[PyMOL] Vacuum Electrostatics error

[Joel Tyndall]

Hi all,

I tried to help Anna with her issue around the colour bar  (which seemed 
unusual) only to find that I cannot generate the electrostatic maps at all on 2 
different PCs running windows (10 I believe).

The error is Pop-error: invalid source selection name ‘assign_tmp1’

Running 2.5.1

Joel


Joel Tyndall | BSc(Hons) PhD

Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Website | pharmacy.otago.ac.nz


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[PyMOL] add hydrogens to .mol2 files

[Joel Tyndall]

Hi all,

I have just noticed that when you add hydrogens to a protein file that is a 
.mol2, hydrogens are added to carboxylates to make them the acid (unionised). 
This does not occur for a pdb file (they are ionised).

Can this be fixed in a future version? I would have thought that the atom 
typing would be such that it recognises the appropriate ionised state (along 
with the residue)

Joel

Joel Tyndall | BSc(Hons) PhD

Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Website | pharmacy.otago.ac.nz


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Re: [PyMOL] save format for molecule files

[Joel Tyndall]

Have you tried .mol2 files. I would expect Maestro to recognise that and it 
should include bond order etc

J


Joel Tyndall, PhD
Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
From: Xavier Fradera 
Sent: Wednesday, May 17, 2023 11:54 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] save format for molecule files

Hi,

I'm trying to save some molecule files (protein+ligand complex) from pymol to a 
format that is readable by maestro. I've tried saving in .mae or .pdb format, 
but bond orders in ligands are lost (all bonds are single). I've played with 
the "PDB options" in the save command and managed to get double bonds right, 
but the aromatic ones are ignored.

Does anyone know how to write files that can be read properly by maestro?

Alternatively, is there a way to convert aromatic bonds into alternating 
single/double bonds, as I think this would be easier to output based on my 
tests?

thanks,
Xavier

--
Xavier Fradera
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Re: [PyMOL] Solid stick between two residues?

[Joel Tyndall]

I agree with Tim, PyMOL simply adds bonds based on the geometry of the 
structure. The salt bridge is very close. The "problem" (if any) lies with the 
crystal structure coordinates

-Original Message-
From: Timofey Tyugashev  
Sent: Tuesday, 6 September 2022 3:17 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Solid stick between two residues?


> Dear pymol users,
> does anybody recognize this type of bond and can explain me what this is? It 
> appears between a Lysine and an Aspartic acid. I expect a hydrogen bond, but 
> for some reason PyMol connects the two amino acids with a stick?
>
> Kind regards,
> Matthias
>
PyMOL generally draws covalent bonds based on geometric distances between 
atoms. Probably in this case the salt bridge between two residues was tight 
enough for the software to mislabel it.


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Re: [PyMOL] Analysis of docking results in multi-model format

[Joel Tyndall]

Hi Enrico,

Which docking protocol are you using as this may already have RMSD to a 
reference ligand and presentation of best poses (based on scoring)

Joel

-Original Message-
From: Enrico Martinez  
Sent: Friday, 25 March 2022 2:11 AM
To: pymol-users 
Subject: [PyMOL] Analysis of docking results in multi-model format

Dear Pymol Users!
I am dealing with the analysis of the results of protein-ligand docking poses 
representing the multi-model pdb.  I need to find a possibility (e.g. via some 
script that could be executed in the pymol) to compare each docking pose with 
the X-ray structure (loaded as the separate model in pymol) in order to find 
automatically the model (= docking solution) which may fit better to it (e.g. 
via estimating RMSD of some part of the ligand in each docking solution 
compared to the X-ray structure).

Assuming that the both pdbs ((docking poses, and X-ray structure)) have been 
superimposed (based on the protein atoms) how could I automatically switch to 
the model (in the ensemble) with the identical position of the ligand as in the 
X-ray structure?  I would be grateful for any suggestions With kind regards, 
Enrico


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Re: [PyMOL] fusing structures

[Joel Tyndall]

Have you tried superimposing the loop (or the main chain of the terminal 
fragments? You could then export the moved loop and edit the pdb

J

From: zeinab masoomi 
Sent: Monday, 22 November 2021 9:52 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] fusing structures

Hi
I want to fuse a modeled loop into a protein structure, is this possible? how 
can I merge two structures into one file to put them close enough and fuse them?
structures are attached below
thank you.
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Re: [PyMOL] Export aligned sequence

[Joel Tyndall]

Please ignore my previous message!

File > Export alignment!

From: Joel Tyndall 
Sent: Tuesday, 19 October 2021 4:24 pm
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Export aligned sequence

Hi folks,

I have two proteins aligned in PyMOL. Is there a way to export the resulting 
sequence alignment?

I have had a very brief look at structural alignment servers but PyMOL seems to 
give me what I want structurallyand sequence wise

J

Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | 
pharmacy.otago.ac.nz<https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpharmacy.otago.ac.nz%2F&data=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7Cf232d9f54d694d443e6f08d992b2d687%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637702120007832511%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=HW9FGLBC%2B0Ah5QHNNwGCylLKHgW3VTNQjo6w5pAOMxw%3D&reserved=0>


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[PyMOL] Export aligned sequence

[Joel Tyndall]

Hi folks,

I have two proteins aligned in PyMOL. Is there a way to export the resulting 
sequence alignment?

I have had a very brief look at structural alignment servers but PyMOL seems to 
give me what I want structurallyand sequence wise

J

Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | pharmacy.otago.ac.nz


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Re: [PyMOL] Recognition and Display of Secondary Structure Cartoon

[Joel Tyndall]

Hi Jessica,

Generally secondary structure is extracted from a pdb file and PyMol would read 
this.

e.g.
HELIX1   1 GLY A   86  THR A   91  1   6
HELIX2   2 GLY B   86  THR B   91  1   6
SHEET1   A 4 GLN A   2  THR A   4  0
SHEET2   A 4 THR B  96  ASN B  98 -1  O  LEU B  97   N  ILE A   3
SHEET3   A 4 THR A  96  ASN A  98 -1  N  THR A  96   O  ASN B  98
SHEET4   A 4 GLN B   2  ILE B   3 -1  N  ILE B   3   O  LEU A  97


Sometimes the pdb file is incomplete or does not display all secondary 
structure. Using the command dss in Pymol can usually help define/display 
correct ss.

https://www.pymolwiki.org/index.php/Dss

Hope this helps
J

From: #JESSICA LIM JIAYING# 
Sent: Saturday, 28 August 2021 6:54 pm
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Recognition and Display of Secondary Structure Cartoon

Hi all,

I am wondering how PyMOL recognises and display secondary structure (like alpha 
helix) when selecting the 'Cartoon' function. I have attached an image of my 
molecule where only certain regions are displayed in the cartoon representation 
whereas there is helical propensity throughout my molecule as seen in the 
image. Hence, how does PyMOL decide on the secondary structure features?

Thank you so much!
Any suggestions/advice on where to look will be greatly appreciated!

Jessica Lim
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Re: [PyMOL] Farewell

[Joel Tyndall]

I can only but agree with al of these comments! Thanks for the support and god 
luck with the future Thomas. 

PyMOL has been my go to software for probably close to 20 years !

Regards

Joel

-Original Message-
From: Jason Key  
Sent: Saturday, 1 May 2021 3:15 AM
To: Thomas Holder 
Cc: Pymol User list 
Subject: Re: [PyMOL] Farewell

Hi Everyone,

I'd like to publicly thank Thomas for his contribution to PyMOL over the last 
decade.

PyMOL is the primary tool the broader scientific community uses to access the 
results we create as structural biologists.
For many researchers, PyMOL is their first window into macromolecular 
structures. And, at the very least, journal covers are MUCH nicer because of it.
It is, without doubt, the most popular title in the SBGrid installation. It 
always has been.

I assure everyone here that creating reliable software that runs on 3 operating 
systems with an open source model and great user support is no easy task.
Sustaining that effort for nearly 10 years is another feat altogether.

If you'd like to see how far PyMOL has come, here's a webinar we did
(live!) in 2013 here :
https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DUHOUFJmj_fM&data=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9b08137f4082497b23a108d90bfc06b3%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637553999355683603%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=4ClB06YR4cNyUz3yLYkq7rA5vAO9BjTP9w%2FMbRZC4KE%3D&reserved=0

Best of luck in your next chapter Thomas!

Cheers,
Jason

--
Jason Key, PhD
Project Lead
SBGrid Consortium, Harvard Medical School


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Re: [PyMOL] Using pyvol in pymall

[Joel Tyndall]

Hi,

I got interested so had a quick look. There is a user manual in the 
doc/directory on github

https://github.com/schlessinger-lab/pyvol

Should give you details of how to use it

Hope this helps

J

From: ALBAYATI SAMAH HASHIM KHALEEL / UPM 
Sent: Wednesday, 18 November 2020 5:40 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Using pyvol in pymall

Hi any one have an idea how to use pyvol plugin pymall to measure the binding 
site volume and how to display different binding site shape.Thanks
Samah Hashim
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Re: [PyMOL] View two proteins from one pdb file

[Joel Tyndall]

Hi Neena,

Use the command “split_states clusters”, just type it into the command line

J

From: Neena Susan Eappen 
Sent: Monday, 8 June 2020 10:01 am
To: pymol-users 
Subject: [PyMOL] View two proteins from one pdb file

Hello PyMOL users,

I have a PDB file with coordinates for two proteins listed one after another 
(attached). However, when i open the file on pymol, I only see one protein 
(shown below) or it might be a sum of those 2 coordinates. How to view both 
structures?

[image.png]

Many thanks, and Take care,
Neena
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Re: [PyMOL] Structure allignmnet in Pymol

[Joel Tyndall]

Hi Maryam,

You can easily align two proteins in Pymol to compare their structures. Read 
both protein structures into the same window under the action option, choose 
align and select which one you want. E.g align to molecule (via alpha carbons)
Hope this is what you wanted
J

[cid:image001.png@01D630FC.D30D62D0]

From: mtaraz...@chem.ucsb.edu 
Sent: Saturday, 23 May 2020 11:18 am
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Structure allignmnet in Pymol

Dear All,
I am a new user in PyMoL and I have a question regarding the structure 
alignment in PyMOL.
I have a protein that its crystal structure is not known. So I used "Modeller" 
software to predict the structure of its closet hit. ( I can easily visualize 
the structure of the closet hit in PyMOL)
Now I want to visualize the structure of initial protein (the one that its  
crystal structure was not known) based on the structure of its closest hit.
I tried that with "Chimera" software using structure alignment. I would like to 
know if PyMoL is able to do that?
Any suggestion would greatly be appreciated.
Best regards
Maryam

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Re: [PyMOL] Comparing same ligands from different proteins

[Joel Tyndall]

Hi,
You can use the pair-ftt function to better overlay the ligands.

