[PyMOL] New PyMOL plugin for analysis of biomolecular channels

[Lukáš Pravda]

Dear PyMOL user,

 

we would like to inform you that there's a new PyMOL plugin available. The
plugin incorporates a functionality of the new tool MOLE 2.0 for detection
and analysis of channels, pores and cavities in biomacromolecules. Further
information with appropriate links to the publication and other details of
this tool can be found at the pymolwiki here
 .

 

Best Regards 

 

MOLE 2.0 authors

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[PyMOL] ALPHA cgo causes COLOR to be ignored

[Lukáš Pravda]

Dear PyMOL users,

 

I'm wondering about coloring CGO objects in PyMOL. In the recent version
1.7. If ALPHA is specified for a cgo object, all the colors are neglected.
In version 1.6 and previous everything works just fine. Is this a bug, an
intension or am I missing a point somewhere? Let's take a following piece of
code. It provides correct colorful triangle, only in the case 'ALPHA' line
is omitted for version of PyMOL 1.7+ (I'm running Windows).

 

data = [

  BEGIN,TRIANGLES,

  ALPHA,1.0,

  COLOR,1.00,0.30,0.30,

  NORMAL,-0.997,-0.057,-0.051,

  VERTEX,52.083,62.446,50.739,

  COLOR,0.6,0.60,0.10,

  NORMAL,-0.999,-0.009,-0.044,

  VERTEX,52.048,63.219,50.739,

  COLOR,1.000,0.567,0.567,

  NORMAL,-0.998,-0.059,0.024,

  VERTEX,52.076,62.446,51.498,

  COLOR,0.600,0.2,0.2,

  END

]

cmd.load_cgo(data,'triangle')

 

Thank you for your answer

 

Lukas

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[PyMOL] ramp_new command always produce symetrical ramp

[Lukáš Pravda]

Dear PyMOL users,

 

I was wondering if it is possible to produce a ramp which is not
symmetrical.  Ie. By command 

 

ramp_new e_pot_color, e_pot_map, [-10, 0, 10], [red, white, blue]

 

I can specify the range of colors red-white-blue in the range -10 0 10. In
case my range would be [-10, 5, 10]. I would like the white color to be more
shifted towards the right value since it corresponds to 5 (or at least the
middle value could be displayed). However, in the current state of the art,
the color spectrum is symmetrical all the time and it appears that the white
color is asserted to 0, which is in this case wrong and, therefore, might be
confounding.

 

 

Thank you for an answer

 

Lukas

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Re: [PyMOL] ligand superimpose (multiple structures) and RMSD value

[Lukáš Pravda]

HI Abdul,

 

Not sure if this is the solution you would like to, but there are several tools 
which are tailored specifically for this purpose (i.e. superimposition of small 
molecules). One of them is SiteBinder 
(http://webchem.ncbr.muni.cz/Platform/App/SiteBinder), it allows you to do 
variety of superimpositions and the results can be loaded back to PyMOl. If you 
need further assistance with SiteBInder, just let me know.

 

Cheers

 

Lukas

From: Abdul Ajees [mailto:a_abdul_aj...@yahoo.com] 
Sent: Saturday, February 7, 2015 7:46 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] ligand superimpose (multiple structures) and RMSD value

 

Dear Pymol users and developers,

 

I need to superimpose more than 200 ligands (same ligand with different 
conformations) to one target ligand and obtain the RMSD value.  

 

for example

 

align 1RGS.pdb 1KMS.pdb

align 1VKS.pdb 1KMS.pdb

align 1CHC.pdb 1KMS.pdb 

...

 

..

 

I can manually do this action but it take long time.  Is there a way to do this 
action quick and automatic using pymol ? For your kind information, I have 
pymol windows and linux version. 

 

 

My idea is to group the 200 ligands into various groups based on their 
conformation.  I found some scripts at 
"http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/";. But it is not working 
for me.  

 It will be highly beneficial to me, if you could kindly suggest any idea. 

