Thread Thomas Holder
Hi Yong and Blaine,

The "alignto" command actually does allow you to specify the "mobile" objects.

PyMOL>alignto ?
Usage: alignto [ target [, method [, selection [, quiet 

For example, you could disable all excluded objects and then use "enabled" as 
the selection:

disable obj1 obj2 obj3
alignto ref, super, enabled

The alternative for such a heavy task would be a custom loop in Python:

python
for name in cmd.get_object_list():
if name != "ref":
cmd.super(name, "ref")
python end


By the way, "alignto" is just a wrapper for "extra_fit", with different 
argument order and default arguments. See also:
https://pymolwiki.org/index.php/Extra_fit

Cheers,
  Thomas

> On Jun 4, 2020, at 12:12 AM, Mooers, Blaine H.M. (HSC) 
>  wrote:
> 
> Hi Yong, 
> 
> Maybe you tried this already, but you might try reducing the use of RAM by 
> superposing all 500 structures represented as CA traces 
> ('ribbons' in PyMOL) or even show the  CA atoms as lines (show lines, name ca 
> and i. *) and then switch representation after alignment. 
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> University of Oklahoma Health Sciences Center
> Oklahoma City, OK 73104-5419
> 
> 
> From: Yong Tang [liutan...@gmail.com]
> Sent: Wednesday, June 03, 2020 3:55 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [EXTERNAL] [PyMOL] protecting a group during subsequent aligment
> 
> Dear all, I have a task to overlay 500+ structures onto a reference structure 
> "ref", as the body of data is big, I decided to do them in chunks, 100 at a 
> time (after crashing pymol on my Windows laptop for a few times attempting 
> it). This is the commend that I used for the first 100:
> 
> alignto ref, method=super.
> 
> This worked perfectly for most entries, but not for all, so I manually 
> adjusted some entries, and then grouped them into chunck1.
> 
> Now I'm ready to move on to the next chunk; I realized I wanted to protect 
> the processed entries from being moved/aligned again as the alignto doesn't 
> allow specification of the "mobile". I applied the /Actions/Movement/Protect 
> on group chunk1, but that didn't seem to prevent the entries in there to be 
> moved/aligned again.
> 
> Any clue how to fix my problem?
> 
> Many thanks, -yong
> 
> 
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Re: [PyMOL] volume representation is extremely dark colored

2020-05-27 Thread Thomas Holder
Hi Vitali,

Try this:

  set precomputed_lighting

Or upgrade to the latest PyMOL version which has this setting by default.

It's an Intel Graphics driver issue, you can read about it in this bug report:
https://github.com/schrodinger/pymol-open-source/issues/15

Cheers,
  Thomas


> On May 27, 2020, at 4:26 AM, Stanevich, Vitali [JRDUS] via PyMOL-users 
>  wrote:
> 
> Hi Blaine,
> 
> Setting ambient to 0.1 didn't change anything. Setting to 0.4 and higher 
> improves brightness but makes representation not very "esthetically pleasing" 
> -  the color is definitively oversaturated.
> 
> Thanks,
> Vitali
> 
> -Original Message-
> From: Mooers, Blaine H.M. (HSC)  
> Sent: Tuesday, May 26, 2020 6:31 PM
> To: Stanevich, Vitali [JRDUS] ; 
> pymol-users@lists.sourceforge.net
> Subject: [EXTERNAL] RE: volume representation is extremely dark colored
> 
> WARNING: This email originated from outside the company. Do not click on 
> links unless you recognize the sender and have confidence the content is 
> safe. If you have concerns about this email, send it as an attachment to 
> 'suspiciousem...@its.jnj.com'.
> 
> Hi Vitali,
> 
> Maybe ambient was set to a large negative value. 
> Doing so has not impact on line drawings.
> 
> Try resetting it to the default value.
> 
> set ambient, 0.1
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology College of Medicine 
> University of Oklahoma Health Sciences Center S.L. Young Biomedical Research 
> Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> 
> From: Stanevich, Vitali [JRDUS] via PyMOL-users 
> [pymol-users@lists.sourceforge.net]
> Sent: Tuesday, May 26, 2020 4:32 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [EXTERNAL] [PyMOL] volume representation is extremely dark colored
> 
> Hello everyone,
> 
> I have a problem of creating useful volume representations in Pymol version 
> 1.8.6.2<https://urldefense.proofpoint.com/v2/url?u=http-3A__1.8.6.2=DwQFAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4=RPm4waFOpdYkr0DWzikqf33ejGbyEIpp1mroeQkUqjc=>.
>  Lines representation behaves as expected, but anything volume related 
> (sticks, surface, cartoon) is drawn as a very dark surface, see example image 
> at the link below:
> https://www.dropbox.com/s/nc8vqs42ki5l0zs/vs1.png?dl=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_nc8vqs42ki5l0zs_vs1.png-3Fdl-3D0=DwMFAg=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4=Wug1vVUQk8jevkmDUEfqd8P7wnR8KN82kBpEqNiWbE8=>
> 
> Is there setting in Pymol which can bring volume-related representation to 
> something more normal? Or do you think it's non-Pymol problem with drivers 
> compatibility and etc issues?
> 
> Thanks in advance!
> 
> Vitali Stanevich, PhD
> Scientist
> Janssen R
> 
> 
> 
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Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

2020-05-22 Thread Thomas Holder
Yes correct, the numbers should be like that. I don't see anything wrong with 
your approach.

Thanks for the background info. Maybe you can give us an update once the study 
is over, sounds interesting!

Cheers,
  Thomas



> On May 22, 2020, at 12:41 AM, Thomas Evangelidis  wrote:
> 
> So, Thomas, you don't see anything wrong in the way I compute the surfaces? 
> The numbers should be like that, right?
> 
> The reason I need both the molecular surface and the SASA in not directly 
> related to a physical quantity. I do SQM scoring of compounds bound to 
> proteins, but the bulkier molecules, which are usually non-binders, tend to 
> yield lower interaction free energies. Thus, I thought to try these two 
> surface types of both the protein and the ligand as descriptors in a machine 
> learning-based attempt to balance these differences and improve the scoring. 
> It remains to be seen in practice which of these two types (molecular surface 
> or SASA) are more useful for my purpose. I also use other molecular 
> descriptors, but I don't want to elaborate on this because it's out of topic.
> 
> Best,
> Thomas
> 
> 
> On Thu, 21 May 2020 at 21:57, Thomas Holder  
> wrote:
> Hi Thomas and Blaine,
> 
> SASA is probably the correct feature to evaluate here, not molecular surface. 
> Of course it may depend the actual goal of this exercise, but typically when 
> talking about interface surface, you're putting that into context with 
> binding energy or solvation effects, and only SASA is meaningful for that as 
> far as I know.
> 
> The difference between SASA and molecular surface is a matter of size and 
> shape. For a very uneven shape (lots of small pockets or protuberances), 
> going from molecular surface to SASA will flatten the surface, which can 
> result in a smaller area, even though the volume is increased.
> 
> You may be interested to check out PISA for this task, it's the tool the PDB 
> uses to determine biological assemblies: https://www.ebi.ac.uk/pdbe/pisa/
> 
> PyMOL's and PISA's results should be similar, but PyMOL is probably easier to 
> handle :-)
> 
> Cheers,
>   Thomas
> 
> 
> > On May 21, 2020, at 4:37 AM, Mooers, Blaine H.M. (HSC) 
> >  wrote:
> > 
> > Hi Thomas,
> > 
> > If you display the SASA of the protein in PyMOL's viewport, 
> > you will see that it and that of the ligand have huge overlaps
> > How do you define the interface in such a situation and how 
> > do you interpret it? 
> > 
> > The interface of the molecular surfaces seems easier to interpret. 
> > 
> > Best regards,
> > 
> > Blaine
> > 
> > Blaine Mooers, Ph.D.
> > Associate Professor
> > Department of Biochemistry and Molecular Biology
> > College of Medicine
> > University of Oklahoma Health Sciences Center
> > S.L. Young Biomedical Research Center (BRC) Rm. 466
> > 975 NE 10th Street, BRC 466
> > Oklahoma City, OK 73104-5419
> > 
> > 
> > From: Thomas Evangelidis [teva...@gmail.com]
> > Sent: Wednesday, May 20, 2020 9:14 AM
> > To: pymol mailinglist
> > Subject: [EXTERNAL] [PyMOL] How to compute the interface surface between 
> > ligand and protein?
> > 
> > Greetings,
> > 
> > I want to compute the interface surface between the ligand and the protein 
> > in batch mode for hundreds of thousands of PDBs, like the attached one 
> > (sample.pdb). I am interested in the interface surface of both of them. 
> > First I create two new molecules, the protein, and the ligand, and I work 
> > with them because the results I get when working with the original molecule 
> > (which contains both protein and ligand) are different.
> > 
> > load sample.pdb
> > create protein, polymer
> > create ligand, resn LIG
> > delete sample
> > 
> > select prot_interface, protein within 3.5 of ligand;
> > set dot_solvent, 0;
> > get_area prot_interface;
> > set dot_solvent, 1;
> > get_area prot_interface;
> > 
> > select lig_interface, ligand within 3.5 of protein;
> > set dot_solvent, 0;
> > get_area lig_interface;
> > set dot_solvent, 1;
> > get_area lig_interface;
> > 
> > protein interface molecular surface = 1216.239 Angstroms^2
> > protein interface SASA = 763.095 Angstroms^2
> > ligand interface molecular surface = 748.867 Angstroms^2
> > ligand interface SASA = 977.608 Angstroms^2
> > 
> > I still don't understand why the interface molecular surface of the ligand 
> > is smaller than the interface SASA, while the opposite happens with the 
> > protein. Could someon

Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

2020-05-21 Thread Thomas Holder
Hi Thomas and Blaine,

SASA is probably the correct feature to evaluate here, not molecular surface. 
Of course it may depend the actual goal of this exercise, but typically when 
talking about interface surface, you're putting that into context with binding 
energy or solvation effects, and only SASA is meaningful for that as far as I 
know.

The difference between SASA and molecular surface is a matter of size and 
shape. For a very uneven shape (lots of small pockets or protuberances), going 
from molecular surface to SASA will flatten the surface, which can result in a 
smaller area, even though the volume is increased.

You may be interested to check out PISA for this task, it's the tool the PDB 
uses to determine biological assemblies: https://www.ebi.ac.uk/pdbe/pisa/

PyMOL's and PISA's results should be similar, but PyMOL is probably easier to 
handle :-)

Cheers,
  Thomas


> On May 21, 2020, at 4:37 AM, Mooers, Blaine H.M. (HSC) 
>  wrote:
> 
> Hi Thomas,
> 
> If you display the SASA of the protein in PyMOL's viewport, 
> you will see that it and that of the ligand have huge overlaps
> How do you define the interface in such a situation and how 
> do you interpret it? 
> 
> The interface of the molecular surfaces seems easier to interpret. 
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> 
> From: Thomas Evangelidis [teva...@gmail.com]
> Sent: Wednesday, May 20, 2020 9:14 AM
> To: pymol mailinglist
> Subject: [EXTERNAL] [PyMOL] How to compute the interface surface between 
> ligand and protein?
> 
> Greetings,
> 
> I want to compute the interface surface between the ligand and the protein in 
> batch mode for hundreds of thousands of PDBs, like the attached one 
> (sample.pdb). I am interested in the interface surface of both of them. First 
> I create two new molecules, the protein, and the ligand, and I work with them 
> because the results I get when working with the original molecule (which 
> contains both protein and ligand) are different.
> 
> load sample.pdb
> create protein, polymer
> create ligand, resn LIG
> delete sample
> 
> select prot_interface, protein within 3.5 of ligand;
> set dot_solvent, 0;
> get_area prot_interface;
> set dot_solvent, 1;
> get_area prot_interface;
> 
> select lig_interface, ligand within 3.5 of protein;
> set dot_solvent, 0;
> get_area lig_interface;
> set dot_solvent, 1;
> get_area lig_interface;
> 
> protein interface molecular surface = 1216.239 Angstroms^2
> protein interface SASA = 763.095 Angstroms^2
> ligand interface molecular surface = 748.867 Angstroms^2
> ligand interface SASA = 977.608 Angstroms^2
> 
> I still don't understand why the interface molecular surface of the ligand is 
> smaller than the interface SASA, while the opposite happens with the protein. 
> Could someone please explain this to me and verify that I am computing the 
> interface surfaces correctly?
> 
> I thank you in advance.
> Thomas
> 
> 
> 
> --
> 
> ==
> 
> Dr. Thomas Evangelidis
> 
> Research Scientist

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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[PyMOL] PyMOL 2.4 released

2020-05-20 Thread Thomas Holder
Greetings,

We are happy to announce the release of PyMOL 2.4. Download ready-to-use 
bundles from https://pymol.org/ or update your installation with "conda install 
-c schrodinger pymol".