You can also display the torsion angles:

In 3-button editing mode, hold control down (PC) and right click on the bond in 
question.

Not sure how to do this command line

Hope this helps
J

From: puneet garg 
Sent: Friday, 12 October 2018 10:34 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Comparing same ligands from different proteins

Hi,
I have two proteins with same oligosacharide (triose) bound to them. I want to 
compare the superposition of the bound ligands. When I superpose the proteins, 
the ligands superpose partially. Is there any way I can calculate all the 
torsion angle different of oligosacchrides.
Thanks


--
Puneet
Structural Biology Lab
Biotechnology Dept.
IIT Madras
Chennai-600036

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Re: [PyMOL] Hbond to backbone cartoon

[Joel Tyndall]

Hi Markus,

Is there still a gap (between atoms and cartoon) when you turn on the backbone 
residues in question?

J

From: Markus Heller 
Sent: Thursday, 6 September 2018 6:26 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Hbond to backbone cartoon

Hi all,

what's the best way to show a hydrogen bond to a backbone atom in the following 
scenario:

Protein shown as cartoon, ligand as sticks, binding site residues (within 5A of 
ligand) shown as lines, and sidechain help is on.

If the ligand forms a hydrogen bond with a backbone atom, the dashes don't 
touch the cartoon, but leave a gap.  What's the recommended solution (or 
workaround) to avoid this gap?

Thanks
Markus
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Re: [PyMOL] Display metal coordination

[Joel Tyndall]

Hi Markus,

I am not aware of this function in pymol but would be interested in one being 
developed.

J

-Original Message-
From: Markus Heller  
Sent: Friday, 24 August 2018 6:28 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Display metal coordination

Hi all,

Is there a way to display the coordination of a metal, e.g. Zn2+ or Mg2+, that 
doesn't require manual selection of atoms and showing of bonds?

I wasn't able to find anything online ...

Thanks
Markus

-- 
Markus Heller, Ph.D.
Senior Scientist, Medicinal Chemistry
Direct: 604.827.1122   Main: 604.827.1147








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Re: [PyMOL] Columb coloring

[Joel Tyndall]

It can easily be done in PyMOL

Select your molecule, then in the right side select A(Action)->Generate->Vacuum 
Electrostatic

Or there are plenty of tutorials on the web for APBS

Hope this helps

J


From: Clarisa Alvarez 
Sent: Thursday, 28 June 2018 3:05 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Columb coloring

Dir Sir/Madam,
I need coloring my protein surface by electrostatic characteristics.
Do I need to install APBS? because i could not do it. If you could help me it 
will be greatful.
Thanks in advance,
Yours,
Clarisa.

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[PyMOL] Protonation of small molecule amines

[Joel Tyndall]

Hi folks,

Is pymol able to protonate an amine e.g. morphine i.e. when you add hydrogens 
to a small molecule, ensure that the amine is charged (at it would be at 
physiological  pH?

I have not been able to do it using the GUI.

Cheers

Joel

Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
School of Pharmacy | Te Kura Mātauraka Wai-whakaora
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | pharmacy.otago.ac.nz


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Re: [PyMOL] Removing unwanted molecules

[Joel Tyndall]

Hi,

Select the one you want e.g. right click, chain select. Under the selection, 
Action > modify > invert > within object..

Or you can select using the sequence viewer

Hope this helps

Joel

From: Mohammad Goodarzi [mailto:mohammad.goda...@gmail.com]
Sent: Friday, 23 June 2017 8:20 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Removing unwanted molecules

Hello,
I want to know how to delete chain B and all ligands except the one that I
want ?
Is there any way to know all molecules which comes with a PDB and then
remove those that you dont want?
Thanks
Mohammad
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Re: [PyMOL] auto_show_cartoon or similar

[Joel Tyndall]

That would be great, my standard is open file, cartoon, ligand sticks

Great idea

-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] 
Sent: Tuesday, 9 February 2016 5:52 AM
To: Ivan Vulovic ; Schubert, Carsten [JRDUS] 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] auto_show_cartoon or similar

Hi Ivan and Carsten,

I can take "auto_show_cartoon" as a feature request. It's trivial to implement.

What also would be nice: automatically showing sticks for ligands. e.g. 
corresponding to the "not polymer" or the "organic" selection. Thoughts?

Cheers,
  Thomas

On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS]  
wrote:

> Hi Ivan,
>  
> you could either try to overload the "load" function in Pymol (not sure this 
> is supported) or write your own custom load function under a different name, 
> which loads the protein, assigns the name of the object, hides lines and 
> shows the cartoon.
>  
> Sorry, this is a rather generic answer but should point you in the right 
> direction.
>  
> Cheers,
>  
> Carsten
>  
> From: Ivan Vulovic [mailto:i...@uw.edu] 
> Sent: Saturday, February 06, 2016 8:18 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] auto_show_cartoon or similar
>  
> Hello 
>  
> Is there a way to make cartoon the default representation, something akin to 
> "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 
> (link below) but I haven't found anything more recent that does what I'd like.
>  
> http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html
>  
> Thanks
> Ivan

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Pymol crashes with older pse files

[Joel Tyndall]

Hi,

Having used Pymol for over a decade, I have a lot of (session) files from 
previous releases of Pymol. Unfortunately I am no longer able to open them in 
1.8.0.0 on a windows 10 machine either from File open session or simply double 
clicking. (pymol.exe has stopped working). I am not convinced it works on a 
windows 8 machine either but it they do work on windows 7 on 1.7.2.0 release. 
When upgraded to 1.8.0 on windows 7 PyMOL crashes. Is there any fix for this or 
am I stuck with the problem?

J


Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
New Zealand’s National School of Pharmacy | Te Kura Mātauraka Wai-whakaora
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Skype: jtyndall
Website | pharmacy.otago.ac.nz


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[PyMOL] pymol fails to open (crash)`

[Joel Tyndall]

Hilist,

Got an annoying issue on my windows 7 and (8 machines). When I open pymol from 
the icon shortcut it crashes with the error "pymol.exe has stopped working... 
close program". Same issue from the start menu. I can open the program by 
double clicking on a pdb file and there are no issues.

Current version is 1.7.6.2

Any idea how to fix this? Might be my hardware but just wondering if others see 
this or there is a fix?
J



_
Joel Tyndall, PhD

Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

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[PyMOL] Unusual error after distance measurement

[Joel Tyndall]

Hi all,

I'm on a PC (windows 7) with the latest incentive 1.7.6.0 version and I have 
seen this problem several times. I have been looking at various structures both 
pdb downloads and local X-ray or homology generated files. For example looking 
at 4xk9, I measure a distance between the ligand and protein which is fine. 
However when I want to do something like say right click on a residue (to 
identify it or) show sticks and the residue number/name is definitely not the 
one being clicked on, i.e. Trp147 is now stating it is His1 (which it is 
clearly not). I have had this problem occur numerous times with different 
proteins and it is a problem as I now need to simply restart the program.

Saving the session maintains the problem. Then selecting the residue in 
sequence view seems to fix the issue but only for that residue


Any thoughts?

J

_
Joel Tyndall, PhD

Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

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[PyMOL] No wheel operation for the slab

[Joel Tyndall]

Hi all,

I seem to be losing the use of  the wheel for the slab adjustment. To be honest 
I find it difficult to replicate or work out what I do to turn it off  (or on).

Anyone else seen this before?

Windows 7, pymol 1.7.2.0 (64 bit)

J



_
Joel Tyndall, PhD

Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

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Re: [PyMOL] Farewell

[Joel Tyndall]

Wishing you all the best Jason, it has been fantastic to be involved with this 
bb with you as the key guy. Always there to answer the questions

From: Jason Vertrees [mailto:jason.vertr...@gmail.com]
Sent: Thursday, 24 April 2014 9:00 p.m.
To: pymol-users; ccp...@jiscmail.ac.uk
Subject: [PyMOL] Farewell

Greetings PyMOLers and CCP4ers worldwide,

It has been my great pleasure to serve the PyMOL community both in a volunteer 
and professional capacity for the past decade. I have recently been given an 
offer I can't refuse—to follow one 
of my dreams—helping lead technology and science at a new 
startup. March 30th marked my last day at 
Schrödinger and supporting PyMOL.

Because of my great fondness for PyMOL and its community, I will continue to 
operate the PyMOLWiki until I find it a suitable home. I started the PyMOLWiki 
in 2005 and since then it's been visited over 15,289,590 times! (If you would 
like to sponsor or host the wiki feel free to email me.) Now I can't imagine 
the PyMOL community without it.

Last, I am truly humbled to have followed in the footsteps of Warren DeLano. He 
was an amazing man whose ideas and actions have touched the lives of millions, 
whether they know it or not. He is missed.

It's been great fun. I wish you all the best.

Cheers,

-- Jason

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Re: [PyMOL] manual superposition with pymol--and another question

[Joel Tyndall]

Haddock?

-Original Message-
From: Lapolla, Suzanne M (HSC) [mailto:suzanne-lapo...@ouhsc.edu] 
Sent: Tuesday, 8 April 2014 7:12 a.m.
To: pymol-users@lists.sourceforge.net
Cc: thomas.hol...@schrodinger.com
Subject: Re: [PyMOL] manual superposition with pymol--and another question

This worked--thanks. I have another ? that may have been addressed previously 
but do not know the answer.  Is there a way to do an alignment (or maybe 
docking is a better word) on two structures/selections and input a constraint 
for that alignment? For example, i am working on generating a model RE a dimer 
of two molecules, and I have some data suggesting a range of distances between 
certain residues of the selection. Is there a way to input that data into Pymol 
before it completes the alignment, or do I need to use other docking programs 
to do that? Hope that makes sense.  Thanks.

From: Lapolla, Suzanne M (HSC)
Sent: Friday, April 04, 2014 5:11 PM
To: Thomas Holder
Subject: RE: [PyMOL] manual superposition with pymol

Thank you! I will try this and get back to you.

From: Thomas Holder [thomas.hol...@schrodinger.com]
Sent: Friday, April 04, 2014 3:16 PM
To: Lapolla, Suzanne M (HSC)
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] manual superposition with pymol

Hi Suzanne,

looks like you only deprotected the CA atoms. If you have this as a named 
selection, try "A > modify > complete > molecules" and deprotect again. Or type:

PyMOL> deprotect bymol (sele)

Instead of working with one object and protecting/deprotecting of subsets of 
atoms, I suggest to extract the selection that you want to move to its own 
object. That's usually easier to handle.

