pymol-users Mailing List for PyMOL Molecular Graphics System

Hello,

I've been trying to use the minimum mesh spacing feature on pymol to make
my meshes more defined and it doesn't seem to do anything.

I use .map.ccp4 files that I generated on ccp4 using .mtz files I generated
on phenix. Any suggestions on what I might be doing wrong and what I could
do to fix this would be really appreciated!

Regards,
Vatsal

-- 

Vatsal Purohit

PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University

PULSe-Biophysics and Structural Biology training group

vp...@pu... <pra...@pu...> | 346-719-9409

Hello,

I've been trying to color my Fo-Fc electron density maps in pymol with the
positive Fo-Fc maps showing as green and negative Fo-Fc maps showing as red
and having no luck with it. They either show up as red or green.

I generate my maps by converting .mtz from phenix to .ccp4 files on ccp4.
Any suggestions about how I can try to color them individually this would
be greatly appreciated!

Regards,
Vatsal

-- 

Vatsal Purohit

PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University

PULSe-Biophysics and Structural Biology training group

vp...@pu... <pra...@pu...> | 346-719-9409

You can select by cordinates, e.g.

select my_selection, z>12.5 (see https://pymolwiki.org/index.php/Selection_Algebra)

So you can select for a range of z-coordinates:

select my_selection, z >12.5 and z< 15

best regards
Annemarie
____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12     



> On 24 Apr 2019, at 03:27, pym...@li... wrote:
> I wanted to ask how to select a plane (perpendicular to zaxis) so that I can select all residues of interest in a protein. Any help is greatly appreciated
> Best Regards,
> Divya?
> 

Thanks Jared for your reply. I apologize for not clear. I want to use the plane to select the residues of interest in protein.


Best Regards,

Divya

________________________________
From: Jared Sampson <jar...@co...>
Sent: Tuesday, April 23, 2019 9:27 PM
To: Divya Kaur Matta
Cc: pymol-users
Subject: Re: [PyMOL] selection of residues in protein using plane perpendicular to Z-axis

Hi Divya -

It's not entirely clear what you're trying to do from your description.  Are you looking to select residues near the plane, or perhaps use the plane to divide residues into "of interest" and "not of interest"?  I think PyMOL can be useful here, but the approach will likely be different depending on your end goal.

Relatedly, if you want to visualize your plane, you can try the Plane Wizard<" rel="nofollow">https://pymolwiki.org/index.php/Plane_Wizard> script, although that won't help with selecting atoms.

Cheers,
Jared


On April 23, 2019 at 7:46:49 PM, Divya Kaur Matta (dm...@gr...<mailto:dm...@gr...>) wrote:

Hi all,

I wanted to ask how to select a plane (perpendicular to zaxis) so that I can select all residues of interest in a protein. Any help is greatly appreciated.


Best Regards,

Divya

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Hi Divya - 

It's not entirely clear what you're trying to do from your description.  Are you looking to select residues near the plane, or perhaps use the plane to divide residues into "of interest" and "not of interest"?  I think PyMOL can be useful here, but the approach will likely be different depending on your end goal.

Relatedly, if you want to visualize your plane, you can try the Plane Wizard script, although that won't help with selecting atoms.

Cheers,
Jared

On April 23, 2019 at 7:46:49 PM, Divya Kaur Matta (dm...@gr...) wrote:

Hi all,

I wanted to ask how to select a plane (perpendicular to zaxis) so that I can select all residues of interest in a protein. Any help is greatly appreciated.

Best Regards,
Divya 
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PyMOL-users mailing list  
Archives: http://www.mail-archive.com/pym...@li...  
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Hi all,

I wanted to ask how to select a plane (perpendicular to zaxis) so that I can select all residues of interest in a protein. Any help is greatly appreciated.