Highlights:

- Incentive PyMOL only:
  - Support for https://lookingglassfactory.com/schrodinger 
  - Pi-Pi and Pi-Cation interactions (A > find > pi-interactions)
  - WaterMap result presets (A > preset > WaterMap ...)
  - APBS Plugin improvements (multi-state assemblies, propka pH calculation)

- Open-Source and Incentive PyMOL:
  - Distinguish .mrc and .ccp4 formats (origin interpretation)
  - Trajectory handling improvements
  - Improved error handling in Python API with exceptions
  - ... many bug fixes

This will be the last release with support for Python 2.7.

Find the complete release notes at:
https://pymol.org/d/media:new24 

We welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schrödinger

--
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Re: [PyMOL] How to inspect contents of 's' and 'p' for an atom?

2020-05-19 Thread Thomas Holder
Hi Mungo,

Introspecting the settings wrapper is a bit more tricky, but also possible:

from pymol import setting, stored
stored.s2dict = lambda s: dict((setting.name_dict[n], s[n]) for n in s)
iterate all, print(stored.s2dict(s))


I've updated the print() syntax in the documentation, thanks for the hint 
Blaine!

Cheers,
  Thomas


> On May 19, 2020, at 1:12 PM, Mungo Carstairs (Staff) 
>  wrote:
> 
> Hi Blaine,
> 
> Thanks for that!
> 
> And is there an equivalent for the settings in 's'?
> So for example I can
> PyMOL> iterate 4zho//A/26/CA,print(s.transparency)
> PyMOL> 0.0
> but how to find all values in 's'?
> 
> Best regards,
> 
> Mungo
> 
> 
> 
>  
>   
> Mungo Carstairs
> Jalview Computational Scientist
> The Barton Group
> Division of Computational Biology
> School of Life Sciences
> University of Dundee, Dundee, Scotland, UK
> www.jalview.org
> www.compbio.dundee.ac.uk 
> g.m.carsta...@dundee.ac.uk
>   
> We're Scottish University of the Year again!
> The Times / Sunday Times Good University Guide 2016 and 2017
> From: Mooers, Blaine H.M. (HSC) 
> Sent: 19 May 2020 11:47
> To: Mungo Carstairs (Staff) ; 
> pymol-users@lists.sourceforge.net
> Subject: RE: How to inspect contents of 's' and 'p' for an atom?
>  
> Hi Mungo,
> 
> See https://pymol.org/dokuwiki/doku.php?id=properties.
> 
> This command will print the dictionary of properties for all of the atoms:
> 
> iterate /4zho//A/*/*, print(properties.all)
> 
> Note the Python3 print() function.
> The documentation needs to be updated.
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> 
> From: Mungo Carstairs (Staff) [g.m.carsta...@dundee.ac.uk]
> Sent: Tuesday, May 19, 2020 2:59 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [EXTERNAL] [PyMOL] How to inspect contents of 's' and 'p' for an 
> atom?
> 
> A PyMOL novice question here.
> 
> I can write custom atom properties to its 'p' dictionary, and print them:
> PyMOL>fetch 4zho
> 
> PyMOL>iterate 4zho//A/26/CA, p.metal_binding='Fe'
> 
> PyMOL>iterate 4zho//A/26/CA, print(p.metal_binding)
> 
> Fe
> 
> but how do I list the contents of the dictionary if I don't know what is in 
> it?
> PyMOL>iterate 4zho//A/26/CA, print(p)
> 
> 
> Same question for 's':
> PyMOL>iterate 4zho//A/26/CA, print(s)
> 
> 
> Better still, where would I find documentation for this?
> 
> Thanks,
> 
> Mungo
> 
> 
> Mungo Carstairs
> Jalview Computational Scientist
> 
> The Barton Group
> Division of Computational Biology
> 
> School of Life Sciences
> 
> University of Dundee, Dundee, Scotland, UK

--
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PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] Capturing scene pixels without writing image to disk

2020-05-07 Thread Thomas Holder
Calling cmd.draw() will schedule a rendering event to be executed in the 
rending loop. This means the command will return before the image was rendered. 
The only way to access the result is with a callback, which will be 
asynchronous with the script you're executing.

Calling cmd.png() is related to that, but will not trigger the callback. It can 
enter a couple of different code paths, depending on the availability of the 
OpenGL context (on-screen display).

1) No OpenGL context (e.g. batch processing) -> Ray tracer will be used. 
Nothing asynchronous here, the PNG file will be available after the function 
call.
2) OpenGL context in different thread -> schedules an async task to be executed 
by the rendering thread. This means cmd.png() returns before the image was 
written (like cmd.draw)
3) Requesting width/height also triggers the async task

So the only option which is guaranteed to be synchronous is the ray tracing. 
Implementing direct numpy array or PNG buffer export would be possible, but the 
performance benefit for your script would probably not be significant.

Cheers,
  Thomas


> On May 6, 2020, at 5:42 PM, Antonio Serrano  wrote:
> 
> Thx for your quick response, Thomas. Please, could you elaborate the previous 
> example a little bit further? I'm a little confused about what you can 
> accomplish using the callback function you posted. Thx

--
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Re: [PyMOL] Capturing scene pixels without writing image to disk

2020-05-06 Thread Thomas Holder
Hi Antonio,

This is currently not possible for ray tracing or for capturing the displayed 
image.

It's possible for deferred on-screen rendering with a callback.

def mycallback(image):
print("got image of dimension", image.shape)

cmd.raw_image_callback = mycallback
cmd.draw()


Cheers,
  Thomas

> On May 4, 2020, at 7:24 PM, Antonio Serrano  wrote:
> 
> So far, I've been able to capture the pixels from the scene in two steps 
> using the png method along with imread:
> p1.cmd.png(image_path)
> img = plt.imread(image_path)
> 
> Since I have to do this quite often in my program, I'd to capture the pixels 
> in a numpy ndarray avoiding writting the image to disk every time. Is that 
> possible? Thx.
> 
> 
> 
> "Este mensaje es privado y confidencial y se dirige exclusivamente a su 
> destinatario. Si usted recibe este mensaje por error, no debe revelar, 
> distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y borre 
> el mensaje y los archivos adjuntos de su sistema. No hay renuncia a la 
> confidencialidad ni a ningún privilegio a causa de una transmisión errónea o 
> por mal funcionamiento". 
> 
> "This message is private and confidential and it is intended exclusively for 
> the addressee. If your receive this message by mistake, you should not 
> disseminate, distribute or copy this e-mail. Please inform the sender and 
> delete the message and attachments from your system. No confidentiality or 
> any privilege regarding the information is waived or lost by any 
> mistransmission or malfunction".
> 
> No me imprimas si no es necesario.
> Don't print me unless it's necessary.
> 
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Re: [PyMOL] For set.view(), there's a Wiki example for the GUI, but not the PyMol API

2020-04-30 Thread Thomas Holder
I've added Python syntax examples to https://pymolwiki.org/index.php/set_view

The argument doesn't have to be a string, it can also be a list or tuple of 
floats. In particular, the return value of cmd.get_view() can be used as input.

Cheers,
  Thomas


> On Apr 29, 2020, at 8:58 PM,  
>  wrote:
> 
> Feature request for Wiki: please add an Example below “PyMol API” like:
>  
> cmd.set_view 
> ("-0.219962522,0.763355076,-0.607366502,0.878539860,0.425617725,0.216765702,0.423973948,-0.485916167,-0.764265418,
>  
> 0.001047601,0.000947788,-48.208724976,-24.094066620,-41.117546082,2.001868963,-84.735671997,181.151062012,
>  -20.0")
>  
> and state N.B. that it’s a vector in a string.   The 9-digit decimal 
> precision is probably not needed, as there aren’t a billion pixels in an 
> image.  Even ray-tracing doesn’t need that level of precision.  
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Re: [PyMOL] incomplete secondary structure

2020-04-16 Thread Thomas Holder
If you need a convenient method for C-alpha only secondary structure 
assignment, I can recommend SST:

https://pymolwiki.org/index.php/Sst

Cheers,
  Thomas

> On Apr 16, 2020, at 2:50 PM, honeg...@bioc.uzh.ch wrote:
> 
> When you look at the coordinate file for 3jav in a text editor, you'll see 
> that for the parts of the structure which give you a "AssignSS-Warning: 
> Ignoring incomplete residue" feedback, the coordinate file contains C-Alpha 
> coordinates only, while in the parts which render the secondary structure 
> properly, you have coordinates for all heavy atoms. The header contains 
> secondary structure information only for those residues where full 
> coordinates are available, and the dss command is unable to assign secondary 
> structure from C-Alpha only.
> 
> If you really want to obtain a cartoon representation for the whole molecule, 
> you either have to use a method to determine the secondary structure from 
> C-alpha atoms only, and assign the secondary structure to the molecule using 
> the "alter" command (laborious), or submit your coordinates to a server 
> capable of modelling a full atom structure from the Alpha trace (e.g. SABBAC 
> 1.3, 
> https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC, 
> caution: you need to submit each chain separately, since the server cannot 
> deal with multi-chain models.
> 
> Annemarie
> 
> 
> Today's Topics:
> 
>1. incomplete secondary structure (h. adam steinberg)
> 
> 
> --
> 
> Message: 1
> Date: Wed, 15 Apr 2020 10:51:07 -0500
> From: "h. adam steinberg" 
> To: pymol-users 
> Subject: [PyMOL] incomplete secondary structure
> Message-ID: <8b4fde28-444e-4f86-be2a-e2982eae4...@gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all,
> 
> When I open 3jav the backbone shows many helices, but Pymol doesn?t draw them 
> as helices when showing the cartoon. Clearly there is something that is not 
> perfect with the deposited cyro structure.
> 
> If I run the dss command, the cartoon structure isn?t fixed, and I get 
> repeats of the following error for each residue from 1-2750 for each chain: 
>  AssignSS-Warning: Ignoring incomplete residue /3jav//D/2750  ?
> 
> Does anyone know how I can fix the secondary structure without having to 
> manually assign it to each helix?
> 
> Thanks!
> 
> 
> Adam
> -- next part --
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Re: [PyMOL] How to hide dihedral angle labels in mdo animation using set_dihedral

2020-02-25 Thread Thomas Holder
Hi Nanna,

These indicators come from the various "pk" selections. The "unpick" command 
will remove them. Just call "unpick" right after "set_dihedral", like this:

mdo 30: set_dihedral sele1, sele2, sele3, sele4, 123; unpick

Hope that helps.

Cheers,
  Thomas

> On Feb 21, 2020, at 7:50 AM, Nanna Holmgaard List  wrote:
> 
> Dear PyMOL, 
> 
> I am using the set_dihedral command in an mdo animation of a dihedral 
> rotation. 
> 
> In addition to rotating the bond, this command introduces three "labels":
> 1) dihedral angle label
> 2) dihedral angle indicator
> 3) circle around the bond, defining the central bond
> 
> I want to have all three "labels" removed in my animation, but cannot figure 
> out how to do it.
> 
> So far, no matter what I tried the circle (3) always remains. I managed a 
> dirty solution to move (1) and (2) outside the picture frame by the "set 
> dihedral_size" and "set dihedral_label_position".
> 
> I would much appreciate any suggestions to a solution, in particular removing 
> the circle (3).
> 
> Thank you very much in advance!
> 
> Best, Nanna H. List
> 
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Re: [PyMOL] Accessing vertex normals from surface representation within PyMOL session

2020-02-25 Thread Thomas Holder
Hi Jared,

Apologies for the late reply. Unfortunately such an API doesn't exist. I agree 
that it would be very useful, I will file a feature request.