Cheers,
  Thomas

On 04 Apr 2014, at 13:38, Lapolla, Suzanne M (HSC)  
wrote:

> I am using pymol 1.3 and having trouble with doing manual 
> superposition with my structures. I am able to download my structures, 
> select the portion I want to move manually and, after deprotecting it 
> using the action menu move it using the shift-mouse editing command. 
> When I do this with my selection shown in cartoon mode, things look 
> great, but then when i switch to show my selected residues as  sticks,  
> the sticks become huge --they  get bigger  and/or  smaller as I move 
> the structure.  Ideas on what I may be doing wrong? Hope this makes 
> sense. Thanks, Suzanne

--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


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Re: [PyMOL] [WAS: polygonal ring] cyclic peptide

[Joel Tyndall]

Hi Jerome,

I am guessing you would be referring to the cartoon representation of the cycic 
peptide. This is only a workaround but I would usually display the sticks of 
the covalently linked N-and C termini (main chain atoms). I feel this provides 
the viewer a better understanding of the peptide itself as you can see where 
residue 1 is (amide linkage) rather than guessing.

Hope this helps

-Original Message-
From: Jerome BENOIT [mailto:g62993...@rezozer.net] 
Sent: Tuesday, 5 November 2013 8:47 p.m.
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] [WAS: polygonal ring] cyclic peptide

Hello Again,

let rephrase my question:
does PyMOL have support for cyclic peptide (ex. 2NS4) ?

Thanks,
Jerome

On 29/10/13 17:37, Jerome BENOIT wrote:
> Hello List,
> 
> So far I use PyMOL to visualize polygonal chain through an expurged PDB data 
> file when the chain is not ring.
> Now I would like to visualize chain rings: what is the best way to make PyMOL 
> understand that the two end points coincide ?
> 
> Thanks in advance,
> Jerome
> 
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[PyMOL] Fading memory

[Joel Tyndall]

Hi folks,

The problem is with "my" memory, not the hardware kind. I am trying to remember 
the name and the relevant webpages to access/ learn how to generate a rotatable 
image within a pdf. I think it is still of limited use and under development 
but could someone help with a link? Something like enhanced images?

Many thanks

Joel

_
Joel Tyndall, PhD

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National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
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Skype: jtyndall

Ph: +64 3 479 7293

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Re: [PyMOL] Unbond two atoms

[Joel Tyndall]

You can also use the builder module. 

Click on the two atoms and then delete bond button

-Original Message-
From: Martin Hediger [mailto:ma@bluewin.ch] 
Sent: Wednesday, 31 July 2013 12:40 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Unbond two atoms

Dear PyMOL users

Sometimes PyMOL draws bonds between atoms which are not supposed to be 
connected. I know it is possible to unbond them using "unbond atom1, atom2", 
however this requires to always select the atoms and rename the selections to 
"atom1" and "atom2", respectively. It would be great if I could just click two 
atoms (using the "Atoms" selection quantifier) and then have them unbonded. How 
could I do that?

Thanks a lot for any hints.
Martin

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[PyMOL] FW: Possible hydrogen addition bug

[Joel Tyndall]

Subject: RE: [PyMOL] Possible hydrogen addition bug

Hi all,

I believe this would be as a result of the "pdb" file not containing the 
hybridisation information. When you manually change that bond to be double 
(using the builder module) and then add hydrogens it is correct. This is not an 
uncommon issue with small molecules from the pdb.

Bob, as an aside, which viewers do read cif files as coordinates? I know 
Mercury does.

Cheers

Joel

-Original Message-
From: Matthew Baumgartner [mailto:mp...@pitt.edu] 
Sent: Friday, 7 June 2013 8:51 a.m.
To: pymol-users
Subject: [PyMOL] Possible hydrogen addition bug

Hi,
I may have found a bug in the way pymol interprets connectivity of atoms. I 
noticed this in one pdb structure that I am working with 1RV1.

Steps to reproduce:
fetch 1RV1

#extract one of the ligands to it's own object extract 'lig', /1RV1//A/110

#add hydrogens
h_add lig

Now look at atom C2 on the ligand and notice that pymol added a hydrogen almost 
along an existing bond to another ring.

I am running pymol 1.5.0.1 on Ubuntu 13.04.

I'm not sure if this has been reported before and has been fixed already in 
1.6. I haven't gotten around to upgrading yet, but I am willing to.

Thanks,
Matt

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Re: [PyMOL] surfaces involving more than one object

[Joel Tyndall]

Hi Bob,

This is probably not the slickest way to do this but  generally I think it is 
one surface one object, so in a simple case of a peptide bound to a protein, I 
would select the peptide chain (right click in the viewer) and extract that 
selection to a new object and then you can generate two separate surfaces.

Hope this helps
Joel

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: Friday, 31 May 2013 6:26 a.m.
To: pymol-users
Subject: [PyMOL] surfaces involving more than one object

PyMOL questions about surfaces:

Simple enough to create a surface for one object. What about for only a portion 
of the object? How to do each of these?
  -- closed surface ignoring a selected set of atoms
  -- open surface not ignoring any atoms, but also not displaying their part

Is the rule, "One surface, one object"? That is, all atoms involved in a 
surface must originate from a single object?

Bob

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Re: [PyMOL] repair the missing loop in crystal structure

[Joel Tyndall]

Try modeller

http://salilab.org/modeller/about_modeller.html


From: yp sun [mailto:sunyep...@yahoo.com.cn]
Sent: Tuesday, 7 May 2013 1:58 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] repair the missing loop in crystal structure

Dear pymol users,


Are there anyone know how to modeling the missing fragment in a crystal 
structure? This missing fragment may be a flexible loop and so its disordered 
the electron density is invisible.Thanks.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
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[PyMOL] export sequence alignment

[Joel Tyndall]

Hi folks,

Sorry if this has already been asked but can I export the sequence alignment 
from PyMOL? I am looking to use cealign to do this (on windows) and I need the 
structural alignment based sequence alignment.

Other tools maybe? I have mustang already

Cheers
Joel

_
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National School of Pharmacy
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Ph: +64 3 479 7293

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[PyMOL] export sequence alignment

[Joel Tyndall]

Sorry forgot to add, I want to use multiple structures

Hi folks,

Sorry if this has already been asked but can I export the sequence alignment 
from PyMOL? I am looking to use cealign to do this (on windows) and I need the 
structural alignment based sequence alignment.

Other tools maybe? I have mustang already

Cheers
Joel

_
Joel Tyndall, PhD

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National School of Pharmacy
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New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

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Re: [PyMOL] How to display .mtz files and work with them

[Joel Tyndall]

Hi Matthias, I can at least try and answer some of your questions:


1.   You can simply click on the command button (rhs side grey window... 
"Command" "Builder" "Volume") to get back to the command info you want. 
Alternatively type in your commands into the viewer window and use escape to 
see the details

2.   At this stage I'm not sure you can generate the volume around your 
protein. The way to get around this is to generate symmetry related molecules 
and look at one of those in the unit cell. (Jason will know more)

3.   Best to generate 2fofc and fofc maps in say ccp4 and display these 
(but not sure if you can use the volume or just the classical mesh)

I too would like to be able to do this to use the great graphics output from  
pymol

Hope this helps

Joel

From: Matthias Haffke [mailto:matze_haf...@hotmail.com]
Sent: Wednesday, 27 February 2013 9:17 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] How to display .mtz files and work with them

Dear all,

I am having some trouble working with PyMOL and the new feature of loading and 
displaying .mtz files.
Sorry for the number of questions (and sorry if most seem trivial...), but I 
couldn't find the answers in the PyMOLWiki and not in the Schrodinger 
documentations.

PyMOL Version is 1.5.0.5 and it's running on Win7 Prof 64 bit.

1.) When loading a .mtz file, you start with the new volume representation. 
Options for color gradients, sigma levels, etc. are displayed in a nice graph 
in the command line window - but the command line is gone and I don't get any 
feedback about commands I write in PyMOL. How do I turn this graphical 
representation of the sigma levels & color gradients on and off?
2.) The volume is represented for one unit cell - and for one unit cell only. I 
would like to display the density just around one molecule in the unit cell or 
around a symmetry mate OUTSIDE the unit cell - which is the command to do so? 
Things like "map_trim" don't work (which is not a surprise - I am obviously not 
displaying a map as one used to do in the older PyMOL versions). You can't 
align the "group", which is created by loading a .mtz file to a selection or 
molecule by using the drop down menus or I couldn't find any other way to limit 
the map to one molecule or one chain in of my .pdb file. Any help on this is 
greatly appreciated.

3.) What I basically want to do (in other words): Open a .pdb file. Open a .mtz 
file. Display the electron density at 2.0 sigma around one specific chain or 
around one specific symmetry mate of my molecule. Can't be that difficult, can 
it? ;-)

Many thanks for any help!

Matthias

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Re: [PyMOL] representing ferrocene in pymol

[Joel Tyndall]

That's pretty slick.

Alternatively you can delete the "drawn bonds" using the builder module. Then 
show nb_sphere for the Fe atom. If you have access to the CSD I would grab one 
from there

Hope this helps

From: Troels Emtekær Linnet [mailto:tlin...@gmail.com]
Sent: Tuesday, 12 February 2013 3:17 a.m.
To: Edward Deira
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] representing ferrocene in pymol

How about.

import select_sites
sites 1a3l
set_bond stick_radius, 0.1, resi 213
extract Fe_atom, resi 213 and name Fe

Wiki
http://www.pymolwiki.org/index.php/Select_sites
http://www.pymolwiki.org/index.php/Set_bond


Best
Troels

Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234

2013/2/11 Edward Deira mailto:edward.de...@gmail.com>>
Dear all,

How can I "accurately" represent ferrocene in pymol, without using CONECT lines 
in the pdb file ?
By "accurately" I mean at least including the C-C bonds; I'd rather not have 
any Fe-C bonds, but if they are present I can live.

I've been trying to figure out how to do this using atom selections, or trying 
to get gonds between the nonbonded...

Any hints are welcome,

all the best
Ed.

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Re: [PyMOL] echo colour

[Joel Tyndall]

Thanks Thomas,

seems to work.

-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] 
Sent: Wednesday, 23 January 2013 10:47 p.m.
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] echo colour

Hi Joel,

the color is stored as a numeric atom property, you can use iterate to get it.

