[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] 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] 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] 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] 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

[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

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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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

[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] 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

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

[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] 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] 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

[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

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

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] 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

[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

[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

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

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

[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] 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] 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] [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

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] 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

[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

[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] 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] 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

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

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] 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

[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

[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] 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

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

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] 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

[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

[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

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

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] 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] 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] 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] 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 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

[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

[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

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] 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

[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] 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

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

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

[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

[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

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

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

[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

[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] 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] 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] 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&#

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 

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] 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

[PyMOL] high end graphics

Hi folks, Is it possible to get graphics output higher than 72 dpi? Cheers 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

[PyMOL] Desparate call for help

appears to be that the nvidia installer (nvidia...6629pkg2.run) is getting confused as to which kernel is running. Has anyone else had these issues/knows any hints. Many thanks in advance J -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago

Re: [PyMOL] ray

earch NMR Spectroscopy, Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherlands _kos...@nmr.chem.uu.nl_ phone: +31-30-2532875 fax: +31-30-2537623 :-) -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pu

Re: [PyMOL] movie question

//ads.osdn.com/?ad_id=6595&alloc_id=14396&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 Ot

[PyMOL] OS-X question

Hi folks, I have recently installed pymol on a friends ibook and it all works fine...but there seems to be no external GUI (as seen on PC and Linux versions). Is it missing on OSX or is my install flawed? It does make it a little easier to use for the novice. Cheers Joel -- Joel Tyndall

[PyMOL] OS-X question

Thanks folks, I did have the hybrid version running but I have now installed the Macpymol version which seems a whole lot easier to install, ie it does it itself! Thanks for your help J -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New

[PyMOL] moving molecules separately

Hi folks, I know the mouse command is out there but I can't seem to find it. I want to move one molecule and not the other (with at least two molecules read in). So I can use it with manual alignment. How do I do it? Cheers J -- Joel Tyndall, PhD Lecturer National School of Pha

[PyMOL] moving molecules separately

! Cheers 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 Fax / Waeawhakaahua +64 3 4797034

[PyMOL] Scene function

't do what its supposed to when you double click on this ie open (or use the hyperlink from powerpoint). It does however work when you open the file from within pymol but doesn't go full screen but opens just like a .pse file. Any suggestions would be helpful. Regards Joel

Re: [PyMOL] Scene function

-Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Joel Tyndall Sent: Monday, May 09, 2005 5:31 PM To: 'PyMOLBB' Subject: [PyMOL] Scene function Hi folks, Firstly the scene functions are really cool and wi

[PyMOL] NMR structures

Hi folks, Hopefully a quick one, How do you display more than one structure (eg all 20 odd) of a pdb ensemble? Cheers Joel -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao

[PyMOL] align/fit

or 1-99 and 101-199). So what I am after is the protein alignment which will align 198 atoms (2 x chain of 99 residues) to give me a pairwise alignment to compare _multiple _structures. Could someone point me in the right direction please. Many thanks Joel -- Joel Tyndall, PhD Lecturer Na

[PyMOL] and another...

So whilst I'm picking your collective brains, how would I set up a superimposition using say 4 different residues usingthe backbones or ca atoms? ie two from each separate chain of the homodimer? Thanks again J -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Ota

Re: [PyMOL] Renumber protein segid

need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id492&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Joel Tyndall, PhD Lecturer Natio

Re: [PyMOL] (no subject)

. Any help, suggestions will be appreciated. Thanks. Regards, Madhavi Kolli Graduate Student UMass Medical School Worcester -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Wha

Re: [PyMOL] Pymol Scenes to Movies

yMOL-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 Pou

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

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] 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

[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] 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

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