Cheers,
  Thomas

> On Feb 14, 2020, at 9:20 PM, Jared Sampson  wrote:
> 
> Hi all -
> 
> Is it possible to access surface triangle mesh position and normal values on 
> a per-selection basis within a PyMOL session?  I know it's possible to get 
> these by writing out and parsing .obj files, but to do this for an entire 
> protein surface in a per-atom/residue fashion would be inefficient.  I 
> imagine there must be a function to access this similar to "dump" for 
> isosurfaces, but haven't been able to find it.
> 
> Thanks a lot!
> 
> Cheers,
> Jared
> 
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Re: [PyMOL] Pymol Rendering

2020-02-25 Thread Thomas Holder
Hi Seán,

Enabling multi-layer transparency should do the trick.

From the menu:
Setting > Transparency > Multi-Layer

From the command line:
PyMOL> set transparency_mode, 1

Hope that helps.

Cheers,
  Thomas


> On Feb 24, 2020, at 10:32 PM, Seán Downey  wrote:
> 
> Hi all, 
> 
> I am trying to render an image of a protein structure with a transparent 
> surface and a slightly less transparent cartoon structure, of the same 
> colour, in order to show both the cartoon structure and a ligand 
> (non-transparent) bound within as well as the surface. Using the ray option, 
> the ligand is visible, but the semi-transparent cartoon is not. Does anyone 
> have any insight into this.  Note I am using version 2.2.3.
> 
> All the best,
> 
> Seán Downey 
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Re: [PyMOL] How to compile pymol with --glut?

2020-02-11 Thread Thomas Holder
Hi Yeping,

This has been asked before (by you :-)), see here:

https://sourceforge.net/p/pymol/mailman/message/36766620/

Cheers,
  Thomas

> On Feb 8, 2020, at 2:12 PM, 孙业平 via PyMOL-users 
>  wrote:
> 
> Dear pymol users,
> 
> I compiled pymol following the guide at 
> https://pymolwiki.org/index.php/Linux_Install in my CentOS 8 system.
> When I tried to launch pymol by the "./pymol" command, I got the following 
> error:
> 
> Qt not available, using GLUT/Tk interface
> Traceback (most recent call last):
>   File 
> "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", 
> line 65, in 
> pymol.launch(args)
>   File 
> "/home/sunyp/software/Pymol/pymol-install/lib64/python/pymol/__init__.py", 
> line 441, in launch
> _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)
> NotImplementedError: compile with --glut
> 
> I then removed the "bin" and the "lib64" directories in the 
> "pymol-open-source-build" directory and recompiled pymol with the following 
> command:
>python3 setup --glut install 
> --prefix=~/software/Pymol/pymol-open-source-build
> 
> However, the newly generated pymol binary file does not work either. Launch 
> pymol give the same "Qt not available, using GLUT/Tk interface" error.
> 
> Could you help me with this?Thank you in advance.
> 
> Best regards.
> 
> 
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Re: [PyMOL] floating external gui

2020-02-11 Thread Thomas Holder
Hi Tamas,

It is currently not possible to start PyMOL with a floating external GUI. The 
most convenient way to get it floating is to double click the empty space of 
the panel which toggles visibility of its title bar, then drag that out. See 
attached screenshot.




Cheers,
  Thomas

> On Feb 8, 2020, at 10:56 AM, Tamas Hegedus  wrote:
> 
> Hi,
> 
> I am using a compiled version of pymol.
> I like the floating window.
> 
> The CNTR-E does not work to toggle floating, I have to use the mouse 
> (display, external gui, toggle floating).
> Is it possible to start pymol with floating external gui?
> 
> Thanks, Tamas
> 
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Re: [PyMOL] Getting session file name

2020-02-11 Thread Thomas Holder
Hi Jason,

This should do it:

name = cmd.get('session_file')


Cheers,
  Thomas

> On Feb 8, 2020, at 5:21 AM, Junsu Park aka. Jason Mosier 
>  wrote:
> 
> Hello, this may be a very simple question that I just can't find the answer 
> to, but I was wondering how I would go about fetching the session name of the 
> .pse currently open? For example, I have two session files: colors and 
> overlays, and I want my code to print something specific for each colors... 
> and overlay... in a text file or whatever based on which one I have open
> 
> Cheers,
> Jason M.
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Re: [PyMOL] How to print the time stample on each frame of the movie for molecular dynamics trajectory in Pymol?

2020-01-20 Thread Thomas Holder
Hi Yeping,

It's possible to create a such a label, but unfortunately it's a bit 
complicated. The following script places a label with 2500 states in the upper 
right corner of the display area.

# create a discrete multi-state object with one labeled atom per state
pseudoatom tmp, label=pending
python
for i in range(2500):
cmd.label("tmp", "'{} ps'".format(i * 80))
cmd.create('timestaple', 'tmp', 1, i + 1, discrete=1)
python end
delete tmp
# anchor the label in the upper right corner
set label_screen_point, [1, 1, 0], timestaple
set label_relative_mode, 1, timestaple
# align the label to the bottom left of the anchor
set label_position, [-1, -1, 0], timestaple


Those label settings are documented here:
https://pymol.org/d/setting:label

Hope that helps.

Cheers,
  Thomas


> On Jan 15, 2020, at 5:22 AM, sunyeping via PyMOL-users 
>  wrote:
> 
> Dear All,
> 
> I load a molecular dynamics (gromacs) trajectory into Pymol and wish to make 
> a movie with it. The trajectory contains 2500 frames, corresponding to 200 ns 
> simulation time, so each frame represents 80 ps. I wish to print time stample 
> on each stample. For example, on the first frame, " 0 ns" is printed; on the 
> second frame, "80 ps" is printed; on the third frame, "160 ps" is printed. 
> How I cannot find any clue how to do this. Could you have any clue how to 
> finish this task? 
> 
> Best regards,
> Yeping Sun
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Re: [PyMOL] diaplay actural sizes in Pymol

2020-01-20 Thread Thomas Holder
Hi Ting,

This will display the assemblies (biological units) in a grid. The result 
should look like in the attached image.

set assembly
set all_states
set grid_mode
fetch 1igt 1s58 3j3i 2ztn 6ui6 5wtf 3iyo, type=mmtf
zoom

The "assembly" setting replaces the use of type=pdb1. It works with type=cif 
and type=mmtf.

https://pymolwiki.org/index.php/Assembly

Hope that helps.

Cheers,
  Thomas




> On Jan 20, 2020, at 7:21 AM, Ting Hu via PyMOL-users 
>  wrote:
> 
> Dear Pymol-users support,
> 
> I want to compare the sizes of different virus and IgG in Pymol. But they are 
> exhibiting similar sizes. how can i change that?
> 
> the commands I enter are as below:
> fetch 1igt, type=pdb1
> fetch 1s58, type=pdb1 set all_states, on
> fetch 3j3i, type=pdb1 set all_states, on
> fetch 2ztn, type=pdb1 set all_states, on
> fetch 6ui6, type=pdb1 set all_states, on
> fetch 5wtf, type=pdb1 set all_states, on
> fetch 3iyo, type=pdb1 set all_states, on
> fetch 1s58, type=pdb1 set all_states, on
> 
> Best regrds
> Ting
>  
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Re: [PyMOL] click and select bug in 2.2

2020-01-10 Thread Thomas Holder
Hi Tamas,

Sounds like one of these bugs:

https://github.com/schrodinger/pymol-open-source/issues/11
https://github.com/schrodinger/pymol-open-source/issues/35

Can you install the latest version from source, like described here?

https://pymolwiki.org/index.php/Linux_Install#Install_from_source

Cheers,
  Thomas

> On Jan 10, 2020, at 4:15 PM, Tamas Hegedus  wrote:
> 
> Hi,
> 
> I use pymol 2.2 (debian stable release).
> Sometimes pymol starts to behave in a strange way. Clicking to an amino acid 
> select a residue somewhere else in the protein.
> (This is not caused by me missing the click in the 3D)
> 
> I would be happy not to downgrade pymol if you have a solution to get around 
> this bug.
> 
> Thanks,
> Tamas
> 
> 
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Re: [PyMOL] Performance of extended commands vs python function

2019-12-18 Thread Thomas Holder
Hi Lorenzo,

Thanks for the script, and great that you could identify cmd.sync() as the 
culprit. I looked at the code, cmd.do("cmd.sync()") literally blocks itself 
until it times out after 1 second. cmd.do() puts commands in a queue, and 
cmd.sync() tries to ensure that all queued commands have been executed. PyMOL 
calls cmd.sync() in a few places right before capturing an image for example.

Not sure how this could be improved. Maybe cmd.sync() should print a warning if 
it times out, that would help to notice a self-lock.

Cheers,
  Thomas


> On Dec 17, 2019, at 11:42 AM, Lorenzo Gaifas  wrote:
> 
> After playing around with it a bit longer, it's clear that I misunderstood. 
> The issue was not with `cmd.alter` nor with `cmd.show_as`, but with 
> `cmd.sync`.
> 
> I was calling many times a smaller function that contained `cmd.sync()`, 
> which resulted - it seems - in all these calls piling up.
> 
> Still, I don't know if it's intended behaviour for `sync` to be so much 
> slower if it's called as a pymol function. Attached you will find a minimal 
> working example to show the difference.
> 
> 
> Il giorno lun 16 dic 2019 alle ore 17:52 Thomas Holder 
>  ha scritto:
> OK thanks. I haven't seen such performance differences before and couldn't 
> reproduce it so far. Could you share your script (and data files if possible) 
> with me?
> 
> Thanks,
>   Thomas
> 
> 
> > On Dec 16, 2019, at 5:42 PM, Lorenzo Gaifas  wrote:
> > 
> > Yes, it does. Both cases are with the GUI and ewual graphical 
> > representation.
> > 
> > On Mon, Dec 16, 2019, 17:37 Thomas Holder  
> > wrote:
> > Hi Lorenzo,
> > 
> > When you say "run from a python script", is that with the graphical GUI? 
> > That "instant update", does that include instant update of visual 
> > representations?
> > 
> > Thanks,
> >   Thomas
> > 
> > 
> > > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas  wrote:
> > > 
> > > Dear Pymol users,
> > > 
> > > I just discovered something I did not expect: the same python function 
> > > can have extremely different performance when called as a python function 
> > > or using the pymol api.
> > > 
> > > To be more specific: I have a function func that (among other things) 
> > > uses cmd.alter several times over a big system to change the properties 
> > > and representation.
> > > 
> > > If I run it calling func() from a python script, its effects are almost 
> > > instant. If I call it with cmd.do('func') (or directly from within pymol 
> > > with func), it’s extremely slow (up to 10 seconds) and Pymol freezes 
> > > completely during this time.
> > > 
> > > I expected this to be due to an overhead of the api itself, but when I do 
> > > the same thing with a simpler function, I see no noticeable difference.
> > > 
> > > Why exactly is this happening? And more importantly, how can I get the 
> > > performance of func even when I call it from within pymol?
> > > 
> > > Thank you,
> > > Lorenzo
> > > 
> > > ___
> > > PyMOL-users mailing list
> > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> > > Unsubscribe: 
> > > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> > 
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> > 
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 

--
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Re: [PyMOL] Performance of extended commands vs python function

2019-12-16 Thread Thomas Holder
OK thanks. I haven't seen such performance differences before and couldn't 
reproduce it so far. Could you share your script (and data files if possible) 
with me?