PyMOL> iterate (first objX), print color

If you need the name of the color, get the index to name mapping as a 
dictionary from PyMOL like this:

PyMOL> stored.cn = dict((i,c) for (c,i) in cmd.get_color_indices()) 
PyMOL> iterate (first objX), print stored.cn[color]

Last but not least, there is the psico.querying.get_color function in the PSICO 
module :)

Cheers,
  Thomas

Joel Tyndall wrote, On 01/23/13 02:04:
> Hi list,
> 
> With the myriad of colours in Pymol, I tend to forget which shade of 
> what I have used. Is there a way/command to print the colour I have 
> used to colour object X?
> 
> Cheers
> 
> Joel
> _____
> 
> Joel Tyndall, PhD
> 
> Senior Lecturer in Medicinal Chemistry National School of Pharmacy 
> University of Otago PO Box 56 Dunedin 9054 New Zealand
> 
> Skype: jtyndall
> 
> Ph: +64 3 479 7293

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[PyMOL] echo colour

[Joel Tyndall]

Hi list,

With the myriad of colours in Pymol, I tend to forget which shade of what I 
have used. Is there a way/command to print the colour I have used to colour 
object X?

Cheers

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

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[PyMOL] Possible (minor) bug

[Joel Tyndall]

Hi Jason/all,

Possible bug. When measuring distances around coordinated metals, I then wanted 
to change the colour of the resulting dashed line. The colour change would only 
appear when you turn the object off (or another). Happens with RNA and protein.

Cheers
J

_
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University of Otago
PO Box 56 Dunedin 9054
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Re: [PyMOL] Can't undo anymore

[Joel Tyndall]

Hi Again,

Thanks Jason for the update. Turns out PyMOL is not broken, but undo is simply 
turned off. See below for details.


In version v1.5 we added a better undo. However, to stop it from eating up all 
your RAM we disabled it for very large systems like proteins. Since it's PyMOL 
you can always change this via the settings. Before you load and edit a large 
molecule, please type,



set suspend_undo_atom_count, 0



This setting when set to X will allow undo on objects with fewer than X atoms. 
If set to 0 it's unlimited and thus works on all objects. So,



set suspend_undo_atom_count, 2500



will allow undo on objects with 2500 or fewer atoms.



Undo prior to v1.5 could only undo 15 levels of atom conformations across one 
protein. Now, undo can handle the following changes:

  * conformational changes

  * multiple object support

  * addition/removal of atoms

  * addition/removal of bonds

  * addition/removal of fragments

  * addition/removal of objects

  * changes in valence

  * changes in atom types

  * editing discrete objects

  * full support in the Builder

Cheers

Joel



From: Joel Tyndall [mailto:joel.tynd...@otago.ac.nz]
Sent: Tuesday, 23 October 2012 11:54 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Can't undo anymore

Hi All,

In previous versions you could move a torsion angle (Ctrl-W click) and if you 
selected the wrong end of the bond, you could undo this. Now it seems that the 
undo is deactivated. Is it possible to have this reinstated? It was very handy.

Currently on 1.5.0.4 on Windows

Cheers

Joel

_________
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Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

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[PyMOL] Can't undo anymore

[Joel Tyndall]

Hi All,

In previous versions you could move a torsion angle (Ctrl-W click) and if you 
selected the wrong end of the bond, you could undo this. Now it seems that the 
undo is deactivated. Is it possible to have this reinstated? It was very handy.

Currently on 1.5.0.4 on Windows

Cheers

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

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Re: [PyMOL] Verify PDB format

[Joel Tyndall]

Hi Martin,

I might be missing something but a little more information might help as to 
what you want to do. agreed, a file extension can be changed to anything but 
viewing the text file should tell you the type (of coordinate file). If you are 
doing this in batch mode then I guess a script would help!

Joel

-Original Message-
From: Martin Hediger [mailto:ma@bluewin.ch] 
Sent: Wednesday, 27 June 2012 10:01 p.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Verify PDB format

Dear PyMOL users
Does anybody know a script to verify that a file contains valid a valid PDB 
formatted structure?
The file extension alone obviously does not provide sufficient validation.

Thanks for any feedback.
Martin

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Re: [PyMOL] different molecules - same scale?

[Joel Tyndall]

Hi Anika,

If you open molecules in the same window then yes they will be the same scale. 
However if you open two different molecules in different windows, the view will 
not necessarily be to scale (e.g. small molecule drug compared to a protein).

Hope this helps

Joel

-Original Message-
From: anika.bra...@unil.ch [mailto:anika.bra...@unil.ch] 
Sent: Wednesday, 6 June 2012 2:17 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] different molecules - same scale?

Hello,
if I import different files in Pymol and watch the molecules for the first time 
in one window, are they automatically in the same scale? I want to make sure 
that the molecules are shown in one scale to align them.

Thanks!
Anika


Anika Braune, PhD student
Pierre Goloubinoff group
Department of Plant Molecular Biology
University of Lausanne
Unil-Sorge, Biophore Building
CH- 1015 Lausanne

anika.bra...@unil.ch

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[PyMOL] My first script?

[Joel Tyndall]

Hi folks,

So I have no scripting skills in python but I can use pymol reasonably well.

I want to superimpose (pair_fit) 4 atoms (all the same) from a library of 
conformers onto a template molecule (similar to clustering after conformational 
searching). I could probably nut out how to do the pairfitting actually I could 
do this easily by command line but I have > 100 molecules so I'm not sure how 
to script this.

Any help would be welcome

Cheers

Joel

_____
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Skype: jtyndall

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Re: [PyMOL] Editing of the pdb structure

[Joel Tyndall]

Surely you could use pymol mutagenesis wizard to do tis.

Also James, It is a good practice to  start a new thread (new email with new 
subject for each set of questions you have

Regards

Joel

From: James Starlight [mailto:jmsstarli...@gmail.com]
Sent: Friday, 27 April 2012 8:25 p.m.
To: pymol-users
Subject: Re: [PyMOL] Editing of the pdb structure

Dear all!

I want to prepare my pdb structure for MD simulation. I've done all required 
things but my protein consist of some missing heavy atoms the list of which 
I've obtained from my pdb hedader

REMARK 470   M RES CSSEQI  ATOMS

REMARK 470 ARG A 220CG   CD   NE   CZ   NH1  NH2

REMARK 470 ARG A 222CG   CD   NE   CZ   NH1  NH2

REMARK 470 ASN B 212OCG   OD1  ND2

REMARK 470 LYS C  43CG   CD   CE   NZ

REMARK 470 GLY C 225O


I've heard that there are some web servers wich could be usefull to build such 
missing atoms.
In particular in my structure there are lack not only side chain atoms but also 
two backbone Oxygens in the Gly and Asn wich could be the main problem of such 
task.


In any case I'll be very thankfull if you provide me with such server

James

26 апреля 2012 г. 12:55 пользователь James Starlight 
mailto:jmsstarli...@gmail.com>> написал:
Thanks Thomas!


Another question-
I have my protein.pdb with some inserted crystall waters within protein 
interiour as well as water surrounded of my protein. I want to remove only 
sorrounding water but prevent internal water ( wich could be functional 
relevant ).

How I could to select such surrounded water ( e.g via some cutoff radius 
relative my protein etc) wich I'd like to remove further ?
26 апреля 2012 г. 11:22 пользователь Thomas Holder 
mailto:spel...@users.sourceforge.net>> написал:

Hi James,

use the alter command:

alter chain "", chain="A"

See also http://pymolwiki.org/index.php/Alter

Cheers,
 Thomas

James Starlight wrote, On 04/26/12 09:18:

Dear PyMol users!


I have some structure.pdb from the md simulation wich consist of 1 chain not 
defined in the pdb file explicitly ( missing chain id in the pdb file). So the 
pymol recognise that chain as the  ' '  . I need to rename this chain to the 
desired name ( e.g to chain A ).

How I could do it?

James

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Re: [PyMOL] How to overlay different structures?

[Joel Tyndall]

Hi Martin,

I do this quite often in Pymol using the pair fit menu pull down.

Wizard > Pair_fitting

You can just click on the three atom pairs you need then "fit 3 pairs". You can 
highlight the residues in question as stick to make it easier.

I'm sure you can use command line too

Pair_fit 1xyz//a/tyr61/cb, 1abc//a/tyr61/cb, 1xyz//a/tyr61/ca, 
1abc//a/tyr61/ca, 1xyz//a/tyr61/c, 1abc//a/tyr61/c

Or something along those lines.

Hope this helps

Joel

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Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
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Skype: jtyndall
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Fax / Waeawhakaahua +64 3 4797034

From: Martin Breugst [mailto:mbreu...@ucla.edu]
Sent: Friday, 13 April 2012 5:34 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] How to overlay different structures?

Dear PyMOL users:

I want to use PyMOL to generate a nice figure showing six different transition 
state structures superimposed in one single picture. I have already tried to 
use the commands pair_fit, overlay, and align but I did not get the results I 
have expected. Is there any way to tell PyMOL to overlay three atoms of each 
structure (in order to define a uniform plane) and if there is, what specific 
command do I have to use?

Thank you very much for your help and suggestions,

Cheers,

Martin

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Re: [PyMOL] Protein Parameters?

[Joel Tyndall]

Hi Shane,

I think I meant weblogo which shows frequency of amino acids

e.g. http://weblogo.berkeley.edu/

Sorry for the confusion
J

_
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Senior Lecturer in Medicinal Chemistry
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University of Otago
PO Box 56 Dunedin 9054
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From: Shane Neeley [mailto:shane.nee...@gmail.com]
Sent: Wednesday, 4 April 2012 10:18 a.m.
To: Joel Tyndall
Subject: Re: [PyMOL] Protein Parameters?

Hi Thanks for the tip Joel.

I checked a few of the sequences for protein motifs but because they are so 
sort and because there really is no known function, i think it is unlikely to 
have any hits.


On Tue, Apr 3, 2012 at 2:58 PM, Joel Tyndall 
mailto:joel.tynd...@otago.ac.nz>> wrote:
Hi Shane,

Whilst I am no expert, I would think possible a sequence motif (based on amino 
acid composition) may help. It may show up certain amino acids at specific 
points. Given the short length of the peptides, the question is what are they 
used for?

Hope this helps
_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: Shane Neeley 
[mailto:shane.nee...@gmail.com<mailto:shane.nee...@gmail.com>]
Sent: Wednesday, 4 April 2012 3:58 a.m.
To: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: [PyMOL] Protein Parameters?

Hi,

This is unrelated to PyMol, but I just wanted to spam the community to see what 
they think about different protein parameters. Let me know if this sort of 
question is inappropriate for the forum.

I have thousands of randomly generated 7 amino acid peptide sequences that are 
within a virus. As we subject this virus to reproduction selective pressure in 
cell lines, we get back functional viruses with certain 7 amino acid sequences, 
while most random sequences are null mutations. So I am now testing the the 
positive sequences to see what they have in common, or what is most important.

I am doing this with a likely structural sequence and a likely surface sequence.

So far I have these params from http://web.expasy.org/protparam/ and ConSurf

1) Isoelectric Point
2) Molecular Weight (may mean bulkiness)
3) GRAVY: grand average of hydropathicity
4) Conservation of AAs at given locations

Do any of you protein experts know of other parameters that I could be testing? 
Maybe something like Phi-value analysis?