 

Thank you,

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Re: [PyMOL] ligand superimpose (multiple structures) and RMSD value

[Lukáš Pravda]

Hi Folmer,

 

Sadly we do not have a UI version without the Silverlight of SiteBInder ready 
yet. The reason is that SiteBinder is the first tool from our WebChemistry 
platform and back at the time of its development, we had expected that 
Microsoft will support it also on other platforms rather than shut it down 
completely J. I think that you can use a cross-platform implementation on linux 
– moonlight (not tested). In Mac, Silverlight is available directly from 
Microsoft and it runs just fine (tested). But, we are planning to port  the 
whole application to the JavaScript/HTML5 in the next version.

 

Anyway, I have compiled for you a binary file of SiteBinder in .NET (for 
linux/mac use you can use mono http://mono-project.com). You can reach it from 
http://is.muni.cz/de/256262/MotiveMatch.zip There are also some test data and 
expected results included. If you execute the application without any 
parameters (MotiveMatch.exe | mono MotiveMatch.exe) you will get a hint what 
the parameters are and how you can use it. 

 

And just to add to that:  For the ligands selection you can use 
our molecular language selection framework (paper in the process of writing) as 
well - webchem.ncbr.muni.cz/Platform/MotiveQuery/Index 

 

If you would have further questions, just let me know.

 

Lukas

 

From: Folmer Fredslund [mailto:folm...@gmail.com] 
Sent: Monday, February 9, 2015 4:21 PM
To: Lukáš Pravda
Subject: Re: [PyMOL] ligand superimpose (multiple structures) and RMSD value

 

Hi Lukes,

That sounds interesting.
Is there a version that does not requires Microsoft Silverlight?

Best regards,
Folmer

 

2015-02-09 11:31 GMT+01:00 Lukáš Pravda :

HI Abdul,

 

Not sure if this is the solution you would like to, but there are several tools 
which are tailored specifically for this purpose (i.e. superimposition of small 
molecules). One of them is SiteBinder 
(http://webchem.ncbr.muni.cz/Platform/App/SiteBinder), it allows you to do 
variety of superimpositions and the results can be loaded back to PyMOl. If you 
need further assistance with SiteBInder, just let me know.

 

Cheers

 

Lukas

From: Abdul Ajees [mailto:a_abdul_aj...@yahoo.com] 
Sent: Saturday, February 7, 2015 7:46 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] ligand superimpose (multiple structures) and RMSD value

 

Dear Pymol users and developers,

 

I need to superimpose more than 200 ligands (same ligand with different 
conformations) to one target ligand and obtain the RMSD value.  

 

for example

 

align 1RGS.pdb 1KMS.pdb

align 1VKS.pdb 1KMS.pdb

align 1CHC.pdb 1KMS.pdb 

...

 

..

 

I can manually do this action but it take long time.  Is there a way to do this 
action quick and automatic using pymol ? For your kind information, I have 
pymol windows and linux version. 

 

 

My idea is to group the 200 ligands into various groups based on their 
conformation.  I found some scripts at 
"http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/";. But it is not working 
for me.  

 It will be highly beneficial to me, if you could kindly suggest any idea. 

 

Thank you,


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Re: [PyMOL] Removing chloride ions from CIF files

[Lukáš Pravda]

Hi Brenton,

Have you specified that cl is element?

remove element cl

should work. At least it worked for me for a different cif structure from
PDB

Hope it helps

Lukas

-Original Message-
From: Brenton Horne [mailto:brentonho...@ymail.com] 
Sent: Tuesday, March 17, 2015 8:49 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Removing chloride ions from CIF files

Hi,

I've been loading a methylphenidate structure I created using
crystallography data and it has a chloride ion I'd like to remove, how do I
do this using PyMOL scripts? I tried

remove [Cl]

hoping it would do something similar to what it does for PDB files if Cl is
replaced by a metal ion's symbol (e.g., Zn, or Mg).