Thanks,
  Thomas


> On Dec 16, 2019, at 5:42 PM, Lorenzo Gaifas  wrote:
> 
> Yes, it does. Both cases are with the GUI and ewual graphical representation.
> 
> On Mon, Dec 16, 2019, 17:37 Thomas Holder  
> wrote:
> Hi Lorenzo,
> 
> When you say "run from a python script", is that with the graphical GUI? That 
> "instant update", does that include instant update of visual representations?
> 
> Thanks,
>   Thomas
> 
> 
> > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas  wrote:
> > 
> > Dear Pymol users,
> > 
> > I just discovered something I did not expect: the same python function can 
> > have extremely different performance when called as a python function or 
> > using the pymol api.
> > 
> > To be more specific: I have a function func that (among other things) uses 
> > cmd.alter several times over a big system to change the properties and 
> > representation.
> > 
> > If I run it calling func() from a python script, its effects are almost 
> > instant. If I call it with cmd.do('func') (or directly from within pymol 
> > with func), it’s extremely slow (up to 10 seconds) and Pymol freezes 
> > completely during this time.
> > 
> > I expected this to be due to an overhead of the api itself, but when I do 
> > the same thing with a simpler function, I see no noticeable difference.
> > 
> > Why exactly is this happening? And more importantly, how can I get the 
> > performance of func even when I call it from within pymol?
> > 
> > Thank you,
> > Lorenzo
> > 
> > ___________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> > Unsubscribe: 
> > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

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Re: [PyMOL] Performance of extended commands vs python function

2019-12-16 Thread Thomas Holder
Hi Lorenzo,

When you say "run from a python script", is that with the graphical GUI? That 
"instant update", does that include instant update of visual representations?

Thanks,
  Thomas


> On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas  wrote:
> 
> Dear Pymol users,
> 
> I just discovered something I did not expect: the same python function can 
> have extremely different performance when called as a python function or 
> using the pymol api.
> 
> To be more specific: I have a function func that (among other things) uses 
> cmd.alter several times over a big system to change the properties and 
> representation.
> 
> If I run it calling func() from a python script, its effects are almost 
> instant. If I call it with cmd.do('func') (or directly from within pymol with 
> func), it’s extremely slow (up to 10 seconds) and Pymol freezes completely 
> during this time.
> 
> I expected this to be due to an overhead of the api itself, but when I do the 
> same thing with a simpler function, I see no noticeable difference.
> 
> Why exactly is this happening? And more importantly, how can I get the 
> performance of func even when I call it from within pymol?
> 
> Thank you,
> Lorenzo
> 
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Re: [PyMOL] [EXTERNAL] Differentiate between bond types by color and representation

2019-12-11 Thread Thomas Holder
Hi Lorenzo and Blaine,

There is a "set_bond" command which can set (some) settings for individual 
bonds.

To change stick color and radius for the bond between atom 2 and 3:

set_bond stick_color, yellow, index 2, index 3
set_bond stick_radius, 0.2, index 2, index 3

Cheers,
  Thomas


> On Dec 11, 2019, at 4:57 PM, Mooers, Blaine H.M. (HSC) 
>  wrote:
> 
> Hi Lorenzo,
> 
> The use the lines instead of sticks may reduce the anticipated hit on 
> performance. 
> There is a line_color setting that use you can.
> 
> Best regards,
> 
> Blaine
> 
> 
> From: Lorenzo Gaifas [bris...@gmail.com]
> Sent: Wednesday, December 11, 2019 9:48 AM
> To: Mooers, Blaine H.M.  (HSC)
> Cc: pymol-users
> Subject: Re: [EXTERNAL] [PyMOL] Differentiate between bond types by color and 
> representation
> 
> Hi Blaine,
> 
> Yes, that's essentially what I'm doing. My worry is that since this doubles 
> the amount of coordinates to keep track of, it will be detrimental to how 
> long a trajectory I can load. Is there any other way to do this?
> 
> On Wed, Dec 11, 2019, 16:31 Mooers, Blaine H.M. (HSC) 
> mailto:blaine-moo...@ouhsc.edu>> wrote:
> Hi Lorenzo,
> 
> You could make an object out of the elastic bonds with the 'create' command, 
> show it as sticks, and use the stick_color setting to color the sticks only.
> You could make different objects for different subsets of the elastic bonds 
> and color them differently.
> 
> Here is an example of the 'create' command that I used to make an object out 
> of six coordinate covalent bonds between a sodium, a N7 nitrogen of an 
> adenine, and five waters.
> 
> cmd.create('coorCov', '(3nd4_0001 and (resi 19 or resi 119 or resi 219 or 
> resi 319 or resi 419 or resi 519 or (resi 3 and name N7)))')
> cmd.set('stick_color','magenta','coorCov')
> cmd.show('sticks','coorCov')
> 
> The color of the atoms, if shown as spheres, will remain the same.
> Although the above two commands are in the Python form, you can paste them 
> onto the top command line in PyMOL.
> 
> By specifying the object as your selection in the argument to the set 
> command, you can also change the thickness of the sticks in only than object 
> so
> you can have sticks of different thickness in the same scene.
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> 
> From: Lorenzo Gaifas [bris...@gmail.com<mailto:bris...@gmail.com>]
> Sent: Wednesday, December 11, 2019 8:38 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] Differentiate between bond types by color and 
> representation
> 
> Dear pymol users,
> 
> I'm trying to properly represent a coarse-grained protein model that has an 
> elastic network.
> 
> I would like to show the bonds that are part of the elastic network with a 
> different color (and possibly representation) from the normal bonds between 
> atoms. However, as far as I know, color settings are atom-based, so I wasn't 
> able to do what I wanted, because all bonds that lead to an atom will always 
> share the same color.
> 
> The only solution I found was to create a copy of the protein with 
> pseudoatoms and draw the elastic network there. However, I expect this has a 
> negative effect on the performance, which is relevant since I plan to use 
> this for molecular dynamics trajectories.
> 
> Am I trying to do this the wrong way? Is it just unfeasible?
> 
> 
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Re: [PyMOL] ModuleNotFoundError: No module named 'pymol._cmd'

2019-11-28 Thread Thomas Holder
Hi Markus,

You mention two directories, maybe you're running PyMOL from the wrong one?

/home/mheller/pymol-2.4/lib/python/pymol
/usr/local/Pymol-2.4/lib/python/Pymol


Cheers,
  Thomas


> On Nov 28, 2019, at 1:00 AM, Markus Heller  wrote:
> 
> Hi,
> 
> This is just an attempt to see if my issue has popped up before.
> 
> I have compiled open source Pymol 2.4, which I used for a few months now.  
> Today, the following error prevents launching Pymol:
> 
> 
> $ pymol
> Traceback (most recent call last):
>  File "/home/mheller/pymol-2.4/lib/python/pymol/__init__.py", line 64, in 
> 
>import pymol
>  File "/home/mheller/pymol-2.4/lib/python/pymol/__init__.py", line 564, in 
> 
>import pymol._cmd
> ModuleNotFoundError: No module named 'pymol._cmd'
> 
> 
> `/usr/local/Pymol-2.4/lib/python/Pymol` contains `cmd.py` and 
> `_cmd.cpython-36m-x86_64-linux-gnu.so`
> 
> I'm baffled as to why Pymol fails to open, as I'm not aware of any changes 
> made to my python setup or related.
> 
> I'd be very grateful for a slight nudge in the right direction ...
> 
> Thanks
> Markus
> 
> 
> 
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Re: [PyMOL] Autosave

2019-11-28 Thread Thomas Holder
It looks like strftime('%s') is not valid on Windows (it works fine for me on 
Linux and macOS). Here is an equivalent alternative that works on all platforms:

filename = '~/pymol-auto-save-{}.pse'.format(int(time.time()))
filename = os.path.expanduser(filename)

Binding a key is also easy. Here is an example which binds saving and rendering 
to the F1 key:

python
@cmd.set_key('F1')
def autosave_and_render():
filename = os.path.expanduser('~/pymol-auto-save.pse')
cmd.set('pse_binary_dump')
cmd.save(filename, quiet=0)
cmd.ray()
python end


Hope that helps.

Cheers,
  Thomas


> On Nov 22, 2019, at 11:48 PM, Junsu Park aka. Jason Mosier 
>  wrote:
> 
> Hello, I'm fairly new to pymol and python in general, but I honestly don't 
> have to self control to save by myself very well and so I was trying to use 
> the proof of concept code for autosaving. However, it was written for a way 
> old version of pymol and so I was wondering if I could get some help with 
> fixing this code up? If that would be too difficult, is there a way that I 
> could bind a key to saving AND then rendering? Or even just clicking on the 
> render button causes it to save before ray tracing? I keep rendering on a 
> weak computer thinking it can handle it and then it crashes and I lose all my 
> progress.
> 
> Link to code: https://pastebin.com/EJJQWc00  
> Link to output:  https://pastebin.com/TNSuA0fH
> 
> Thanks,
> -Jason
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Re: [PyMOL] Problem loading Amber trajectory

2019-11-28 Thread Thomas Holder
Hi Martin,

Would it be possible to share those files with me?

Thanks,
  Thomas

> On Nov 28, 2019, at 6:00 PM, Rosellen, Martin  
> wrote:
> 
> Dear all,
> 
> I have issues loading Amber trajectories. First, I load the the topology
> like this:
> 
> load WT.prmtop, WT, 1, top
> 
> output:
> 
>   ObjectMolecule: Attempting to read Amber7 topology file.
>   TOPStrToCoordSet: Warning: can't currently image a truncated octahedron...
> 
> 
> load_traj WT.trj, WT
> 
> output:
> 
> ObjMolLoadTRJFile-Error: Failed to read expected coordinate value.
>This traj. does not match the loaded parameter/topology file.
>Likely cause: either the atom count or the periodic box settings
>are inconsistent between the two files.
> 
> 
> My guess is that pymol somehow changes the atom count because it cannot
> image the truncated box which causes the error with the trajectory.
> 
> I was thinking about putting the trajectory in a PDB but that would be a
> file of <20GB in the end.
> 
> Any comment, positive or negative, would be very much appreciated.
> 
> cheers
> 
> Martin
> 
> 
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[PyMOL] Admins for Pymol-script-repo needed

2019-11-15 Thread Thomas Holder
Hi PyMOL User -

Are you proficient with Python and Git? Then we could need your help with the 
Pymol-script-repo! The project currently has 6 admins, but it seems that most 
of them have moved on and are no longer available to help out.

What's needed? Code review on pull requests, giving feedback to the author if 
needed, and merging the pull request when it looks good. Also any sort of 
maintenance on the code base you feel is necessary and appropriate.

https://github.com/Pymol-Scripts/Pymol-script-repo

The Pymol-script-repo is not owned or managed by Schrödinger, it's a community 
project (which doesn't stop Schrödinger from contributing, we're part of the 
community as well :-)). The repository hosts most of the scripts and (single 
file) plugins from the PyMOLWiki.

There is currently one open pull request from Pedro:
https://github.com/Pymol-Scripts/Pymol-script-repo/pull/105

So if you want to become a Pymol-script-repo admin, please send me an email.

Thanks,
  Thomas

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Re: [PyMOL] Pymol Qt Wayland

2019-11-05 Thread Thomas Holder
Hi Quyen,

This works for me:

  export QT_QPA_PLATFORM=xcb
  pymol

Hope that helps.

Cheers,
  Thomas



On Sun, Nov 3, 2019 at 6:15 AM RDirective  wrote:
>
> Dear all,
>
> I have a slight problem with Pymol on Fedora 31. The vanilla distribution 
> runs Gnome on Wayland.  Pymol complains that [qt.qpa.plugin: Could not find 
> the Qt platform plugin "wayland" in ""]. The GUI and 3D render will still 
> work but if I were to install qt5-qtwayland-devel to provide the plugin, then 
> the GUI will load but the 3D render no longer shows anything. It is just a 
> blank frame.  What can be done about this?
>
> Best,
> Quyen
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Re: [PyMOL] Get surface coordinates

2019-10-30 Thread Thomas Holder
Hi Pedro,

There is a "dump" command which exports all surface points and normals to a 
text file.

  dump /tmp/dump.txt, acceptor_17

Each line will have 6 numbers, 3 for the position, and 3 for the normal.

For cmd.get_volume_field you need the map name, not the surface name.

  data = cmd.get_volume_field('acceptor')
  print(data)


Hope that helps.