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Re: [PyMOL] Protein Parameters?

[Joel Tyndall]

Hi Shane,

Whilst I am no expert, I would think possible a sequence motif (based on amino 
acid composition) may help. It may show up certain amino acids at specific 
points. Given the short length of the peptides, the question is what are they 
used for?

Hope this helps
_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
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From: Shane Neeley [mailto:shane.nee...@gmail.com]
Sent: Wednesday, 4 April 2012 3:58 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Protein Parameters?

Hi,

This is unrelated to PyMol, but I just wanted to spam the community to see what 
they think about different protein parameters. Let me know if this sort of 
question is inappropriate for the forum.

I have thousands of randomly generated 7 amino acid peptide sequences that are 
within a virus. As we subject this virus to reproduction selective pressure in 
cell lines, we get back functional viruses with certain 7 amino acid sequences, 
while most random sequences are null mutations. So I am now testing the the 
positive sequences to see what they have in common, or what is most important.

I am doing this with a likely structural sequence and a likely surface sequence.

So far I have these params from http://web.expasy.org/protparam/ and ConSurf

1) Isoelectric Point
2) Molecular Weight (may mean bulkiness)
3) GRAVY: grand average of hydropathicity
4) Conservation of AAs at given locations

Do any of you protein experts know of other parameters that I could be testing? 
Maybe something like Phi-value analysis?


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Re: [PyMOL] where does PyMOL install to on Windows?

[Joel Tyndall]

Hi Nat,

In mine its

C:\Program Files\PyMOL\PyMOL\PyMOL.exe

Hope this helps

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


-Original Message-
From: Nat Echols [mailto:nathaniel.ech...@gmail.com] 
Sent: Monday, 26 March 2012 5:52 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] where does PyMOL install to on Windows?

I'm trying to figure out how to launch PyMOL automatically from a script on 
Windows.  I'm stuck with the 0.99 build for now, where the .exe is

C:\Program Files\DeLano Scientifc\PyMOL\PyMOL.exe

Is this now

C:\Program Files\Schrodinger\PyMOL\PyMOL.exe

in the newer versions, or somewhere else?

thanks,
Nat

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Re: [PyMOL] How to tell what amino acids are in view?

[Joel Tyndall]

Shane,

The simplistic option is to use the shift key and drag your mouse across the 
viewer window. With the sequence displayed this will select those residues in 
view and highlight them also. This is the static option and I'm guessing not 
quite what you may be after

Joel


_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
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Re: [PyMOL] Changing ligand conformation

[Joel Tyndall]

Mark,

You could always simply edit the pdb file (remove the trans option). Simply 
open up the pdb file in a text editor (gedit/notetab/wordpad) and delete the 
lines corresponding to the trans form. The pdb file (compare with the mol or 
mol2 files) is simple to edit manually. The others require connectivity etc to 
be edited.

The last pdb file I saw with an alt conf looked like this:

ATOM 53  CG2AVAL A   6  -5.306 -11.323  22.865  0.50 11.50  AC
ATOM 54  CG2BVAL A   6  -7.334 -10.108  21.413  0.50 12.94  AC
ATOM 55  CVAL A   6  -8.805 -10.428  23.682  1.00 11.53  A  
  C
ATOM 56  OVAL A   6  -9.347 -11.540  23.573  1.00 12.73  A  
  O

Where the AVAL and BVal correspond to different orientations.

Hope this helps
_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand    
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


-Original Message-
From: Mark Bostock [mailto:mjb...@cam.ac.uk] 
Sent: Saturday, 10 December 2011 10:26 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Changing ligand conformation

I have a pdb file of a protein which contains a lysine residue bound to a 
ligand. The ligand has two conformations due to a cis/trans isomerisation. I 
have created a pdb file (also .mol and .mol2) of lysine attached to the cis 
form and would like to replace the
lysine-ligand(trans) form which is currently in the protein structure with the 
lysine-ligand(cis) form. Does anyone know how to do this; mutagenesis only 
gives me the option of standard amino acids and also does not remove the 
existing ligand.

Many thanks,

Mark.



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Re: [PyMOL] about Display CCP4 Maps

[Joel Tyndall]

Hi Lina,

Could you be more specific about what you are trying to do. E.g." I have a 
structure from the pdb and I would like to display the density."

If it is this option then you can automatically generate ccp4 type maps from 
http://eds.bmc.uu.se/eds/ assuming the structure factors have been deposited. 
You can them load these into pymol (file.ccp4)

"Or I am determining the structure of a protein ligand complex and I wish to 
calculate the electron density map ."

If this is the case I would suggest some further reading of the ccp4 tutorials. 
These come with ccp4i

Hope this helps

Joel

_________
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
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-Original Message-
From: lina [mailto:lina.lastn...@gmail.com] 
Sent: Wednesday, 26 October 2011 1:27 a.m.
To: Thomas Holder
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] about Display CCP4 Maps

On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder  
wrote:
> Hi Lina,
>
> do you already have any electron density or reflection file (*.map, 
> *.mtz,
> ...) or do you want to create a "fake" density from your structure? 
> It's not


I don't have the reference electron density file.

mainly wish to calculate a density map based on the structure?

> clear from your question.
>
> Cheers,
Thanks for asking.

>  Thomas
>
> On 10/25/2011 10:28 AM, lina wrote:
>>
>> Hi,
>>
>> I went through the pymolwiki and cross this page:
>>
>> http://www.pymolwiki.org/index.php/Display_CCP4_Maps
>>
>> I have some questions:
>>
>> 1] do I need generate the map from ccp4
>>
>>  (I have already installed the ccp4i, but seems not easy to know how 
>> to get the map)
>>
>> 2] For small molecular (ligand), the ccp4 is the best way to obtain 
>> its  electron density map?
>>
>> Seems those questions are not so-pymol-related, but I wish if someone 
>> are familiar with this, can give me some advice??
>>
>> Those questions might be easy, but to me at present it seems very 
>> confusing.
>>
>> Thanks with best regards,
>
> --
> Thomas Holder
> MPI for Developmental Biology
>

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Re: [PyMOL] pdb of ice

[Joel Tyndall]

A quick google search found this:

http://www.nyu.edu/pages/mathmol/library/water/ 

hope this helps

_
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Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
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-Original Message-
From: H. Adam Steinberg [mailto:a...@steinbergs.us] 
Sent: Friday, 21 October 2011 9:31 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] pdb of ice

Hi all,

Does anyone know of a pdb that was created for the structure of water molecules 
in ice? I have not been able to find one and am not looking forward to creating 
one! :)

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] get atom name

[Joel Tyndall]

Hi Lina,

If you have an atom that you want to identify you can right click on the atom 
which give you the atom name (pdb format).

Your command "select o, name o" does work on the latest windows install 1.4.1 
where it selects all oxygens and creates a selection called (o).

Hope this helps

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: lina [mailto:lina.lastn...@gmail.com]
Sent: Sunday, 25 September 2011 11:11 p.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] get atom name

Hi,

how can I get the atoms name (except label)

when I use
select o, name o

not work.

Here I will the .pse file in the following email.

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Re: [PyMOL] Script for Torsion angles

[Joel Tyndall]

Hi Martin,

Whilst I have no competence what so ever in scripting, I believe the 
measurement wizard does offer you the "torsion angle" option only it is listed 
as a "dihedral".

Hope this helps

Joel 

_________
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
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-Original Message-
From: Martin Hediger [mailto:ma@bluewin.ch] 
Sent: Friday, 2 September 2011 9:49 p.m.
To: pymol-users
Subject: [PyMOL] Script for Torsion angles

Dear List
Does anyone have a script to calculate torsion angles lying around?
Ideally, i would like to be able to enter x1, x2, x3, x4 and get the
(smaller) angle between the two normals of the planes defined by x1, x2,
x3 and x2, x3, x4, respectively. For some odd reason the measurment wizard in 
my PyMOL install does not display torsion angles..!?

Kind regards and thanks for any feedback.
Martin

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[PyMOL] mtz files and ray tracing

[Joel Tyndall]

Hi folks,

Just worked out how to open the mtz files in v1.4.1 which is great (and I now 
know what the volume tab is). Nice work

Two questions:

How can I extend the map around my protein as it appears to cross the 
boundaries of the asu?

When I ray trace, the map disappears...so we can't use the excellent graphics

I am using both a phenix generated mtz (works with File>open mtz) and a ccp4 
generated one (File > open)

Cheers

Joel



_____
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

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[PyMOL] Generating peptides with structure in Pymol

[Joel Tyndall]

Hi all,

I just wanted to raise an issue a colleague pointed out recently. When you 
generate an ideal peptide in the form of an alpha helix using the builder 
function in Pymol, the intra-molecular H-bonds that characterise an alpha helix 
(I to i+4) are too close (2.2 Angstrom O-N). If you generate such a peptride, 
save it then reopen in Pymol, extra bonds are drawn between N-H and O= 
indicating the close proximity. Whilst I realise Pymol is not currently 
designed to "Model" structures, could this be updated.

Cheers

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

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Re: [PyMOL] Display main chain amides after preset

[Joel Tyndall]

Hi Jason,

Thanks for that. From a teaching-learning perspective, I would like to see a 
"correct" option added, or indeed the current option updated to include amides 
(turning off the helper), but just a suggestion. 

Cheers

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
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New Zealand   
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-Original Message-
From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] 
Sent: Friday, 5 August 2011 3:24 p.m.
To: Joel Tyndall
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Display main chain amides after preset

Hi Joel,

The preset commands make changes that are sometimes undoable. In this case, 
PyMOL sets "cartoon_side_chain_helper" on a selection and then deletes the 
selection. To do what you want, you need to perform the actions in the command 
without the cartoon_side_chain_helper setting:

# fetch an example protein

fetch 1hpv, async=0

# detect ligand sites

preset.ligand_sites("1hpv")

# show the dashes in the polar contacts

show dashes, 1hpv_pol_conts

# show the cartoon

show cartoon, rep ribbon

# hide surface and ribbon
hide surface
hide ribbon


Should we add some more options for preset visualizations?