Thanks for your time,
Brenton


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Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

[Lukáš Pravda]

Hi Brenton,

 

fetch 4v7y, type=cif 

 

is the command you are looking for

 

All the best

 

Lukas Pravda

---

CEITEC - Central European Institute of Technology

Masaryk University

Brno, Czech Republic

---

 

From: Brenton Horne [mailto:brentonho...@ymail.com] 
Sent: Thursday, March 19, 2015 4:55 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

 

Hi,

I have noticed that for some PDBs wwPDB doesn't contain PDB files (e.g., 4V7Y 
 ), but rather 
they have mmCIF files instead and I was wondering if it was possible to get the 
fetch command to fetch these mmCIFs instead of PDBs. Now to be clear, I do 
understand how to load mmCIFs that I have downloaded manually from wwPDB by 
going to File->Open... but I'd like to know how to get PyMOL to fetch these 
files from wwPDB and load them. 

Thanks for your time,
Brenton

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Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

[Lukáš Pravda]

Which version of PyMOL do you have? Mine is 1.7.4 and it is working just fine. 
So in case you have and older version(< 1.3 I guess) it might not work properly.

 

Lukas

 

From: Brenton Horne [mailto:brentonho...@ymail.com] 
Sent: Friday, March 20, 2015 12:02 AM
To: Lukáš Pravda
Subject: Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

 

Thanks for ya help but I'm afraid this isn't working. See it saves the fetched 
file as .sf format which it then fails to recognize. 




PyMOL>fetch 4V7Y, type = cif
 please wait ...
PyMOL>as cartoon
 CmdLoad: ".\4v7y.sf" loaded as "4V7Y".

 

On 19/03/2015 9:31 PM, Lukáš Pravda wrote:

Hi Brenton,

 

fetch 4v7y, type=cif 

 

is the command you are looking for

 

All the best

 

Lukas Pravda

---

CEITEC - Central European Institute of Technology

Masaryk University

Brno, Czech Republic

---

 

From: Brenton Horne [mailto:brentonho...@ymail.com] 
Sent: Thursday, March 19, 2015 4:55 AM
To: pymol-users@lists.sourceforge.net 
<mailto:pymol-users@lists.sourceforge.net> 
Subject: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

 

Hi,

I have noticed that for some PDBs wwPDB doesn't contain PDB files (e.g., 4V7Y 
<http://www.rcsb.org/pdb/explore/explore.do?structureId=4V7Y> ), but rather 
they have mmCIF files instead and I was wondering if it was possible to get the 
fetch command to fetch these mmCIFs instead of PDBs. Now to be clear, I do 
understand how to load mmCIFs that I have downloaded manually from wwPDB by 
going to File->Open... but I'd like to know how to get PyMOL to fetch these 
files from wwPDB and load them. 

Thanks for your time,
Brenton

 

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Re: [PyMOL] show the long helix filament

[Lukáš Pravda]

Hi Yeping,

 

What is the PDB id you are working with? Perhaps you have to download the 
biological assembly rather than asymmetric unit. I’d suggest you to go to the 
PDBe entry (pdbe.org/PDBID) and from the quick links select download ‘Assembly 
composition XML’. Take a look which assembly id has ‘preferred’ attribute se to 
‘True’ and download corresponding assembly. 

 

Hope it helps

 

Lukas Pravda

Central European Institute of Technology (CEITEC)

 

From: sunyeping [mailto:sunyep...@aliyun.com] 
Sent: Wednesday, January 13, 2016 9:31 AM
To: pymol-users 
Subject: [PyMOL] show the long helix filament

 

 

Dear all,

 

I am studying a published protein molecule which was claimed to be helical 
symmetric. The pdb file contain 3 copies of this molecule arranged in 
head-to-tail patern. The author claims that this interation is repeated in a 
directional manner along the P31 screw axis. Does anyone know how to show the 
whole long helix filament rather that just three protomer of this molecule? Can 
pymol do this?

 

Best regards.

Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

 

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[PyMOL] Grammar for PyMOL selection algebra

[Lukáš Pravda]

Dear PyMOL users, 

 

I am trying to add support for pymol-like selection algebra into one of your
software tools. Therefore, I was wondering, if there is any formal
description of the language available in for example as context-free
grammar. I was trying to find something in the source code rather
unsuccessfully.

 

All the best

 

Lukas Pravda

 

CEITEC | Central European Institute of Technology

http://webchem.ncbr.muni.cz/

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