Cheers,
  Thomas


> On Oct 30, 2019, at 6:42 AM, Pedro Lacerda  wrote:
> 
> And cmd.get_volume_field is returning -1.
> 
> Em qua, 30 de out de 2019 às 02:00, Pedro Lacerda  
> escreveu:
> Hi,
> 
> How can I access the underlying coordinates of acceptor, donor and apolar 
> surface objects on the given session given by the following server? Coords 
> akin to dot representation would suffice.
> 
> http://fragment-hotspot-maps.ccdc.cam.ac.uk/results_table
> http://fragment-hotspot-maps.ccdc.cam.ac.uk/result/1542
> 
> An example of session is attached.
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> 
>  ARSB_hotspots.pse
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
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[PyMOL] Open position for PyMOL Software Engineer

2019-10-23 Thread Thomas Holder
Greetings,

Schrödinger is looking to hire a Software Engineer to join the PyMOL team in 
New York. We would be very excited if there is a talented member from the PyMOL 
community who can fill this position. Interested? Please follow the link:

https://hire.withgoogle.com/public/jobs/schrodingercom/view/P_AADAADpO9VyJDPz7O7

Cheers,
The PyMOL Team at Schrödinger

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Re: [PyMOL] dots with/without ray tracing

2019-10-17 Thread Thomas Holder
Hi Vaheh,

Try this:

set dot_radius, 0.1
set dot_as_spheres

Cheers,
  Thomas


> On Oct 15, 2019, at 9:53 PM, Oganesyan, Vaheh 
>  wrote:
> 
> Hello PyMOLers,
>  
> Figure that contains dots getting unwanted metamorphosis after ray tracing 
> (figures before ray tracing and after are attached). Any suggestion how to 
> overcome it?
> Thank you.
> Regards,
>  
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> 
> AstraZeneca
> R | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T:  301-398-5851
> vaheh.oganes...@astrazeneca.com
>  
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Re: [PyMOL] feature request

2019-10-17 Thread Thomas Holder
Hi Jared and Vaheh -

We've implemented two modes and pushed the change to the github repository.

set internal_gui_name_color_mode, 
set internal_gui_name_color_mode, 2

Mode 1 is color by first carbon color. We think this is the most relevant use 
case and what the user typically would expect. This only affects molecular 
objects of course, other object types will appear in the default color (white).

Mode 2 is object color. It applies to all object types.

I learned that the "C > by element > ..." menu options also update the object 
color with the same color that is applied to carbons.

A neat way to transfer atom color to object color is with this command:

  iterate (name CA), cmd.set_object_color(model, color)

Other selections are possible of course.

Cheers,
  Thomas


> On Oct 2, 2019, at 7:31 PM, Jared Sampson  wrote:
> 
> Hi Thomas - 
> 
>> When I said it's easy to implement, I was only thinking of object color. 
>> Among the various cases you describe, the "dominant color" is probably the 
>> most important one, as it might not be obvious to the user that object color 
>> can be different from atom colors.
> Indeed, I was among those for whom "it might not be obvious" that there are 
> separate object and atom colors!  I had thought all coloring was done at the 
> atom level (as you show using the selection), and didn't realize there is a 
> separate object-level color, nor did I know about the `set_object_color` 
> command.
> 
> Thanks for the explanation, Thomas!
> 
> Cheers,
> 
> Jared
> 

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Re: [PyMOL] feature request

2019-10-02 Thread Thomas Holder
Hi Jared and Vaheh -

Jared, you've put way more thought into this than I did :-) When I said it's 
easy to implement, I was only thinking of object color. Among the various cases 
you describe, the "dominant color" is probably the most important one, as it 
might not be obvious to the user that object color can be different from atom 
colors.

color blue, (obj);# only changes atom colors
color blue, obj  ;# changes object and atom colors
cmd.set_object_color("obj", "blue")  ;# only changes object color

More complex situations like spectrum or per-representation colors can be 
neglected I think - I wouldn't know how to map those to a label color in a 
useful way.

As a first step, I can add internal_gui_name_color_mode=1 with object colors.

Cheers,
  Thomas


> On Oct 1, 2019, at 9:31 PM, Oganesyan, Vaheh 
>  wrote:
> 
> Thomas and Jared,
> I’m not sure what will be the best solution, but as a start, color of the 
> object name may stay white if more than one color is used. Because you both 
> found this as an interesting idea allows me to ask similar question now 
> regarding labels. What if we can get label_color match the residue color. I 
> vaguely remember something like this discussed x number of years ago, but do 
> not remember why not. Could label become property of the object and not just 
> a property of a session?
>  
> Thank you.
>  
>  
> From: Jared Sampson  
> Sent: Tuesday, October 1, 2019 2:45 PM
> To: Oganesyan, Vaheh ; Thomas Holder 
> 
> Cc: pymol-users 
> Subject: Re: [PyMOL] feature request
>  
> Hi Thomas and Vaheh - 
>  
> This is indeed an interesting idea.  I was thinking about this in terms of 
> implementation, and what the edge cases might be.  I wonder what would be the 
> mechanism for assigning the color if the object is not just a single color.  
> Would it be the color that is the dominant color of the object over all 
> (visible) representations?
>  
> What about a spectrum-colored object?  Would it be possible to color the 
> object name according to the colors in the spectrum (like the "spectrum" and 
> "rainbow" menu items already in the OpenGL menu)?
>  
> And what if there are different coloring schemes for the different 
> representations—would there be a hierarchy in terms of choosing , e.g. 
> surface > cartoon > stick > line, etc.?
>  
> I definitely like Thomas' idea of a global `internal_gui_name_color_mode` 
> setting to turn the menu object name coloring on/off.  (Perhaps different 
> modes could correspond to different ways of choosing the displayed color.)  
> It might also be useful to include object-level (or named-selection-level) 
> settings to override the global setting and specify the color or spectrum 
> directly, e.g.:
>  
> set internal_gui_name_color, red, obj1
> set internal_gui_name_spectrum, rainbow, obj1
>  
> Really interesting suggestion, Vaheh.  Looking forward to seeing how it might 
> work!
>  
> Cheers,
> Jared
>  
> On October 1, 2019 at 5:13:07 AM, Thomas Holder 
> (thomas.hol...@schrodinger.com) wrote:
> 
> Hi Vaheh,
> 
> I see that this can be useful, and it's fairly easy to implement. We can add 
> a new setting to turn this on and off, like "internal_gui_name_color_mode" 
> (or do you have a suggestion for a better name?).
> 
> Cheers,
> Thomas
> 
> 
> > On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh 
> >  wrote:
> > 
> > Thomas and other PyMOL developers,
> > 
> > It looks as if we color the object name similar to the object color it will 
> > be easier to distinguish which structure am I manipulating now. While 
> > models can be colored, the names of the models can't.
> > Anybody else think it might be helpful?
> > 
> > Thank you.
> > Regards,
> > 
> > Vaheh Oganesyan, Ph.D.
> > Scientist, Biologic Therapeutics
> > 
> > AstraZeneca
> > R | Antibody Discovery and Protein Engineering
> > One Medimmune Way, Gaithersburg, MD 20878
> > T: 301-398-4640 M: 240-398-0046 
> > vaheh.oganes...@astrazeneca.com
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> 
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Re: [PyMOL] feature request

2019-10-01 Thread Thomas Holder
Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a 
new setting to turn this on and off, like "internal_gui_name_color_mode" (or do 
you have a suggestion for a better name?).

Cheers,
  Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh 
>  wrote:
> 
> Thomas and other PyMOL developers,
> 
> It looks as if we color the object name similar to the object color it will 
> be easier to distinguish which structure am I manipulating now. While models 
> can be colored, the names of the models can't.
> Anybody else think it might be helpful?
> 
> Thank you.
> Regards,
> 
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> 
> AstraZeneca
> R | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T:  301-398-4640  M:  240-398-0046 
> vaheh.oganes...@astrazeneca.com

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Re: [PyMOL] "Qt not available" error from compilation with python2 but not python3

2019-09-19 Thread Thomas Holder

> On Sep 14, 2019, at 8:46 AM, sunyeping via PyMOL-users 
>  wrote:
> 
> Even if I re-compile with --glut:
> python2 setup.py install --prefix=~/pymol-install-py2
> the same error occurs.

Remove the "build" directory before you re-compile with --glut:

  rm -rf build
  python2 setup.py --glut install --prefix=~/pymol-install-py2

Hope that helps.

Cheers,
  Thomas

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Re: [PyMOL] PyMol: incomplete replacement of b- and q-factors

2019-09-13 Thread Thomas Holder
Hi Joe,

There can be atoms without coordinates. In particular, when loading mmCIF 
files, PyMOL fills in dummy-CA atoms for missing residues, to provide a 
complete sequence display in the sequence viewer.

"alter" iterates over all atoms, including those without coordinates. 
"iterate_state" only includes those *with* coordinates.

Your issue can be handled in several ways:

1) Make a selection on the atoms with coordinates in state 1:
   select mysele, state 1, enable=0
   alter mysele, b = next(di)
   spectrum b, selection=mysele

2) Or just remove atoms which don't have coordinates in state 1:
   remove not state 1
   alter all, b = next(di)
   spectrum b

See "Coordinates" section here:
https://pymolwiki.org/index.php/Selection_Algebra

Cheers,
  Thomas

> On Sep 12, 2019, at 6:09 PM, Heffron, Joseph  
> wrote:
> 
> Hello all, 
> 
> I am trying to color several proteins by different factors, e.g., distance 
> from a given point (here the origin). To do this, I replace the q-factor (or 
> b-factor) with my variable of choice. However, most of my files have one or a 
> few residues that are for some reason not affected by the alter_state (e.g., 
> pdb = 1ihm). I can't see any distinction in these residues compared to the 
> others.  
> 
> example code: 
> 
> fetch 1ihm
> alldist = []
> iterate_state 1, all, alldist.append((x**2+y**2+z**2)**0.5)
> di = iter(alldist)
> alter all, b = next(di)
> spectrum b
> 
> Thank you, 
> Joe 
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Re: [PyMOL] amino acids displayed for mutagenesis. Hyp? PTMs? (Bruce Onisko)

2019-09-05 Thread Thomas Holder
Hi Bruce,

Worked for me without issues, on all platforms (Windows, Linux, Mac).

Installation:
1) Open PyMOL
2) Plugin > Plugin Manager > Install New Plugin
3) Install from PyMOLWiki or any URL
   URL: https://pymolwiki.org/index.php/Pytms
4) Click "Fetch"

Test Usage:
1) Load something:
fetch 1ubq
as lines
2) Plugin > Legacy Plugins > PyTMs
3) Click "Acetylation" on the left
4) Click "Modify: Acetylation!" in the bottom right

Cheers,
  Thomas

> On Sep 5, 2019, at 6:22 AM, Bruce Onisko  wrote:
> 
> Dear all,
> 
> I just read "PyTMs: a useful PyMol plugin for modelling common 
> post-translational modifications" and it looks great for my needs.
> 
> However after an hour of frustration I have not been able to download and 
> install the plugin.  (I had no trouble downloading, installing and using the 
> SwissModel plugin...)
> 
> Has anyone done this recently?  If so maybe point me to a working link, or 
> step me through the process please?
> 
> Thanks!
> 
> Bruce

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Re: [PyMOL] aberrant behavior of mouse clicks in PyMOL

2019-08-22 Thread Thomas Holder
Hi Vaheh,

Which version of PyMOL do you use? Could it be this issue? 
https://github.com/schrodinger/pymol-open-source/issues/35

Cheers,
  Thomas

> On Aug 21, 2019, at 10:04 PM, Oganesyan, Vaheh 
>  wrote:
> 
> Hi All,
>  
>  
> I’m experiencing very annoying behavior of mouse clicks when there are more 
> than one molecule in ASU. Upon opening the window cartoon mode is showing. If 
> I click on the part of first listed molecule then all look good. However, if 
> I click on the part of the second molecule then another residue gets picked 
> up from the first one. Now, if I do “show as cartoon” while it is already 
> showing cartoon, then the behavior goes back to normal.
> Question: Do I have computer hardware issue, (personal hardware issue ), or 
> this is a bug?
> Thank you.
>  
> Regards,
>  
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> 
> AstraZeneca
> R | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T:  301-398-4640  M:  240-398-0046
> vaheh.oganes...@astrazeneca.com
>  
>  
>  
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Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