Cheers,

-- Jason

On Thu, Aug 4, 2011 at 6:22 PM, Joel Tyndall  wrote:
> Hi folks/Jason,
>
>
>
> I have been playing with PyMOL again lately for teaching and have 
> noticed that when you run the menu command Action>preset>ligand site 
> >cartoon which looks great... if there are any H-bonds with a protein 
> chain amide carbonyl, then the carbonyl is not displayed. If you use 
> "Show>lines or sticks" this does not then show them. I'm sure there is 
> a background (python) setting to adjust this but is it possible to 
> include the carbonyl's in question with the initial preset? HIV protease is a 
> good example to show this.
>
>
>
> Cheers
> Joel
>
>
>
> _
>
> Joel Tyndall, PhD
>
> Senior Lecturer in Medicinal Chemistry National School of Pharmacy 
> University of Otago PO Box 56 Dunedin 9054 New Zealand
>
> Skype: jtyndall
> http://www.researcherid.com/rid/C-2803-2008
>
> Pukeka Matua
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 56 Otepoti 9054
> Aotearoa
>
> Ph / Waea   +64 3 4797293
> Fax / Waeawhakaahua +64 3 4797034
>
>
>
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[PyMOL] Display main chain amides after preset

[Joel Tyndall]

Hi folks/Jason,

I have been playing with PyMOL again lately for teaching and have noticed that 
when you run the menu command Action>preset>ligand site >cartoon which looks 
great... if there are any H-bonds with a protein chain amide carbonyl, then the 
carbonyl is not displayed. If you use "Show>lines or sticks" this does not then 
show them. I'm sure there is a background (python) setting to adjust this but 
is it possible to include the carbonyl's in question with the initial preset? 
HIV protease is a good example to show this.

Cheers
Joel

_________
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

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Re: [PyMOL] Downloading the biological assembly from the PDB

[Joel Tyndall]

Hi Martin,

You can download the biological assembly directly from the pdb website. Under 
download files (RHS) usually the last entry is Biological Assembly. Once 
downloaded you can unzip it and change the file suffix back to pdb e.g. 
1AVD.pdb1  ==> 1AVD_1.pdb

Hope this helps

Joel

_____
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
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-Original Message-
From: Martin Hediger [mailto:ma@bluewin.ch] 
Sent: Wednesday, 4 May 2011 8:00 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Downloading the biological assembly from the PDB

Dear all
I would like to ask how it is possible to download the coordinate file for the 
biological assembly of a protein structure from the PDB.
Naturally, this is not a question directly related to PyMOL, but I thought I'll 
be reaching at least a couple of Biochemists/Chrystallographers who know how to 
do this.
As an example, when downloading the PDB file of "1AVD", I get a file with two 
chains. The biological assembly would be a tetramer, so I wonder what URL I 
would require to write into a script that does the downloading.

Thanks for help on this.
Martin

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[PyMOL] Virtual machines and graphics cards

[Joel Tyndall]

Hi folks,

I am looking at running virtual linux on a windows XP machine and I noticed 
that pymol runs but without graphics acceleration. Its all installed on the 
windows side and I have searched the web to see if I can activate enhanced 
graphics on a linux guest. I don't think you can do it with VMWare player but 
virtual box looks possible (not sure though)


Comments appreciated

J

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
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Re: [PyMOL] Question about ray

[Joel Tyndall]

Try setting your Pymol viewer to square dimensions first:

Viewport 600,600

Then try the ray command

This should work

Joel

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


-Original Message-
From: Gudrun Lotze [mailto:gudrun.lo...@gmx.net] 
Sent: Wednesday, 23 June 2010 12:30 p.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Question about ray

Dear Pymol-Users,

I tried to ray my protein to get a good looking picture. I tried set  
ray_trace_mode, 0 and ray 1200, 1200. I always go a square around my  
protein and parts where not visible.
How can I get rid of that black border line and how can I ray my  
protein so it is on the whole page visible and not in a box cut off.
Thank you and kind regards
Gudrun Lotze


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Re: [PyMOL] pymol dies when minimizing

[Joel Tyndall]

Hi,

Yeah I have a similar issue and have been meaning to post it. On windows 7 
following minimization, the viewer doesn't update when you open it again, no 
menus either. Using PyMOL 1.2r2

Looking forward to a solution

J

_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

From: Robin Emig [mailto:re...@pacificbiosciences.com]
Sent: Wednesday, 2 June 2010 7:34 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] pymol dies when minimizing

Does anyone else have the problem where pymol dies, or wont update the display 
after minimizing on windows? Is there a way to fix this?
-Robin
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Re: [PyMOL] Align different Structures

[Joel Tyndall]

Hi Martin,

I think it would be good to use pair_fit

Someone else may be able to help with a scdropt buut if you have a stretch of 
residues you can align them such as:

Pair_fit a///79-85/ca, b///89-95 , a///150-175/ca, b///183-208/ca

(this aligns a to b) You could also renumber chain A to match the numbers of 
chain B (if it doesn't already match)

I'm pretty sure this will give you what you want. It is at least one method

Joel
_
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


-Original Message-
From: Martin Hediger [mailto:ma@bluewin.ch] 
Sent: Thursday, 25 March 2010 10:51 p.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Align different Structures

Hi all,
My problem is:
I have two structures, A and B. Both are part of a protein and contain 
residues from the active site. A is a subset of B in a sense that B is 
contains residues even further from the active site (generated by the 
expand command).
I ran a QM calculation on the active site in the minimal set A to obtain 
a transition state for an enzymatic reaction (ester cleavage). So A is 
not in its original configuration anymore, i.e. some of the residues 
have moved.
What I want to do is this: the same calculation on the expanded model B 
would be too expensive. So I want to align B as reasonably as possible 
to A, since I know what the transition state looks like in the simple 
model. How do I do this in the smartest way? By pair-fitting in Pymol? I 
believe to issue the align command is not the best idea, since i dont 
want an overlay, I want the catalytically relevant residues to be 
superimposed.
I would very much appreciate any suggestions.

Martin

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[PyMOL] FW: Slightly off topic

[Joel Tyndall]

Thanks folks, will start with FC11

J

From: Joel Tyndall [mailto:joel.tynd...@otago.ac.nz]
Sent: Tuesday, 15 December 2009 4:33 p.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Slightly off topic

Hi folks,

Sorry for the off topic post. I have just got a new whizz bang laptop and I'm 
wondering whether I have gone too high spec. It is 64 bit LED ASUS ul50v 
series. I am running linux centos 5.4 but can't get the nvidia driver going 
(LED screen perhaps) and I just had an initial problem with pymol. (I want to 
run modeler, sybyl and gold also ) This is not to mention the fact that the 
kernel doesn't have wireless or Ethernet drivers.

Should I "downgrade" or persist.

Many thanks for comments

_____
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
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[PyMOL] Slightly off topic

[Joel Tyndall]

Hi folks,

Sorry for the off topic post. I have just got a new whizz bang laptop and I'm 
wondering whether I have gone too high spec. It is 64 bit LED ASUS ul50v 
series. I am running linux centos 5.4 but can't get the nvidia driver going 
(LED screen perhaps) and I just had an initial problem with pymol. (I want to 
run modeler, sybyl and gold also ) This is not to mention the fact that the 
kernel doesn't have wireless or Ethernet drivers.

Should I "downgrade" or persist.

Many thanks for comments

_____
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
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[PyMOL] broken

[Joel Tyndall]

Hi again folks,

Having tried to install both versions on my PC, then delete versions I can now 
only start pymol using the pymol.exe and any other automatic links bring the 
error:

Error: Pymol failed to launch "Aw Shucks"

I can get around this but it would be nice to restore to the original status 
quo.

Thanks for any help

J


_____

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

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[PyMOL] (no subject)

[Joel Tyndall]

PS is it possible to run two versions at once on a PC (a quick test failed)


_

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

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[PyMOL] Education

[Joel Tyndall]

Hi folks,

I'm using the latest version 1.2r1 of pymol for research etc and we have 0.99 
in our lecture theatres (this is in the process of being upgraded to edu1_1 
version - all windows. The problem is when I generate a nice presentation in 
1.2r1 using align, surfaces etc it doesn't translate to the older versions.

I can provide files if required

Is the only option to generate "educational" presentations for my lectures 
using the edu version?

Thanks

J


_________

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

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Re: [PyMOL] Extracting Amino Acid Sequence from PDB File

[Joel Tyndall]

You can also download the sequence directly from the pdb

J
_

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
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Aotearoa

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-Original Message-
From: Buz Barstow [mailto:b...@mac.com] 
Sent: Friday, 14 August 2009 9:35 a.m.
To: pymol-users@lists.sourceforge.net; ccp...@jiscmail.ac.uk
Subject: [PyMOL] Extracting Amino Acid Sequence from PDB File

Hi All,

Does anyone know of a program that can extract the amino sequence of a  
protein from a PDB file and output it as a FASTA file?

Thanks! and all the best,

--Buz



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Re: [PyMOL] selecting one model from multiple structures

[Joel Tyndall]

Hi Bala,

Start with "split_states your_object". If its an NMR structure with multiple 
solutions, then this will make each a separate object. I find this much 
easierto deal with. Also works for Biological units with multiple units 
involved.

J


_____

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


From: Bala subramanian [mailto:bala.biophys...@gmail.com]
Sent: Thursday, 16 July 2009 3:46 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] selecting one model from multiple structures

Friends,

I have a single pdb file with multiple models like that in NMR structures. How 
do i select a particular model of interest  from the pdb in pymol.

Thanks,
Bala
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[PyMOL] Rigimol/ipymol

[Joel Tyndall]

Hi folks,

I was wondering if anyone can help. I have made some nice morphs using 
rigimol/ipymol based on Warren's examples (Thanks Warren). I was wondering if 
anyone has any scripts to do the following.

I have generated a morph with two structures with two different ligands  where 
there is a conformational change of the protein between the two ligands. There 
exists an intermediate structure which I would like to include also. How can I 
include this i.e. I want to morph from 1 to 2 then to 3 and show the ligands 
(changing) as well?

Many thanks for any help in advance.

Joel


_____

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

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[PyMOL] surface area cross section

[Joel Tyndall]

Hi folks,

Apologies for the relatively off topic question but I figured someone may be 
able to help.

Does anyone know of a tool that will calculate the cross-sectional area of a 
(small) molecule?

Cheers Joel


_

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

Re: [PyMOL] depiction of ligands

[Joel Tyndall]

Dear Jhon,

You want to use the show sticks option. Using the sequence viewer, this will 
show your ligands etc. Select these by clicking on them in the sequence viewer 
then under selection pick show sticks. From this point once you have displayed 
the selected residues it would be best to use the measurement wizard. You can 
turn off the actual distance using the label option. Pymol will only identify 
H-bonds you will have to identify the rest yourself.

