[PyMOL] Vacuum Electrostatics error

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 ___ PyMOL-users

[PyMOL] add hydrogens to .mol2 files

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

Re: [PyMOL] save format for molecule files

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

Re: [PyMOL] Solid stick between two residues?

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.s

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

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

Re: [PyMOL] fusing structures

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 m

Re: [PyMOL] Export aligned sequence

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 seque

[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

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

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

Re: [PyMOL] Farewell

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: Pym

Re: [PyMOL] Using pyvol in pymall

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-

Re: [PyMOL] View two proteins from one pdb file

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 list

Re: [PyMOL] Structure allignmnet in Pymol

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@01

Re: [PyMOL] Comparing same ligands from different proteins

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 Oc

Re: [PyMOL] Hbond to backbone cartoon

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

Re: [PyMOL] Display metal coordination

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

Re: [PyMOL] Columb coloring

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.ne

[PyMOL] Protonation of small molecule amines

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

Re: [PyMOL] Removing unwanted molecules

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

Re: [PyMOL] auto_show_cartoon or similar

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 Subjec

[PyMOL] Pymol crashes with older pse files

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

[PyMOL] pymol fails to open (crash)`

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

[PyMOL] Unusual error after distance measurement

s? 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

[PyMOL] No wheel operation for the slab

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

Re: [PyMOL] Farewell

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] Fa

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

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 work

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

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

[PyMOL] Fading memory

Something like enhanced images? Many thanks 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

Re: [PyMOL] Unbond two atoms

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

[PyMOL] FW: Possible hydrogen addition bug

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 uncom

Re: [PyMOL] surfaces involving more than one object

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 tw

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

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 mode

[PyMOL] export sequence alignment

_ 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 -- Minimize network downtime and

[PyMOL] export sequence alignment

mustang already 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

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

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 s

Re: [PyMOL] representing ferrocene in pymol

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:

Re: [PyMOL] echo colour

or] 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 pr

[PyMOL] echo colour

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

[PyMOL] Possible (minor) bug

_ 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 -- Keep yourself connected to Go Parallel

Re: [PyMOL] Can't undo anymore

l 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: T

[PyMOL] Can't undo anymore

_ 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 -- Everyone

Re: [PyMOL] Verify PDB format

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 woul

Re: [PyMOL] different molecules - same scale?

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

[PyMOL] My first script?

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 _____ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy Unive

Re: [PyMOL] Editing of the pdb structure

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-us

Re: [PyMOL] How to overlay different structures?

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 _____ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy U

Re: [PyMOL] Protein Parameters?

Hi Shane, I think I meant weblogo which shows frequency of amino acids e.g. http://weblogo.berkeley.edu/ Sorry for the confusion J _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin

Re: [PyMOL] Protein Parameters?

_ 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

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

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

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

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 Poutape

Re: [PyMOL] Changing ligand conformation

-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

Re: [PyMOL] about Display CCP4 Maps

p4i 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 Putaia

Re: [PyMOL] pdb of ice

A quick google search found this: http://www.nyu.edu/pages/mathmol/library/water/ 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

Re: [PyMOL] get atom name

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

Re: [PyMOL] Script for Torsion angles

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

[PyMOL] mtz files and ray tracing

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 Otag

[PyMOL] Generating peptides with structure in Pymol

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, P

Re: [PyMOL] Display main chain amides after preset

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, P

[PyMOL] Display main chain amides after preset

f 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 __

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

oel _____ 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 Pou

[PyMOL] Virtual machines and graphics cards

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

Re: [PyMOL] Question about ray

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

Re: [PyMOL] pymol dies when minimizing

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 Lectur

Re: [PyMOL] Align different Structures

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 

[PyMOL] FW: Slightly off topic

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&#

[PyMOL] Slightly off topic

al 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 Sen

[PyMOL] broken

e 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

[PyMOL] (no subject)

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

[PyMOL] Education

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

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

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

Re: [PyMOL] selecting one model from multiple structures

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 _____ Jo

[PyMOL] Rigimol/ipymol

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 Poutape

[PyMOL] surface area cross section

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

Re: [PyMOL] depiction of ligands

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

Re: [PyMOL] depiction of ligands

ence 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

[PyMOL] pymol doing interesting things on windows

. 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 Aote

[PyMOL] Website

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

[PyMOL] install/upgrade

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 Che

Re: [PyMOL] Molecule galleries

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

[PyMOL] Test - please ignore

_ 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

[PyMOL] Crash on a PC

x27;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 Puken

Re: [PyMOL] how to add acetyl group nto peptide by pymol

lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- 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 Poutapet

Re: [PyMOL] align states

: 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 Unive

Re: [PyMOL] how to modify side chain angle

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

Re: [PyMOL] Movie to Powerpoint

p;dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Ku

Re: [PyMOL] Displaying Disulphide bonds using Pymol

sier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/l

Re: [PyMOL] Saving .psw files

57&dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand

Re: [PyMOL] pymol transitions recorded as movie?

Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Joel Tyndall, PhD Lecturer Nat

[PyMOL] Sequence view print out

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 -- Jo

[PyMOL] viewing multi-sdf files

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

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

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

Re: [PyMOL] mesh for 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

Re: [PyMOL] Saving Images

et https://lists.sourceforge.net/lists/listinfo/pymol-users -- 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

[PyMOL] Nvidia question (7676 driver)! - NOT SOLVED

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

[PyMOL] Another Nvidia question (7676 driver)! - SOLVED -use 7664

n 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 Ph / Waea

[PyMOL] Another Nvidia question (7676 driver)!

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

Re: [PyMOL] displaying protein with propeptide

cation Exam for All Training Attendees Through End of 2005. For more info visit: http://ads.osdn.com/?ad_idv28&alloc_id845&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-use

Re: [PyMOL] Superimpose

L-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- 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

Re: [PyMOL] Creating PDB files from Primary Sequence

ing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- 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 P

Re: [PyMOL] sessions and movies

;op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand

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