2019-08-21 Thread Thomas Holder
Hi Yeping,

The return value of cmd.align() is documented here:

https://pymolwiki.org/index.php/Align#PyMOL_API

Cheers,
  Thomas

> On Aug 20, 2019, at 5:15 AM, sunyeping via PyMOL-users 
>  wrote:
> 
> Hello Mat,
> 
> Thank you for your reply.
> I followed your codes in the second line and get a series of output, which 
> look like:
> 
> (9.949092864990234, 267, 0, 9.949092864990234, 267, 420.0, 226)
> 
> I guess the first and the fourth float numbers are the rmsd, but what are 
> other numbers in the line?
> 
> Best regards.
> 
> Yeping
> --
> From:Istvan Kolossvary 
> Sent At:2019 Aug. 20 (Tue.) 00:29
> To:Mateusz Bieniek 
> Cc:孙业平 ; pymol-users 
> Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD 
> simulation trajectory and a reference structure?
> 
> Superpose all states of an object to one of the states.
> print cmd.intra_fit("my-trajCA", 1)Do the same, but this time the 
> target/reference is a different object.
> for s in range(cmd.count_states()): print(cmd.align('my-traj', 'ref', 
> mobile_state=s + 1, target_state=1, cycles=0, transform=0))
> 
> On Mon, Aug 19, 2019 at 9:25 AM Mateusz Bieniek  wrote:
> There is also intra_rms and instra_fit commands: 
> https://pymol.org/pymol-command-ref.html#intra_rms
> https://pymol.org/pymol-command-ref.html#intra_fit
> 
> For example:
> intra_fit name CA and resid 1326-1350, 0
> 
> Maybe they will be useful. 
> 
> Best, Mat
> 
> On Mon, 19 Aug 2019 at 13:54, sunyeping  wrote:
> Hello Mateusz,
> 
> Thank you very much for your reply to my inquiry. Before I try the PyMOL 
> extension you mentioned, I want to try scripting language in pymol. I wrote a 
> attemptive one (align.py):
> 
> cmd.load("A.gro")
> cmd.load("A.xtc")
> cmd.load("ref.pdb")
> for i in range(1, 5001):
>cmd.align(ref, A,target_state=i)
> 
> I ran it in pymol command line, but it doesn't work. I am new to pymol 
> scripting. Could you write a correct one for me? Thank you very much.
> 
> Best regards,
> 
> Yeping 
> 
> 
> --
> From:Mateusz Bieniek 
> Sent At:2019 Aug. 19 (Mon.) 20:32
> To:孙业平 
> Cc:pymol-users 
> Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD 
> simulation trajectory and a reference structure?
> 
> Hi Sunyeping,
> 
> Besides using the scripting language in pymol, you might want to consider the 
> experimental PyMOL extension created by the PyMOL Fellows (me and Paul Smith, 
> https://pymol.org/fellowship/). The extension relies on the MDAnalysis 
> package and so far includes RMSD as an example. Here is the link to the right 
> github branch 
> https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
> 
> If you compile it, you can use the RMSD this way: 
> mda_load systemX.gro
> mda_load_traj systemX.xtc
> mda_rmsd 
> 
> 
> Kind Regards, 
> Mateusz
>  
> 
> On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users 
>  wrote:
> Dear everyall,
> 
> I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames 
> and a reference structure (B.pdb) into pymol. I wish to get the rmsd value 
> between each state of the MD simulation trajectory and the reference 
> structure, but I don't know how. I can use the align command as: "align A, 
> B", but this only gives one rmsd value. Could you tell me how to get the rmsd 
> value between each state of the MD simulation trajectory and the reference 
> structure?
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Re: [PyMOL] HELIX and SHEET records not read by Pymol

2019-08-21 Thread Thomas Holder
Hi Chris,

Works for me. Do you have an example file that doesn't work for you?

"Works for me" steps to reproduce:
- remove everything but ATOM records from 1ubq.pdb (raw.pdb)
- run stride on raw.pdb
- paste stride output on website
- paste website result into PDB file (stride.pdb)
- load stride.pdb and raw.pdb with PyMOL
-> Result: Cartoons differ

Cheers,
  Thomas

> On Aug 20, 2019, at 11:05 AM, Chris Fage  wrote:
> 
> Dear All,
> 
> Pymol seems to ignore the HELIX and SHEET records in my coordinate file, and 
> instead assigns secondary structural features according to the default 
> method. Unless my understanding is flawed, these records should override 
> Pymol's assignment...?
> 
> I generated the records with the Stride Web Interface and converted them to 
> PDB format with Emma Rath's website 
> (http://www.canoz.com/sdh/STRIDEtoPDBsecondarystruct.pl). 
> 
> Does anyone have any ideas? Thanks!
> 
> Best wishes,
> Chris
> 
>   Virus-free. www.avg.com
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Re: [PyMOL] count_atoms and states

2019-08-15 Thread Thomas Holder

> On Aug 12, 2019, at 2:56 PM, Christian Cole French 
>  wrote:
> 
> Maybe the nonexistent state warning is something that should be implemented 
> elsewhere as well.

Selecting state 0 is now an error:

https://github.com/schrodinger/pymol-open-source/commit/c09ce287d447e6c703e57d31ae3e5d53f8359ee1

Cheers,
  Thomas

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Re: [PyMOL] Label volume

2019-08-15 Thread Thomas Holder
Hi Pedro,

it's only possible to label atoms. If you need an independent label, create a 
pseudo atom:

pseudoatom label="Hello World"

You can move the atom (or the label) in 3-Button Editing mouse mode while 
holding CTRL and dragging with the left mouse button.

Cheers,
  Thomas

> On Aug 12, 2019, at 7:01 PM, Pedro Lacerda  wrote:
> 
> And how to place a single arbitrary label on the object or segment?
> 
> Em seg, 12 de ago de 2019 às 13:55, Pedro Lacerda  
> escreveu:
> Hi PyMOL list,
> 
> Is possible toshow  a label independent of the associated object be enabled?
> 
> Or is possible to label a volume or map?
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
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Re: [PyMOL] Plugin upload.

2019-07-12 Thread Thomas Holder
Hi Will,

You need a GPL-compatible license for your plugin which uses PyQt. This could 
be GPL (of course) but also BSD-3-Clause or Apache License.

By the way, PyMOL also works with PySide (which is LGPL). So strictly speaking, 
your plugin will not depend on PyQt, you could always set up Open-Source PyMOL 
with PySide and use that instead. The compatibility module is pymol.Qt (do 
"from pymol.Qt import QtWidgets" instead of "from PyQt5 import QtWidgets").

Hope that helps.

Cheers,
  Thomas

> On Jul 11, 2019, at 3:53 PM, William Tao  wrote:
> 
> Hi Wael,
> 
> I'm somehow curious whether you have used PyQt in your plugin. 
> 
> Nowadays, people usually upload released code onto repositories like GitHub. 
> But I'm not sure which open source license we need to use if PyQt is used. 
> 
> Hope anyone who is familiar with this issue could help.
> 
> Many thanks.
> 
> Will
> 
> 
> Wael Azzam via PyMOL-users  于2019年7月9日周二 
> 上午3:11写道:
> To whom it may concern,
> 
> I am writing to you in the hopes of knowing how to upload a PyMol plugin that 
> I developed on the page PyMolWiki ?
> 
> Best regards,
> 
> Wael Azzam
> B.S in Bioinformatics 
> Lebanese American University, Beirut

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Re: [PyMOL] Plugin upload.

2019-07-12 Thread Thomas Holder
Hi Wael,

Of course you can add it to the PyMOLWiki!

If your plugin is a single Python file, then the easiest thing to do is to add 
it to the Pymol-script-repo. Just fork 
https://github.com/Pymol-Scripts/Pymol-script-repo and make a pull request.

If your plugin is more complex (multiple files), then it will be better if you 
make your own github project for it. Users can download your repo as a ZIP file 
from github and install that zip file with PyMOL's plugin manager (if you 
follow a layout like https://github.com/Pymol-Scripts/pymol2-demo-plugin ).

In addition to uploading your plugin to github, you should create a page on the 
PyMOLWiki with instructions how to use it.

Cheers,
  Thomas


> On Jul 11, 2019, at 10:10 PM, Wael Azzam via PyMOL-users 
>  wrote:
> 
> Hello Will,
> 
> Thank you for your reply!!
> 
> No, I used Tkinter for Gui with no implementation of PyQt whatsoever.
> So, i cannot make it to the PyMolWiki plugins category?
> 
> Best,
> Wael
> 
> 
> 
> On 11 Jul,2019, at 16:53, William Tao  wrote:
> 
>> Hi Wael,
>> 
>> I'm somehow curious whether you have used PyQt in your plugin. 
>> 
>> Nowadays, people usually upload released code onto repositories like GitHub. 
>> But I'm not sure which open source license we need to use if PyQt is used. 
>> 
>> Hope anyone who is familiar with this issue could help.
>> 
>> Many thanks.
>> 
>> Will
>> 
>> 
>> Wael Azzam via PyMOL-users  于2019年7月9日周二 
>> 上午3:11写道:
>> To whom it may concern,
>> 
>> I am writing to you in the hopes of knowing how to upload a PyMol plugin 
>> that I developed on the page PyMolWiki ?
>> 
>> Best regards,
>> 
>> Wael Azzam
>> B.S in Bioinformatics 
>> Lebanese American University, Beirut

--
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PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] The 'select' command for complex residue selection

2019-07-09 Thread Thomas Holder
The last parentheses is not the ASCII character ")" (code 41), but the unicode 
character ")" (code U+FF09) and PyMOL can't handle that.

https://www.compart.com/en/unicode/U+FF09

Cheers,
  Thomas


> On Jul 9, 2019, at 5:47 AM, Kevin Jude  wrote:
> 
> Strange, I get the same error and can't figure out why it doesn't like the 
> parentheses around the second term, though here are a few formulations that 
> give the correct result without syntax errors:
> 
>  select sele, protein_A and chain A and (resi 29-33 or resi 70-73 or resi 
> 116-119) or protein_A and chain C and resi 87-95
>  select sele, (protein_A and chain C and resi 87-95) or (protein_A and chain 
> A and (resi 29-33 or resi 70-73 or resi 116-119))
>  select sele, protein_A and chain C and resi 87-95 or (protein_A and chain A 
> and (resi 29-33 or resi 70-73 or resi 116-119))
>  select sele, protein_A and chain C and resi 87-95 or (protein_A and chain A 
> and resi 29-33 or resi 70-73 or resi 116-119)
> 
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
> 
> On Mon, Jul 8, 2019 at 7:40 PM sunyeping via PyMOL-users 
>  wrote:
> Dear all, 
> 
> In pymol I loaded two protein: protein_A and protein_B. I want to make a 
> selection of some incontinuous residues from two chains of protein_A, for 
> example, residue 30-34, 71-74 and 117-120 from chain A and residue 88-96 from 
> chain C. How should I write the select command? I tried the following:
> 
>select sele, (protein_A and chain A and (resi 29-33 or resi 70-73 or resi 
> 116-119)) or (protein_A and chain C and resi 87-95)
> 
> but it returns syntax error. So what is the correct command for this?
> 
> Thank you in advance

--
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PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] Errors in "Label" page on PyMOL Wiki

2019-07-08 Thread Thomas Holder
Hi Jared,

I can confirm this. There is a  tag in the page, if I remove the
tag the page loads fine.

I've sent an email to SBGrid to let them know.

Cheers,
  Thomas

On Mon, Jul 8, 2019 at 4:53 AM Jared Sampson  wrote:
>
> Hi PyMOLers -
>
> I'm currently not able to access the label page on PyMOL Wiki, which prints 
> out a string of PHP errors. Weirdly, it appears to be specific to that page, 
> as others (off the top of my head, I visited load and save) appear to be 
> working fine.
>
> Can anyone else confirm this?  If so, I wonder if it can be fixed by an admin.
>
> Cheers,
> Jared
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Re: [PyMOL] `selection` argument in load_traj

2019-06-26 Thread Thomas Holder
Hi Lorenzo,

You are correct, it's doing nothing for most trajectory formats. Only the 
implementation for AMBER .trj files uses it. It looks like it allows selecting 
a subset of atoms.