I hope this helps. For further information look at the pymol wiki. It is also 
better to post these requests to the bulletin board so others cab see the 
results

Regards


Joel Tyndall, PhD



Senior Lecturer in Medicinal Chemistry

National School of Pharmacy

University of Otago

PO Box 56 Dunedin 9054

New Zealand



Pukenga

Te Kura Taiwhanga Putaiao

Te Whare Wananga o Otago

Pouaka Poutapeta 913 Otepoti 9054

Aotearoa



Ph / Waea +64 3 4797293

Fax / Waeawhakaahua +64 3 4797034






From: Jhon Thomas [mailto:jhon1.tho...@gmail.com]
Sent: Friday, 27 March 2009 8:20 p.m.
To: Joel Tyndall
Subject: Re: [PyMOL] depiction of ligands

Hi joel

Thanks for your reply...
I want to show my ligand (sulpahete) in my figure and its interaction with the 
selcted atoms of the selected residues (Hbonds, ionic etc). as well as i want 
to show the interaction (hbonds) with the selected atoms of the selected 
residues. shwing sphere wouldnot be a good way. i will appreciate your help.

Thank you

Thomas
On Thu, Mar 26, 2009 at 1:51 AM, Joel Tyndall 
mailto:joel.tynd...@otago.ac.nz>> wrote:

Hi there,



There are many ways to do this. You can also try Action>preset>ligands. This 
will show the ligands (hetatms) and their interactions. Unfortunately this 
doesn't highlight metal ions everytime (unless it interacts with the ligands). 
You can usually view this using the sequence option. [show the sequence - S 
button bottom right, move the slider to the end of the protein (usually) and 
select the metal(s) show spheres of selection]



Hope this helps



J



_________

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034



From: Jhon Thomas [mailto:jhon1.tho...@gmail.com<mailto:jhon1.tho...@gmail.com>]
Sent: Thursday, 26 March 2009 5:30 a.m.
To: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: [PyMOL] depiction of ligands



Hi all

I would like to know, how we can show the ligands in pymol. Although i can see 
the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms l;ike 
sulphate  and metal ions. I will appreciate the suggestions.

Thanks in advance

Thomas

Re: [PyMOL] depiction of ligands

[Joel Tyndall]

Hi there,

There are many ways to do this. You can also try Action>preset>ligands. This 
will show the ligands (hetatms) and their interactions. Unfortunately this 
doesn't highlight metal ions everytime (unless it interacts with the ligands). 
You can usually view this using the sequence option. [show the sequence - S 
button bottom right, move the slider to the end of the protein (usually) and 
select the metal(s) show spheres of selection]

Hope this helps

J


_

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034


From: Jhon Thomas [mailto:jhon1.tho...@gmail.com]
Sent: Thursday, 26 March 2009 5:30 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] depiction of ligands

Hi all

I would like to know, how we can show the ligands in pymol. Although i can see 
the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms l;ike 
sulphate  and metal ions. I will appreciate the suggestions.

Thanks in advance

Thomas

[PyMOL] pymol doing interesting things on windows

[Joel Tyndall]

Hi again folks,

I've been having some strange things happening with pymol starting on my 
windows machine (windows XP; NVIDIA GeForce 8400 GS; LG LCD screen; pymol 
version 1.1r). Attached is the most resent problem. Previously upon start up 
pymol decided to simply go very slowly when starting up. This repaired itself 
on restart as did the latest issue.

I'm really not sure what the issue could be and just figured this is the 
logical place to start. My feeling is that it may be one of those mystery bugs 
only ever experienced by me but I thought I'd throw it out there.

Cheers

Joel


_____

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

<>

[PyMOL] Website

[Joel Tyndall]

Hi Warren,

I notice the FAQ link is missing from the website. I found the page but no 
link, was looking so my students can cite pymol appropriately. Will it be 
reinstated?

Cheers

J

_

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

[PyMOL] install/upgrade

[Joel Tyndall]

Hi folks,

Just updated my pymol version to 1.1 on my linux boxes and I get an error 
"floating point".
I am running centos 4.6 32 bit...any suggestions? I've got nothing. 1.0r2 works 
fine.

J


_____

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034

Re: [PyMOL] Molecule galleries

[Joel Tyndall]

Hi there,

The gallery is currently in 2D format. Any plans to generate 3D galleries?

J

_

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034




-Original Message-
From: pymol-users-boun...@lists.sourceforge.net 
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of X-raylab info
Sent: Thursday, 4 September 2008 3:54 a.m.
To: x-ray...@spider.med.jhmi.edu
Cc: scit...@lists.apple.com; x-ray...@spider.med.jhmi.edu; 
o-i...@origo.imsb.au.dk; objcryst-de...@lists.sourceforge.net; 
comc...@iucr.org; pymol-users@lists.sourceforge.net; cn...@yahoogroups.com; 
gnu-darwin-po...@lists.sourceforge.net; 
blueobelisk-disc...@lists.sourceforge.net; ccp...@jiscmail.ac.uk; 
gnu-darwin-distribut...@lists.sourceforge.net; corecifc...@iucr.org; 
vm...@ks.uiuc.edu
Subject: [PyMOL] Molecule galleries


I have automated the process to make molecule galleries, which I am
finding very useful to my research, so I thought that I would share the
opportunity and take requests.  It is quick and easy.  I did a bisphenol
search today, and as I expected, the search turned up a few stilbenes,
which is the same molecular family as resveratrol.  Strikingly,
Bisphenol A is a noted teratogen, which shows that care must be taken
when using such molecules during development.  Here is a link to the
bisphenol gallery.

http://molecules.gnu-darwin.org/mod/Bisphenol-more.html

If you would find it useful, I am definitely interested in taking
requests for molecule galleries.   Just send me the name of your
favorite molecule.  As you may be able to tell, we have access for
galleries to about 1% or 0.5 million structures, in the total archive
thus far, but it is already quite useful. The automated jobs are
underway to fill in the rest.  The next milestone is the capability to
index and make galleries for the remaining millions of molecules for
which we have pdb files already, which would be 5-10% complete.  Any
comments or suggestions are also welcome.

Regards,

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Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293
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[PyMOL] Crash on a PC

[Joel Tyndall]

Hi folks,

Having a few problems trying to view some docking results. When I open a 
.mol2 file its fine. If I try to open another, pymol crashes and 
disappears (no error given). It is sort of repeatable but has happened 
at different points (mostly early in a session.


The key is I have ssh'd the files from my Linux machine (all works fine 
there) and the problem is on the PC. And the docked poses are generated 
from GOLD.


Any help?

J

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293 
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Re: [PyMOL] how to add acetyl group nto peptide by pymol

[Joel Tyndall]

You can use the builder functionality to add a carbonyl and then  a 
methyl to your lysine amine terminus. Unfortuantely you cannot optimize 
in Pymol. You could use Prodrug or CNS if you have some experience.


Cheers

Joel

LIU Changdong wrote:

Hi,evreyone:
 I've got a pdb file of short peptide (11aa),I want to add an acetyl group
on Lys residue and optimize the structure.Is there anyone who can tell me
how to do it?

Best
Dong


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Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293 
Fax / Waeawhakaahua +64 3 4797034

Re: [PyMOL] align states

[Joel Tyndall]

Hi andrea,

you can easily do this by

split_states my_struct
dele my_struct


for the NMR ensemble, then I would use the action menu, align function 
and align them  to state_1. This is in effect aligning the separate 
states as objects, unless I misunderstood you


J

Andrea Spitaleri wrote:

Hi all,
in pymol is it possible to align states rather than object. I mean, I
have loaded a pdb file with n-structures and I'd like to align each of
them on the first one of the bundle.
Thanks in advance

Regards

andrea




  


--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293 
Fax / Waeawhakaahua +64 3 4797034

Re: [PyMOL] how to modify side chain angle

[Joel Tyndall]

Hi Marcela,

in 3-button editing mode control right click on a bond brings up an 
angle display (you can pick two different bits of the bond depending on 
which end you want to rotate. then control left click and drag and you 
can rotate your dihedral angle. Control z undoes the move.


Hope this helps

J

Marcela NUNEZ wrote:

Hi everybody!

I would like to modify a side chain angle of an histidine residue of a
pdb file. Does anybody know how to do that?.


  


--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

Ph / Waea   +64 3 4797293 
Fax / Waeawhakaahua +64 3 4797034

Re: [PyMOL] Movie to Powerpoint

[Joel Tyndall]

Video mach seems to work

chiradip chatterjee wrote:

Hi Friends
I am a new Windows pymol user.
I made a movie in Pymol and saved the 120 ray traced
*.png frames.
Now I want to convert the *.png files to MPEG files
and then directly convert/run the movie in the
Powerpoint presentation.
can anyone please help me in this regard
Thanks
Chiradip




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PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
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Ph / Waea   +64 3 4797293 
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Re: [PyMOL] Displaying Disulphide bonds using Pymol

[Joel Tyndall]

Dear Nagesh,

If you upgrade to the latest version (0.99) there is an option do 
display the disulfides under the show menu


J

Nagesh Chakka wrote:

Hi Jerome,
Thanks for the mail. The web address you gave is about obtaining 
information about Cys involved in bond formation. In my case, I do know 
which pair of Cys are involved in it and this information is also 
provided in the PDB file but I am unable to display the bridge in the 
PyMOL viewer.
Also I need to display the structure in a particular orientation. Can 
this information be be added in my script.

Thanks
Nagesh

Jerome Pansanel wrote:

  

Hello,

You can find some documentation about sulfur bonds on this page:
http://www.pymolwiki.org/index.php/Process_All_Files_In_Directory

If you are not successfull by using this resource, don't hesitate to post
again.

Cheers,

Jerome Pansanel

Selon Nagesh Chakka :

 



Hello everyone,
I am unable to display disulphide bonds using PyMOL (version 0.97). My 
understanding is that PyMOL can connect Cys that are within bonding 
distance. The PDB file (ID 1AG2) defines residues involved in the SSBond


formation. I  also tried to  use the command "bond" to connect the 
residues but without any success. I am not sure if I am doing anything 
wrong. Any suggestion in this regard is appreciated.

Thanks
Nagesh


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Lecturer
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University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea   +64 3 4797293 
Fax / Waeawhakaahua +64 3 4797034

Re: [PyMOL] Saving .psw files

[Joel Tyndall]

Hi Miguel,

This seems like a big in the program. Save the file as per usual (.pse) 
Change the suffix of the file to .psw and that works fine


J

Miguel Alejandro Pabon Sanclemente wrote:


PyMOL community,

I want to assemble a short animation using the PyMOL movie-making 
capabilities.  I tried to save several scenes  as a .psw file (as previously 
suggested) but by default PyMOL saves the file as .pse.  How can I make PyMOL  
save the file as .psw? I'm working with PyMOL version 0.99.


Thanks beforehand!!




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Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea   +64 3 4797293 
Fax / Waeawhakaahua +64 3 4797034

Re: [PyMOL] pymol transitions recorded as movie?