Best Regards,

Divya

Hi Elmira,

If you are using windows, Open Source PyMOL for python3.6 can be found here:
https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol

If you are using Mac, Open Source PyMOL via macports still depends on Python2.7 by default. 
However, you can install PyMOL built with the macports python3.6 interpreter by using the variant flag python36.
(e.g., sudo port install pymol +python36). 
See https://www.macports.org/ports.php?by=library&substr=pymol

I tested this command this morning, and it worked for me with the Mohave OS. 
It takes about twenty minutes for the dependencies to install.  
I was able to "import pymol" and run "print pymol.__path__", which returned the path to macports python3.6.
Earlier, I had made a kernel for mapcorts python3.6 so this interpreter could be used in jupyter notebook.

If you are using Linux, see the PyMOL wiki for help https://pymolwiki.org/index.php/Linux_Install.

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: Elmira Nazarshodeh [elm...@gm...]
Sent: Tuesday, April 23, 2019 8:35 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Problem with pymol in python 3.6

Hello

I am going to work with pymol through python 3.6. When I type (from pymol import cmd) in the jupyter notebook, I get the following error:

ModuleNotFoundError: No module named 'pymol'


Could you please help me how can I fix the problem? How can I install a version of pymol that is compatible with python 3.6.?

Best Regards

Hello

I am going to work with pymol through python 3.6. When I type (from pymol
import cmd) in the jupyter notebook, I get the following error:

ModuleNotFoundError: No module named 'pymol'

Could you please help me how can I fix the problem? How can I install
a version of pymol that is compatible with python 3.6.?


Best Regards

  1. Ray tracing after morphing (Pascal Egea)

Which version of PyMOL are you using? In the free edu version, Raytracing is suppressed.
In the incentive version, you find under the movie menu the option “ray trace frames” which you need to check.
You may also want to first set your viewport (https://pymolwiki.org/index.php/Viewport)  to a larger size to get a better resolution.

Of course, both of these actions will increase the time it takes to render your movie


____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12     



> On 22 Apr 2019, at 14:00, pym...@li... wrote:
> 
> Send PyMOL-users mailing list submissions to
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>   1. Ray tracing after morphing (Pascal Egea)
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> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 21 Apr 2019 08:58:52 -0700
> From: Pascal Egea <pa...@ms...>
> To: pym...@li...
> Subject: [PyMOL] Ray tracing after morphing
> Message-ID:
> 	<CAO...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear All,
> 
> I have been making a morph in pymol and saved the different states using
> the mpng command in the active window. However, I cannot figure out how to
> get ray-traced images to make a high quality movie in quicktime, right now
> it is quite pixelated.
> Is there a way to ray0trace each state of the morph?
> Thanks in advance.
> -- 
> Pascal F. Egea, PhD
> Assistant Professor
> UCLA, David Geffen School of Medicine
> Department of Biological Chemistry
> Boyer Hall room 356
> 611 Charles E Young Drive East
> Los Angeles CA 90095
> office (310)-983-3515
> lab      (310)-983-3516
> email     pegea at mednet.ucla.edu
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Hello pymol-users, fyi ...

26th Annual Tcl/Tk Conference (Tcl'2019)
https://www.tcl-lang.org/community/tcl2019/

November 04 - 08, 2019
Crowne Plaza Houston River Oaks
2712 Southwest Freeway, 77098
Houston, Texas, USA

[ NEWS
 * [Submission is open](https://www.tcl-lang.org/community/tcl2019/cfp.html)
]

Important Dates:

Abstracts and proposals due   September 09, 2019
Notification to authors       September 16, 2019
WIP and BOF reservations open August 12, 2019     ** may change **
Registration opens            September 09, 2019     ** may change **
Author materials due          October 14, 2019
Tutorials Start               November 04, 2019
Conference starts             November 06, 2019

Email Contact:                tcl...@go...

Submission of Summaries

Tcl/Tk 2019 will be held in Houston, Texas, USA from November 04, 2019 to November 08, 2019.