Cheers,
  Thomas

> On Jun 25, 2019, at 4:05 PM, Lorenzo Gaifas  wrote:
> 
> Dear pymol users,
> 
> What is the purpose of the `selection` argument in the `load_traj` command?
> 
> My intuition would say that it allows to somehow select which atoms to load 
> into pymol before the actual loading happens. However, it seems to do nothing 
> whatsoever. What am I missing?
> 
> Thanks,
> Lorenzo
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Re: [PyMOL] Thermal ellipsoid plot

2019-06-26 Thread Thomas Holder
Hi Koji,

Yes it is my understanding that sphere_scale 1.1932 would correspond to 30% 
probability.

Cheers,
  Thomas

> On Jun 25, 2019, at 12:26 PM, koji naka  wrote:
> 
> Dear Mr. Thomas Holder,
> 
> Thank you very much for your kind reply.
> I am very happy to know the scale factor for the 50% probability, but I don't 
> understand well.
> From the table, can I take a value the scale? For example, in case of 30% 
> probability, is it ok to set " set sphere_scale,  1.1932"? or not?
> 
> I am sorry for bothering you again.
> 
> Best regards,
> Koji
> 
> 2019年6月25日(火) 18:49 Thomas Holder :
> Hi Koji,
> 
> Interesting question, I wasn't aware of the ellipsoid_probability setting.
> 
> The probability to radius conversion is done with a lookup table, see:
> https://github.com/schrodinger/pymol-open-source/blob/d1359f125d/layer2/RepEllipsoid.cpp#L114
> 
> To get sphere scaling equivalent of ellipsoid_probability=0.5, you can do:
> 
> set sphere_scale, 1.53820
> 
> I calculated this value with the following script:
> 
> problevel = [ \
>   0.4299, 0.5479, 0.6334, 0.7035, 0.7644, \
>   0.8192, 0.8694, 0.9162, 0.9605, 1.0026, \
>   1.0430, 1.0821, 1.1200, 1.1570, 1.1932, \
>   1.2288, 1.2638, 1.2985, 1.3330, 1.3672, \
>   1.4013, 1.4354, 1.4695, 1.5037, 1.5382, \
>   1.5729, 1.6080, 1.6436, 1.6797, 1.7164, \
>   1.7540, 1.7924, 1.8318, 1.8724, 1.9144, \
>   1.9580, 2.0034, 2.0510, 2.1012, 2.1544, \
>   2.2114, 2.2730, 2.3404, 2.4153, 2.5003, \
>   2.5997, 2.7216, 2.8829, 3.1365, 6. ]
> 
> iprob = int((cmd.get_setting_float('ellipsoid_probability') + 0.01) * 50 - 1)
> pradius = problevel[iprob]
> 
> cmd.set('sphere_scale', pradius * cmd.get_setting_float('ellipsoid_scale'))
> 
> Hope this helps.
> 
> Cheers,
>   Thomas
> 
> 
> > On Jun 24, 2019, at 7:21 AM, koji naka  wrote:
> > 
> > Dear all,
> > 
> > The size of isotropic atoms plotted by using "alter all, vdw = 
> > sqrt(b/8)/pi" and "show sphere" looks small compared with the size of 
> > anisotropic atoms displayed by "show ellipsoid" in PyMOL default setting 
> > with 50% probability.
> > 
> > How can I plot the isotropic atoms with 50% probability?
> > 
> > The data is a pdb file converted from a cif through Mercury software.
> > 
> > Thank you very much for your help.
> > 
> > Best regards,
> > Koji
> > 
> > 
> > ___________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> > Unsubscribe: 
> > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

--
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Re: [PyMOL] set transparency for selected elements of secondary structure

2019-06-26 Thread Thomas Holder
Hi James and Ali,

Are you using PyMOL 2.3 yet?

"As of PyMOL version 2.3, cartoon transparency is now an atom-level setting."

https://pymolwiki.org/index.php/Cartoon_transparency

Cheers,
  Thomas

> On Jun 26, 2019, at 10:26 AM, Ali Kusay  wrote:
> 
> Hi James,
> 
> I am not sure what the exact cause of your issue is but I think if you make a 
> selection first then apply the transparency to the selection that should 
> work, i.e.:
> 
> sele ss H+S
> set cartoon_transparency, 0.5, sele
> 
> Something to do with selection based transparency settings not enabling newer 
> ones to be made
> 
> Cheers,
> 
> Ali
> 
> On 26/6/19, 6:18 pm, "James Starlight"  wrote:
> 
>Dear pymol users!
> 
>I am trying to set transparency based on the secondary structure using
>pymol selection algebra
> 
># set transparency to all helix and sheets but not loops
>set cartoon_transparency, 0.5, ss H+S
> 
>which produce the following output
>PyMOL>set cartoon_transparency, 0.5, ss H+S
> Setting: cartoon_transparency set for 144 atoms in object 
> "0190_before_minim".
> 
>but actually do nothing in terms of visualization.
> 
>Could you suggest me how it would be possible to fix it?
> 
>Thanks in advance!
> 
> 
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Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread Thomas Holder
If you want to rename multiple chains at once, make a selection like (chain 
A+B+C). This list selection syntax is documented here: 
https://pymolwiki.org/index.php/Property_Selectors

cmd.load(pdb)
cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
cmd.save('output.pdb')

Cheers,
  Thomas


> On Jun 25, 2019, at 4:14 PM, James Starlight  wrote:
> 
> thanks so much Thomas, for this example!
> 
> Actually, your python script does exactly what my bash script -
> produces number of pdbs for each of the renamed chain.
> I would like rather to produce at the end ONE pdb with all chains
> renamed to empty chain...
> I guess I need to save the result outside of the loop something like this
> 
>  hop hey lalaley #
> from pymol import cmd
> pdb = "Ev_complex_model_final.pdb"
> chains_array = ["A", "B"] # add more chains in case of more complex pdb
> 
> # loop over chains to rename it
> for chain in chains_array:
>cmd.load(pdb)
>cmd.alter('chain ' + chain, 'chain=""')
>cmd.delete('*')
> ##
> 
> # save output as pdb
> # I need to add something in the name of output indicating how much
> chains have been renamed
> # like output_withoutAB.pdb
> cmd.save('output_'  + '.pdb')
> 
> thanks in advance for help!

--
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Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread Thomas Holder
> generally if I integrate a pymol silent script inside my
> bash script, I do not need to use cmd.* syntax, right?

Correct. The -d argument takes PyMOL commands, like a .pml script. Python 
syntax is optional.

Python syntax (cmd.*) is necessary and most useful if you write a Python script 
(.py extension) and run that with PyMOL. You could write your multi-chains loop 
as a Python script:

 example.py ##
from pymol import cmd
pdb = "my.pdb"
chains_arrays = ["A", "B", "C", "D", "E", "F", "G"]

for chain in chains_array:
cmd.load(pdb)
cmd.alter('chain ' + chain, 'chain=""')
cmd.save('output_' + chain + '.pdb')
cmd.delete('*')
##

Then run it with PyMOL:
pymol -ckqr example.py

See also:
https://pymolwiki.org/index.php/Launching_From_a_Script
https://pymolwiki.org/index.php/Python_Integration

Cheers,
  Thomas

> On Jun 25, 2019, at 3:08 PM, James Starlight  wrote:
> 
> one extra programming question:
> 
> imagine now in my pdb I have severals chain which I would like to
> rename to blank chain.
> 
> I can do it simply like this
> # a case for 3 chains to be renamed
> 
> #!/bin/bash
> pdb="my.pdb"
> output=$(pwd)
> pymol -c -d "
> cmd.load('${pdb}')
> cmd.alter('(chain A)', 'chain=\"\"')
> cmd.alter('(chain B)', 'chain=\"\"')
> cmd.alter('(chain C)', 'chain=\"\"')
> cmd.save('${output}/output.pdb','all')
> "
> 
> or for multi-chain protein I can alternatively create external loop,
> thus running pymol 3 times iteratively (which is not good realization)
> providin array info from external shell session
> 
> # this example save 7 different pdbs renaming one chain in each of them
> #!/bin/bash
> pdb="my.pdb"
> output=$(pwd)
> chains_arrays=( A B C D E F G )
> 
> for i in "$chains_array[@]}"; do
> pymol -c -d "
> cmd.load('${pdb}')
> cmd.alter('(chain $i)', 'chain=\"\"')
> cmd.save('${output}/output_$i.pdb','all')
> "
> done
> 
> would it be possible rather to make an array and loop inside the pymol
> to rename all chains into the blank chain during one execution of
> pymol?
> 
> Thanks in advance!
> 
> вт, 25 июн. 2019 г. в 14:50, James Starlight :
>> 
>> I have got the idea!
>> thank you so much Thomas!
>> One question: generally if I integrate a pymol silent script inside my
>> bash script, I do not need to use cmd.* syntax, right?  In what cases
>> cmd.* sytax might be usefull?
>> 
>> Thank you again!
>> 
>> вт, 25 июн. 2019 г. в 12:05, Thomas Holder :
>>> 
>>> 
>>>> On Jun 25, 2019, at 11:48 AM, James Starlight  
>>>> wrote:
>>>> 
>>>> so what I need is just to update my pymol, keep using the same command?
>>> 
>>> Yes
>>> 
>>>> P.S.would the following integration of the code into bash script be
>>>> usefull to remove chains in no gui mode?
>>>> 
>>>> pymol -cQkd "
>>>> from pymol import cmd
>>>> fetch $pdb, type=pdb, tmp
>>>> cmd.alter('(chain A)',chain='')
>>>> "
>>>> I am not sure whether I used here cmd.alter in correct way ..
>>> 
>>> 
>>> With fetch, use "async=0" or use Python syntax. And keyword arguments 
>>> (type=) must be after positional arguments (tmp).
>>> 
>>> It's easier if you don't use Python syntax for alter, otherwise you'll need 
>>> three levels of nested quotes, which gets ugly:
>>> 
>>> pymol -cQkd "
>>> fetch $pdb, tmp, type=pdb, async=0
>>> alter (chain A), chain=''
>>> "
>>> 
>>> With Python syntax (note the ugly escaping of quotes):
>>> 
>>> pymol -cQkd "
>>> cmd.fetch('$pdb', 'tmp', type='pdb')
>>> cmd.alter('(chain A)', 'chain=\"\"')
>>> "
>>> 
>>> Cheers,
>>>  Thomas
>>> 
>>> --
>>> Thomas Holder
>>> PyMOL Principal Developer
>>> Schrödinger, Inc.
>>> 

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Re: [PyMOL] Thermal ellipsoid plot

2019-06-25 Thread Thomas Holder
Hi Koji,

Interesting question, I wasn't aware of the ellipsoid_probability setting.

The probability to radius conversion is done with a lookup table, see:
https://github.com/schrodinger/pymol-open-source/blob/d1359f125d/layer2/RepEllipsoid.cpp#L114

To get sphere scaling equivalent of ellipsoid_probability=0.5, you can do:

set sphere_scale, 1.53820

I calculated this value with the following script:

problevel = [ \
  0.4299, 0.5479, 0.6334, 0.7035, 0.7644, \
  0.8192, 0.8694, 0.9162, 0.9605, 1.0026, \
  1.0430, 1.0821, 1.1200, 1.1570, 1.1932, \
  1.2288, 1.2638, 1.2985, 1.3330, 1.3672, \
  1.4013, 1.4354, 1.4695, 1.5037, 1.5382, \
  1.5729, 1.6080, 1.6436, 1.6797, 1.7164, \
  1.7540, 1.7924, 1.8318, 1.8724, 1.9144, \
  1.9580, 2.0034, 2.0510, 2.1012, 2.1544, \
  2.2114, 2.2730, 2.3404, 2.4153, 2.5003, \
  2.5997, 2.7216, 2.8829, 3.1365, 6. ]

iprob = int((cmd.get_setting_float('ellipsoid_probability') + 0.01) * 50 - 1)
pradius = problevel[iprob]

cmd.set('sphere_scale', pradius * cmd.get_setting_float('ellipsoid_scale'))

Hope this helps.