[Joel Tyndall]

Hi Eva,

If you save your scenes (conformations) as a psw file (under save as) 
you can then use a hyperlink in powerpoint and this will launch pymol in 
presentation mode and you can just use page down to scroll through the 
scenes. Pymol is still active so you can rotate the molecules in the 
presentation.


Hope this helps

J

Eva Vanamee wrote:


I regularly use the F function keys in PyMol to store
conformations and call them back in a presentation.
I really like the transition effects. Is it possible to record those
transitions as a movie and use them in a Powerpoint presentation?
Thanks in advance,
- Eva




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Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea   +64 3 4797293 
Fax / Waeawhakaahua +64 3 4797034

[PyMOL] Sequence view print out

[Joel Tyndall]

Hi all,

I'm not sure if this has been asked before and I'm not sure if its 
possible...but here goes anyway. Is there a way to print/export the 
sequences in the viewer window? It would be an easy way to translate 
actual secondary structure to a sequence alignment


Thanks

J

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
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[PyMOL] viewing multi-sdf files

[Joel Tyndall]

Hi folks,

hopefully an easy solution but how do I read all the molecules (scroll 
thru) in a multi-sdf file or mol file. I have tried the split states 
command but that only reads the first molecule.


Any help would be appreciated.

J

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
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Re: [PyMOL] display of multiple NMR structures stored in one PDB file

[Joel Tyndall]

Check out the list under NMR and my name (I asked the same question). Answer 
also pasted below

J

To see them all at once:

load my_struct.pdb
set all_states

Or if you want them separated into individual objects:

unset all_states
split_states my_struct
dele my_struct



Michael Weber wrote:


Hello,
I have a short question concerning the display of multiple NMR 
structures stored in one PDB file. When loading NMR .PDB files with 
SWISS-PDB-VIEWER, the number of NMR structures present in that file is 
initially displayed during the loading process and one can select how 
many and which of the structures are going to be loaded.
 
In pyMOL, when trying to load for example 1JOX.pdb (which contains 4 
NMR models), only one single structure is displayed. How can I 
visualize the remaining three?
 
Thanks for your help, ;-)

Michael.



--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
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Re: [PyMOL] mesh for compound molecule

[Joel Tyndall]

Hi Lena,

I know it might not be the best way but you can change the hetatm name 
to atom and then create a separate object in pymol. or read in a 
separate file with the above change


J

len...@gmx.de wrote:


Hello PyMOL-users,

I was wandering how to show the mesh on the compound molecule (i.e. other
structures that amino acids inside of a protein).  Any visualization similar
to electron density would be also useful.

Thanks!!
lena

 



--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

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Re: [PyMOL] Saving Images

[Joel Tyndall]

If you would like appropriately scaled images then you can set up your 
viewer to the appropriate dimensions eg for a square


viewport 700,700

or rectangle

viewport 800,400

If using a square I then use

ray 1800,1800

this ray traces an image larger than your pymol window and allows you to 
save it. This will help with higher resolution images. Newer versions 
show a preview. You canuop the resolution by increasing the ray pixels


Hope this helps

J

Peter Adrian Meyer wrote:


Hi everyone,
Each time I try to save images, Pymol writes 640x480
pixel image to the file. I wonder if there is a way to
save images (png format) other than 640X480 pixel that
is default.
Any help will be appreciated.
Thanks.
   



Images are saved as either the size of the viewer window, or the ray
traced size.  The easiest way to get a larger image is to maximize the
viewer window, and then save.  To get an arbritray size, use the
ray-tracer (ray 1024,768 ; png BigImage.png).

Pete



Pete Meyer
Fu Lab
BMCB grad student
Cornell University



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Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea   +64 3 4797293 
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[PyMOL] Nvidia question (7676 driver)! - NOT SOLVED

[Joel Tyndall]

Hi folks,

I was a little pre-emptive. The flicker is back! so no solution yet.

J

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea   +64 3 4797293 
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[PyMOL] Another Nvidia question (7676 driver)! - SOLVED -use 7664

[Joel Tyndall]

Hi folks,

Thanks to those who responded. I uninstalled the 7676 driver and 
installed an earlier driver (7664) which seems to be a trusted nvidia 
driver (see mailing list) and has solved the problem (and pymol doesn't 
crash. I did try the 6629 but the x sever refused to start ( at least on 
my system).


Anyway thanks again

J

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

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[PyMOL] Another Nvidia question (7676 driver)!

[Joel Tyndall]

Hi folks,

Sorry for the slightly of topic question but I figure you guys know 
whats going on.


I have a linux box with RHE WS 4 and I have just installed the nvidia 
driver (7676 x86) which at least works so far! The problem is that the 
screen will occasionally (and randomly) start flickering badly rendering 
pymol and any other program essentially useless (flicker is the whole 
screen and the desktop shape changes to a trapezoid shape).


Any body know how to fix this. Have people tested this driver? Should I 
load an earlier driver?


Many thanks

Joel

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

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Re: [PyMOL] displaying protein with propeptide

[Joel Tyndall]

Hi Ann,

I would change the chain id of the propeptide in a text editor, to say P 
and remove the P from after the residue numbers.


J

Anne Mølgaard wrote:


Hi,

I am having problems displaying proteins with unusual residue numbering,
such as proteins with propeptides. An example is 1cs8, which starts off like
this:

ATOM  1  N   SER A   1P-32.762  23.978  22.929  0.00 34.26
N  
ATOM  2  CA  SER A   1P-32.360  24.645  21.660  0.00 34.08
C  
ATOM  3  C   SER A   1P-32.303  26.162  21.821  0.00 33.91
C  
ATOM  4  O   SER A   1P-32.838  26.712  22.786  0.00 33.82
O  
ATOM  5  CB  SER A   1P-33.338  24.274  20.541  0.00 34.28
C  
ATOM  6  OG  SER A   1P-34.684  24.406  20.971  0.00 34.36
O  
.

.
.
And later on comes the sequence corresponding to the mature protein:

ATOM   1060  N   ALA A   1  11.470  66.852  16.148  1.00 22.69
N  
ATOM   1061  CA  ALA A   1  11.282  65.561  15.491  1.00 20.80
C  
ATOM   1062  C   ALA A   1  10.621  65.677  14.113  1.00 20.33
C  
ATOM   1063  O   ALA A   1   9.920  66.649  13.835  1.00 18.43
O  
ATOM   1064  CB  ALA A   1  10.451  64.636  16.393  1.00 19.50
C  
Etc. 


If I open 1cs8 with PyMol, I can see everything in the "lines", "sticks" and
"surface" representation, but in ribbon or cartoon mode only part of the
protein is shown. What do I have to do to show the whole sequence?

How do I select residues with a "P" appended to the residue number? If I say
"select resi 1P-5P" I get both 1P-5P and 1-5. 


Any help will be appreciated! (I am using PyMol version 0.98 for Windows).

- Anne 



Anne Mølgaard, Ph.D.
Center for Biological Sequence Analysis
BioCentrum-DTU, Building 208
DK-2800 Lyngby

Email:  a...@cbs.dtu.dk 
Phone:  (+45)4525 2472
 





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--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea   +64 3 4797293 
Fax / Waeawhakaahua +64 3 4797034

Re: [PyMOL] Superimpose

[Joel Tyndall]

Hi Michael,

I notiuced no-one has posted anything so here goes.

Start with
align 1abc, 1target
which will superimpose 1abc onto 1target
then from here you can select the non homologous regions (using display 
sequence and highlight from here and colour to your hearts content. I'm 
sure there are other ways to do this but this is one way!


Cheers

J

Michael Morbious wrote:


Hi everyone,
I have two similar (closely related) multi-chain
structures. I want to merge them and highlight the
regions that do not superimpose. However, I do not
know how to superimpose these two structures and how
to select non-intersecting residues. 
Any help will be appreciated.
Thanks.  




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Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea   +64 3 4797293 
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Re: [PyMOL] Creating PDB files from Primary Sequence

[Joel Tyndall]

Hi James,

Sounds like you want a homology model type set up, ie generate 
coordinates based on a template. Modeller can do this and an easier way 
is via the  swissmodel


http://swissmodel.expasy.org//SWISS-MODEL.html

If however you want a relatively random structure then pymol _can_ do 
this. Click on builder (top right og GUI) and then select protein. From 
here you can generate any sequence you want. You can then export this 
and use the program of your choice to run dynamics etc


Hope this helps

J

James R. Graham wrote:


Hello,

This may be slightly off-topic, but I was wondering whether PyMol  
would allow one to enter a peptide sequence (generally short in  
length) to create a template structure that can then be used for  
structural refinements (minimizations, etc.) elsewhere.


If PyMol cannot do this, is anyone aware of any program (preferably  
Mac OS X or linux compatible) that would be able to do this?


Any info would be greatly appreciated.

And apologies if this question is too far off-topic.

Regards,
james




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--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea   +64 3 4797293 
Fax / Waeawhakaahua +64 3 4797034

Re: [PyMOL] sessions and movies

[Joel Tyndall]

Hi Nadine,

To answer the first part, there is a much easier way...use the scene 
function in 0.98 version. This allows you to jump between individual 
"screenshots". You can then save this as a .psw file and view it as full 
screen or embed it in powerpoint. (See my previous post "Pymol scenes to 
movies"). Essentaially you set up view 1 and hit append, then view 2 , 
append etc. you can then scroll thru your views.


The second question, can't help.

Cheers

J

Nadine Atwood wrote:



Hi,

I have come across a problem that I cannot find a way around and would 
greatly appreciate some help. I have made a movie showing several 
protein models and numerous distances to illustrate residue 
interactions in different structures. This movie is rather long, and I 
wanted to make a very short version containing certain "screenshots" 
of the original. I have created *.pse files corresponding to the 
frames I would want in the short movie, but cannot find a way of 
loading these in a script. (I can view them "manually" by opening them 
one at a time through the command line, but that rather defeats the 
point.) I wanted to load these using mset and mdo commands, but of 
course, as soon as I load the first one, PyMOL's memory returns to the 
state that was saved and the new movie is deleted. I suppose I need to 
save these files in another format, but have not been able to find 
anything that seems appropriate.


I have also encountered another small problem that I do not need a 
solution to but thought I would mention as it might be a bug (though 
it could be due to my very amateurish programming): when running the 
long movie (which creates and deletes a large number of distances), if 
the movie is stopped and then start again, some distances (I suppose 
corresponding to commands given in frames where the movie was stopped) 
are not deleted, whereas if the movie is run without interruption, all 
distances are handled correctly. (I am using version 0.97)


I am not very computer literate, so a simple explanation would be 
fantastic.;)

Thanks for your advice.

Nadine

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--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea   +64 3 4797293 
Fax / Waeawhakaahua +64 3 4797034