The program committee is asking for papers and presentation proposals
from anyone using or developing with Tcl/Tk (and extensions). Past
conferences (Proceedings: https://www.tcl-lang.org/community/conferences.html)
have seen submissions covering a wide variety of topics including:

* Scientific and engineering applications
* Industrial controls
* Distributed applications and Network Managment
* Object oriented extensions to Tcl/Tk
* New widgets for Tk
* Simulation and application steering with Tcl/Tk
* Tcl/Tk-centric operating environments
* Tcl/Tk on small and embedded devices
* Medical applications and visualization
* Use of different programming paradigms in Tcl/Tk and proposals for new
  directions.
* New areas of exploration for the Tcl/Tk language

Submissions should consist of an abstract of about 100 words and a
summary of not more than two pages, and should be sent as plain text
to tcl...@go... no later than September 09, 2019. Authors of accepted
abstracts will have until October 14, 2019 to submit their final
paper for the inclusion in the conference proceedings. The proceedings
will be made available on digital media, so extra materials such as
presentation slides, code examples, code for extensions etc. are
encouraged.

Printed proceedings will be produced as an on-demand book at lulu.com
Online proceedings will appear via
	https://www.tcl-lang.org/community/conferences.html

The authors will have 30 minutes to present their paper at
the conference.

The program committee will review and evaluate papers according to the
following criteria:

* Quantity and quality of novel content
* Relevance and interest to the Tcl/Tk community
* Suitability of content for presentation at the conference

Proposals may report on commercial or non-commercial systems, but
those with only blatant marketing content will not be accepted.

Application and experience papers need to strike a balance between
background on the application domain and the relevance of Tcl/Tk to
the application. Application and experience papers should clearly
explain how the application or experience illustrates a novel use of
Tcl/Tk, and what lessons the Tcl/Tk community can derive from the
application or experience to apply to their own development efforts.

Papers accompanied by non-disclosure agreements will be returned to
the author(s) unread. All submissions are held in the highest
confidentiality prior to publication in the Proceedings, both as a
matter of policy and in accord with the U. S. Copyright Act of 1976.

The primary author for each accepted paper will receive registration
to the Technical Sessions portion of the conference at a reduced rate.

Other Forms of Participation

The program committee also welcomes proposals for panel discussions of
up to 90 minutes. Proposals should include a list of confirmed
panelists, a title and format, and a panel description with position
statements from each panelist. Panels should have no more than four
speakers, including the panel moderator, and should allow time for
substantial interaction with attendees. Panels are not presentations
of related research papers.

Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather
sessions (BOFs) are available on a first-come, first-served basis
starting in August 12, 2019. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in August 12, 2019. Some WIP and BOF time slots will be held open
for on-site reservation. All attendees with an interesting work in
progress should consider reserving a WIP slot.

Registration Information

More information on the conference is available the conference Web
site (https://www.tcl-lang.org/community/tcl2019/) and will be
published on various Tcl/Tk-related information channels.

To keep in touch with news regarding the conference, subscribe to the
tcl...@go... list. See:
https://groups.google.com/forum/#!forum/tclconference for list
information, archive, and subscription.

To keep in touch with Tcl events in general, subscribe to the
tcl-announce list. See: https://code.activestate.com/lists/tcl-announce
for list information, archive, and subscription.

Conference Committee

   * Andreas Kupries
   * Arjen Markus    Deltares
   * Brian Griffin   Mentor - A Siemens Business
   * Gerald Lester   KnG Consulting LLC
   * Joe Mistachkin  Mistachkin Systems
   * Ronald Fox      CAEN Technologies
                     NSCL @ Michigan State University

Contact Information     tcl...@go...

Tcl'2019 would like to thank those who are sponsoring the conference:

   * FlightAware
   * Mentor - A Siemens Business
   * Noumena Corp

Dear All,

I have been making a morph in pymol and saved the different states using
the mpng command in the active window. However, I cannot figure out how to
get ray-traced images to make a high quality movie in quicktime, right now
it is quite pixelated.
Is there a way to ray0trace each state of the morph?
Thanks in advance.
-- 
Pascal F. Egea, PhD
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
Boyer Hall room 356
611 Charles E Young Drive East
Los Angeles CA 90095
office (310)-983-3515
lab      (310)-983-3516
email     pegea at mednet.ucla.edu

Hello all,

Yesterday, when I installed Chimera UCSF on my computer, and found to run
Pymol become extremely slowly, particularly when generating graph using ray
function. Usually it can be done in a minute, but now takes forever. So I
uninstalled Chimera, but didn't work out.
Then I uninstalled pymol again, and reinstall a new one, but it still runs
very slowly. Have you seen this situation before? Looking forward to
receiving any feedback and comments.