Cheers,
  Thomas


> On Jun 24, 2019, at 7:21 AM, koji naka  wrote:
> 
> Dear all,
> 
> The size of isotropic atoms plotted by using "alter all, vdw = sqrt(b/8)/pi" 
> and "show sphere" looks small compared with the size of anisotropic atoms 
> displayed by "show ellipsoid" in PyMOL default setting with 50% probability.
> 
> How can I plot the isotropic atoms with 50% probability?
> 
> The data is a pdb file converted from a cif through Mercury software.
> 
> Thank you very much for your help.
> 
> Best regards,
> Koji
> 
> 
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Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread Thomas Holder
Hi James,

pdb_use_ter_records works in PyMOL 2.3.0, but not in previous versions (was 
broken and then removed). See 
https://pymolwiki.org/index.php/pdb_use_ter_records

Cheers,
  Thomas

> On Jun 25, 2019, at 10:25 AM, James Starlight  wrote:
> 
> Dear Pymol Users!
> 
> I need to process input PDB via pymol (this time no need to do it via
> no-gui mode!!) to remove chain id from PDB.
> 
> I am using alter command to do it with the following syntax
> #rename chain A to phantom chain :-)
> alter (chain A),chain=''
> 
> the problem that in my initial PDBs there are many TER records (e.g.
> to separate protein from ligand etc), which should be keeped after
> such post-processing in the form of original PDB (with chain A).
> 
> I have tried to do this before saving of the PDB
> get pdb_use_ter_records
> 
> however, as the result, all the TER records were removed from the
> processed pdb. How I could fix it?
> 
> Many thanks in advance!
> 
> 
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Re: [PyMOL] possible bug mouse coordinates

2019-06-14 Thread Thomas Holder
Hi Arnaud,

This should be fixed now, see
https://github.com/schrodinger/pymol-open-source/commit/af28e453c6

Cheers,
  Thomas

> On Jun 13, 2019, at 5:46 PM, Thomas Holder  
> wrote:
> 
> Hi Arnaud,
> 
> I can reproduce both issues, at least with "sticks" representation. 
> Apparently PyMOL is missing pick color invalidation somewhere.
> 
> As a workaround, click the "Rebuild" button (upper right button box), or type 
> the "rebuild" command. After that, picking should be correct again.
> 
> Cheers,
>  Thomas
> 
>> On Jun 13, 2019, at 4:21 PM, Arnaud Basle  wrote:
>> 
>> Dear All,
>> 
>> We found that our home compiled version has the problem just even doing:
>> 
>> load a pdb
>> 
>> change the colour
>> 
>> and then the mouse coordinates are wrong... Anyone else?
>> 
>> Cheers,
>> 
>> Arnaud
>> 
>> 
>> On 13/06/2019 14:33, Arnaud Basle wrote:
>>> Dear All,
>>> 
>>> We may have found a bug where pymol does not get the correct mouse location 
>>> on the screen.
>>> 
>>> We are using Version 2.3.0a0 on linux Mint 19 (~ubuntu).
>>> 
>>> Maybe people can try to reproduce the bug:
>>> 
>>> open a pdb file
>>> 
>>> display sticks
>>> 
>>> try to select residues or recenter and it should work fine.
>>> 
>>> Now, reduce the top part window of pymol with the log output, movie buttons 
>>> and command line (the mouse pointer will change then click and drag).
>>> 
>>> repeat selecting/centering and it should work.
>>> 
>>> Then use a menu entry, for example Display>Background>White
>>> 
>>> And if not only us now it seems we click on a residue but another one is 
>>> selected. It looks like there is a bug where pymol cannot determine the 
>>> correct mouse co-ordinates?
>>> 
>>> Cheers,
>>> 
>>> Arnaud
>>> 
>>> 
>> -- 
>> Dr Arnaud Basle         X-ray facilities manager
>> Newcastle Structural Biology Laboratory
>> University of Newcastle
>> Medical School
>> ICAMB
>> Framlington place
>> NE2 4HH Newcastle upon tyne
>> Phone 0191 208 8931
>> 
>> 
>> 
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>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

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Re: [PyMOL] Advice on plugin creation

2019-06-14 Thread Thomas Holder
Hi Ed,

The tutorial doesn't consider that the "dialog" variable must not go out of 
scope. It needs an additional reference to keep it alive, e.g. a global will 
work:

dialog = None

def run_plugin_gui():
   from pymol.Qt import QtWidgets

   global dialog

   if dialog is None:
   dialog = QtWidgets.QDialog()
   # TODO: FILL DIALOG WITH WIDGETS HERE

   dialog.show()

The full example plugin on github doesn't suffer from this problem, it's kept 
alive by circular references - at least until you run the Python garbage 
collector (ouch!).

Cheers,
  Thomas


On Wed, Jun 12, 2019 at 7:02 PM Edward Lowe  wrote:
> 
> Hello,
> 
> I'm trying to create what I think should be a fairly simple plugin to
> use pymol to showcase structures for a University Open day - all it
> needs to do is load up coordinate files and maps and present a very
> simple GUI that visitors can use to move between pre-defined scenes.
> 
> I've constructed a PyQt plugin following the tutorial on pymolwiki
> which works up to a point...
> If I display the window using dialog.show() as in the tutorial example,
> the window disappears immediately on opening.
> If I change this to using dialog.exec() my widget opens correctly and
> everything works - but since this is now a modal window it is not
> possible to return to the main pymol gui and interact with the
> structure.  This was the point of the exercise an why I'm not just
> making a movie!
> 
> Does anyone have any advice on what could be done to fix this
> behaviour?  It probably goes without saying that I am very much a
> novice at this!
> 
> Thanks,
> Ed.
> --
> Dr. E.D. Lowe   edward.l...@bioch.ox.ac.uk
> Department of Biochemistry  Tel: ++44 (0)1865 (2)75392
> University of Oxford
> Oxford UK, OX1 3QU
> 
> 
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Re: [PyMOL] possible bug mouse coordinates

2019-06-13 Thread Thomas Holder
Hi Arnaud,

I can reproduce both issues, at least with "sticks" representation. Apparently 
PyMOL is missing pick color invalidation somewhere.

As a workaround, click the "Rebuild" button (upper right button box), or type 
the "rebuild" command. After that, picking should be correct again.

Cheers,
  Thomas

> On Jun 13, 2019, at 4:21 PM, Arnaud Basle  wrote:
> 
> Dear All,
> 
> We found that our home compiled version has the problem just even doing:
> 
> load a pdb
> 
> change the colour
> 
> and then the mouse coordinates are wrong... Anyone else?
> 
> Cheers,
> 
> Arnaud
> 
> 
> On 13/06/2019 14:33, Arnaud Basle wrote:
>> Dear All,
>> 
>> We may have found a bug where pymol does not get the correct mouse location 
>> on the screen.
>> 
>> We are using Version 2.3.0a0 on linux Mint 19 (~ubuntu).
>> 
>> Maybe people can try to reproduce the bug:
>> 
>> open a pdb file
>> 
>> display sticks
>> 
>> try to select residues or recenter and it should work fine.
>> 
>> Now, reduce the top part window of pymol with the log output, movie buttons 
>> and command line (the mouse pointer will change then click and drag).
>> 
>> repeat selecting/centering and it should work.
>> 
>> Then use a menu entry, for example Display>Background>White
>> 
>> And if not only us now it seems we click on a residue but another one is 
>> selected. It looks like there is a bug where pymol cannot determine the 
>> correct mouse co-ordinates?
>> 
>> Cheers,
>> 
>> Arnaud
>> 
>> 
> -- 
> Dr Arnaud Basle X-ray facilities manager
> Newcastle Structural Biology Laboratory
> University of Newcastle
> Medical School
> ICAMB
> Framlington place
> NE2 4HH Newcastle upon tyne
> Phone 0191 208 8931
> 
> 
> 
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Re: [PyMOL] Question about Pymol method / ESP rendering

2019-06-11 Thread Thomas Holder
Hi Taka,

Your ESP.cube file doesn't look like an electrostatic potential map, it looks 
like electron density. You need two map files, one for the density, and one for 
the ESP.

Cheers,
  Thomas

> On Jun 8, 2019, at 12:39 AM, Taka Seri  wrote:
> 
> Dear Pymol users,
> I am newbie of Pymol.
> I have a question of coloring method. I would like to draw isosurface with 
> ESP and would like to set color with ramp_new function.
> Attached files are example.
> When I load ESP file and type following command, I could get isosurface.
> But I could get only blue colored surface after setting color with ramp_new 
> function.
> 
> > isosurface esp_surf, ESP, 0.2
> > ramp_new color_map, ESP, [-0.1, 0.1]
> 
> I read following url and it worked well.
> https://pymolwiki.org/index.php/Ramp_New
> 
> Is something wrong in my ESP file or approach? Any advice or suggestions will 
> be greatly appreciated.
> 
> Kind regards,
> 
> Taka
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Re: [PyMOL] [EXTERNAL] Absymal performance when creating large numbers of bonds

2019-05-26 Thread Thomas Holder
Hi Lorenzo,

Looks like the cmd.bond() function is indeed very inefficient. I've found a "TO 
DO: optimize for performance" comment in the code - that speaks for itself.

https://github.com/schrodinger/pymol-open-source/blob/master/layer2/ObjectMolecule.cpp#L4492

Parallelization is not the solution. You are probably right that a new API 
function is needed which allows you to directly add a bond by atom indices 
instead of atom selections.

Cheers,
  Thomas

> On May 25, 2019, at 5:11 PM, Lorenzo Gaifas  wrote:
> 
> Hi Blaine,
> 
> Thanks for your help.
> I don't think what you suggest is going to solve the problem. The loop itself 
> is quite fast, and I don't need to perform anything else in the loop other 
> than adding those bonds.
> I already have a list of tuples [(atom1, atom2), (atom3, atom4)] and all I 
> need to do is create a bond between each pair. The bottleneck is the bond 
> function, not the loop itself.
> 
> Also, I doubt simply the speed difference between C++ and Python could 
> explain such a drastic difference (minutes against fractions of a second). 
> There is clearly a difference in the way the `bond` command is implemented 
> and the way bonds are generated at startup.
> 
> What I think is needed, is either a way for pymol to perform those actions in 
> parallel (unlikely) or a way to get my hands on the way bonds are generated 
> at startup and use those functions or at least the same approach.
> 
> Thank you,
> Lorenzo
> 
> Il giorno sab 25 mag 2019 alle ore 16:23 Mooers, Blaine H.M. (HSC) 
>  ha scritto:
> Hi Lorenzo,
> 
> You can import numpy  and replace your lists of coordinates with NumPy 
> arrays. 
> Operations with numpy arrays can be >100 times faster than with lists in for 
> loops. 
> See the last example the following blog post for inspiration: 
> 
> https://medium.freecodecamp.org/if-you-have-slow-loops-in-python-you-can-fix-it-until-you-cant-3a39e03b6f35.
> 
> Please recall that PyMOL is collection of C and C++ programs wrapped by 
> Python. 
> The fast display of bonds inside the viewport is due to C or C++ programs. 
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> 
> From: Lorenzo Gaifas [bris...@gmail.com]
> Sent: Saturday, May 25, 2019 5:48 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [EXTERNAL] [PyMOL] Absymal performance when creating large numbers 
> of bonds
> 
> Dear pymol users,
> 
> I'm working on a script, using the python API, that needs to add a very large 
> number of bonds to the loaded structure.
> 
> I thought simply using cmd.bond() in a for loop would do the trick, but -even 
> though it works- it is extremely slow. I figured something was fishy, since 
> pymol at startup is almost istantaneous and there, too, it has to compute, 
> draw and even guess equally large numbers of bonds.
> 
> I also tried to parallelise the command, but by now I *think* this can't be 
> done due to the Global Intepreter Lock.
> 
> I feel like there must be something I'm missing (maybe a way to prevent pymol 
> from updating the rendering between each cmd.bond call?) or at least an API 
> function that better exposes the bond generation procedure. Does someone have 
> suggestions on how to solve this problem?
> 
> Cheers,
> Lorenzo
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