Thanks,

Bio

Hi, I would like to store in a variable the primitives number gained
from cmd.ray(renderer=2). I am trying to redirect output using StringIO
module but seems not to work. Is there an other way to do this?

Hi Shahzad - 

In your session file, these residues are part of a protein structure, so "bringing them closer together" (e.g. with the `translate` command) would distort the geometry of the protein and I would advise against it. I would recommend simply adjusting the camera position to zoom on the selected residues.

```
# create a selection for your residues of interest and zoom on them
select my_residues, resi 132+137+215+254+256+265+375
zoom my_residues

# or set the camera explicitly with the mouse (then copy using the "Get View" button and paste at command prompt)
set_view (\
     0.565557718,   -0.809213281,   -0.159118786,\
     0.178787529,   -0.068047501,    0.981527865,\
    -0.805093408,   -0.583563268,    0.106191292,\
     0.000148047,   -0.000042731,  -66.173744202,\
     0.539898396,   36.191528320,   51.672920227,\
    49.509685516,   82.788223267,  -20.000000000 )
```

If you don't want empty space between them, you could add a cartoon/ribbon/other representation, and make it some neutral color and/or semitransparent to make it unobtrusive, while providing some context for the highlighted residues.

```
show ribbon
set ribbon_color, grey90
set ribbon_as_cylinders, 1
set ribbon_transparency, 0.5
```

Hope that helps.

Cheers,
Jared

On April 12, 2019 at 8:59:33 AM, Dr Shahzad A. Pandith (drs...@uo...) wrote:

Dear all,
I am a PyMol user from past two years now. I need to know 'how can we bring two amino acid residues closer in the PyMol window' to avoid huge spacing in between.
Attached is a PyMol session file for reference.

Thanks and regards.
Shahzad

--
With best wishes
Shahzad A. Pandith, PhD
INSPIRE Faculty
Department of Botany
University of Kashmir
Voice: +91 959 660 6625, +91 941 935 4745
Email: pan...@ya...

http://bit.ly/1OzSxln |  http://bit.ly/1VIePTn  |  http://bit.ly/1IQCShp

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This is a reminder that the upcoming registration deadline (Apr 15th, 2019), please submit your application before the deadline if you are interested in attending this year's school.

Thanks.

Charles, Garib and Qingping


On 1/3/19 8:09 AM, Qingping Xu wrote:

Dear Colleagues,

We are pleased to announce the 12th annual CCP4 crystallographic school “From data collection to structure refinement and beyond” will be held on June 17-24, 2019 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2019/index.php.

Dates: June 17 through 24, 2019

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA

The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website.

Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.

Application: Application deadline is April 15th, 2019. To apply, visit https://www.ccp4.ac.uk/schools/APS-2019/application.php.

Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals).

We hope to see you at the school.

Charles, Garib and Qingping

Dear all,
I am a PyMol user from past two years now. I need to know 'how can we bring
two amino acid residues closer in the PyMol window' to avoid huge spacing
in between.
Attached is a PyMol session file for reference.

Thanks and regards.
Shahzad

-- 
*With best wishes*
*Shahzad A. Pandith, PhD*
*INSPIRE Faculty*
*Department of Botany*
*University of Kashmir*
*Voice: +91 959 660 6625, +91 941 935 4745*
*Email: **pan...@ya... <pan...@ya...>*

http://bit.ly/1OzSxln |  http://bit.ly/1VIePTn  |  http://bit.ly/1IQCShp

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04/10/19,
5:25:20 PM

Thank you Jared for the detailed explanation!

Neena

On Tue, 9 Apr 2019 at 12:35, Jared Sampson <jar...@co...>
wrote:

> Hi Neena -
>
> PyMOL shows all the potential H-bonds, but not all of them will be formed
> at all times. Any single proton can only participate in one H-bond at a
> time, but remember a crystal structure is an average structure based on the
> ensemble of states present in the protein crystal (or on the EM grid for
> cryo-EM structures).  It's ok to have "too many" polar contacts...it just
> means the atoms have options for where to interact.
>
> Also, a carbonyl oxygen has 2 lone pairs, so can accept 2 H-bonds.  See
> perhaps McDonald & Thornton, JMB (1994)
> https://doi.org/10.1006/jmbi.1994.1334 for a more detailed discussion.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On April 4, 2019 at 11:25:17 PM, Neena Susan Eappen (
> nee...@gm...) wrote:
>
> Hello PyMOL users,
>
> Hydrogen bond finder on Pymol sometimes gave me unexpected observations
> like:
> more than 3 H bonds to Lysine, more than 1 to a carbonyl oxygen and so on.
> This is even after setting H-bond center cutoff to 3.0 A. Any insight would
> be appreciated.
>
> Thank you for sharing your knowledge,
> Neena
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Hi Neena - 

PyMOL shows all the potential H-bonds, but not all of them will be formed at all times. Any single proton can only participate in one H-bond at a time, but remember a crystal structure is an average structure based on the ensemble of states present in the protein crystal (or on the EM grid for cryo-EM structures).  It's ok to have "too many" polar contacts...it just means the atoms have options for where to interact.

Also, a carbonyl oxygen has 2 lone pairs, so can accept 2 H-bonds.  See perhaps McDonald & Thornton, JMB (1994) https://doi.org/10.1006/jmbi.1994.1334 for a more detailed discussion.

Hope that helps.

Cheers,
Jared 


On April 4, 2019 at 11:25:17 PM, Neena Susan Eappen (nee...@gm...) wrote:

Hello PyMOL users,

Hydrogen bond finder on Pymol sometimes gave me unexpected observations like:
more than 3 H bonds to Lysine, more than 1 to a carbonyl oxygen and so on. This is even after setting H-bond center cutoff to 3.0 A. Any insight would be appreciated.

Thank you for sharing your knowledge,
Neena
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Hi Julia,

As a student, you can register for a free educational license:

https://pymol.org/edu/

Cheers,
  Thomas


> On Apr 4, 2019, at 8:54 PM, Julia Garcia <jmi...@uc...> wrote:
> 
> Hello, 
> 
> I am currently a student and I am using pymol in one of my classes. I was able to download the software, but I am confused on whether I need to activate it or skip the activation (image attached below). I was told that this software was free to use as a student, but in order to activate it I have to pay for a subscription. If you could help clarify how to properly set up pymol on my computer that would be greatly appreciated.
> 
> Thank you,
> 
> Julia Garcia

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello PyMOL users,

Hydrogen bond finder on Pymol sometimes gave me unexpected observations
like:
more than 3 H bonds to Lysine, more than 1 to a carbonyl oxygen and so on.
This is even after setting H-bond center cutoff to 3.0 A. Any insight would
be appreciated.

Thank you for sharing your knowledge,
Neena

Hello,

I am currently a student and I am using pymol in one of my classes. I was
able to download the software, but I am confused on whether I need to
activate it or skip the activation (image attached below). I was told that
this software was free to use as a student, but in order to activate it I
have to pay for a subscription. If you could help clarify how to properly
set up pymol on my computer that would be greatly appreciated.

Thank you,

Julia Garcia

Dear PyMOL community,

 

We are in the process of redesigning the ligand pages of PDBe and we would be grateful if you could fill out a short survey to help us understand what information about small molecules / ligands you would find useful. The survey is available at https://bit.ly/2FFmHFG

 

Recently, we have introduced protein-specific aggregated views on the structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in Europe Knowledge Base (PDBe-KB). We highlight the available information related to structures of specific proteins, including structural and functional annotations, domains, ligand-binding sites and interfaces. In the next step we would like to present a similar aggregated view from a small molecule / ligand perspective. 

 

Thank you for your time,

Lukas

 

 

--

Lukas Pravda, Ph.D.

Bioinformatician/Scientific Programmer

 

Protein Data Bank in Europe (PDBe)

European Bioinformatics Institute (EMBL-EBI)

Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD

United Kingdom