[PyMOL] Molecular surface area

2019-05-19 Thread Andreas Tosstorff
Hi all, I am looking for the method by which the get_area command calculates the molecular surface area when dot_solvent=0. It is described for SASA in the mailing list but I could not find it for the default method. Thanks a lot for your help! Andreas

[PyMOL] Pandas module in Pymol

2018-11-21 Thread Andreas Tosstorff
onda3/lib/python3.6/site-packages/pymol/parsing.py", line 533, in run_file execfile(file,global_ns,local_ns) File "/home/andt88/anaconda3/lib/python3.6/site-packages/pymol/parsing.py", line 528, in execfile exec(co, global_ns, local_ns) File "/home/andt88/Dropbox/PhD

Re: [PyMOL] Pymol 2.1 graphics error

2018-05-11 Thread Andreas Tosstorff
ely, even on a wired local network. On May 9, 2018, at 8:01 PM, Andreas Tosstorff wrote: Hi all, I just installed PyMol 2.1 on my system (Centos 7) and there are some issues with displaying any structures. I get the following error, however I'm not sure whether that's what&#

[PyMOL] Pymol 2.1 graphics error

2018-05-09 Thread Andreas Tosstorff
)   GL_VERSION:  3.0 Mesa 17.0.1 GL_ERROR : 1282" I'm new to Pymol and Linux so please excuse me if I'm missing something. Thanks, Andy -- M.Sc. Andreas Tosstorff Lehrstuhl für Pharmazeutische Technologie und Biopharmazie Department Pharmazie LMU München Butenandtstr. 5-13 ( Haus B)

Re: [PyMOL] Enable selected atoms of disabled object

2017-06-19 Thread Andreas Warnecke
Hej, a disabled object will not show any display, but you can easily work with selections, provided that a selection is defined. Try something like: hide everything object show sticks selection Cheers, Andreas On Jun 19, 2017 6:00 AM, "Vijay Masand" wrote: > Dear All, >

Re: [PyMOL] PyTMs

2017-04-12 Thread Andreas Warnecke
Hej Raag, my name is Andreas and I wrote PyTMs back for my PhD. It essentially uses PyMOLs basic editing functions to build PTMs onto protein models. PyTMs is a simple tool and has its clear restrictions, but generally it is nice to play around with and explore hypotheses with. The challenge is

Re: [PyMOL] PyMOL for iPad issues

2017-02-28 Thread Andreas Forster
Dear João, type set grid_mode, on to see your models side by side. You might have to align them first. Use the command super model1, model2 for that. All best. Andreas On Tue, Feb 28, 2017 at 5:27 PM, João Oliveira Jr. wrote: > Hi > > Please, when using PyMOL app for iPa

Re: [PyMOL] Coordinates of an atom

2016-12-01 Thread Andreas Forster
Dear Mohsen, when I Google "pymol coordinates atom", the top hit is this: https://pymolwiki.org/index.php/Get_Coordinates_I Worth a try. All best. Andreas On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi all, > > >

Re: [PyMOL] Coordinates of an atom

2016-12-01 Thread Andreas Warnecke
Hej, try this command and specify the atom selection: cmd.get_atom_coords('atom selection') see also: https://pymolwiki.org/index.php/Get_Coordinates_I Cheers, Andreas On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi all, > &

Re: [PyMOL] Detecting holes/cavities in surface

2016-07-19 Thread Andreas Warnecke
I haven't used it before, but I there is a PyMOL plugin called KVfinder that detects cavities. Potentially this offers an approach for you. On Jul 20, 2016 12:05 AM, "Daniel James" wrote: > Hi all, > > I haven't used this list before but can't find an answer to my question > elsewhere. I am selec

Re: [PyMOL] Selective valency on bond

2016-06-14 Thread Andreas Warnecke
The easiest way to deal with this is setting the valence or valence_mode individually for the object. set valence, 0, object1 set valence, 1, object2 Cheers, Andreas On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick wrote: > Dear PyMol users, > > I have a crystal structure of m

[PyMOL] Electrostatic Map for a molecule containing a citrulline

2016-02-25 Thread Andreas Warnecke
Dear all, a colleague is interested in generating an electrostatic map of a protein containing a citrulline. Does anybody have any experience with this and could recommend any approach? Cheers, Andreas -- Site24x7 APM

Re: [PyMOL] on PDB

2015-11-25 Thread Andreas Forster
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures Andreas On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu wrote: > Dear Shane, > > get_view is a nice command. Is any way to change the original PDB based on > what we get by set_view to get the new pdb? > > Smit

Re: [PyMOL] Pymol for inorganic chemists - dealing with bonds

2015-11-20 Thread Andreas Warnecke
er by "dash"). Hope this may help, otherwise there may be other approaches, Cheers, Andreas On Thu, Nov 19, 2015 at 3:54 PM, Henrique C. S. Junior < henrique...@gmail.com> wrote: > Dear Pymol users, > As an inorganic chemist, to represent metallic centers and ligands

Re: [PyMOL] on using pymol scripts

2015-11-19 Thread Andreas Forster
that. To download the script from the PyMOL website, you'll have to modify the address above accordingly. All best. Andreas On Thu, Nov 19, 2015 at 9:02 AM, Smith Liu wrote: > Dear All, > > If I want to use a pymol script, for example the script on centroid, will > you plea

Re: [PyMOL] APBS problem

2015-10-08 Thread Andreas Forster
ak reading http://www.catb.org/~esr/faqs/smart-questions.html and then ask better question. The answer to your problem: /tmp/1-PE0.dx needs to be generated. That's all I can infer from the information you gave. All best. Andreas On Thu, Oct 8, 2015 at 4:30 PM, Albert wrote: > Hello: >

Re: [PyMOL] Viewing Electrostatic Potential maps for multimeric complexes

2015-06-08 Thread Andreas Warnecke
You could try to split the states and subunits in PyMOL, then save them as individual .pdb's and then use those to generate multuple .dx files. On Jun 8, 2015 2:38 AM, "Rahul Sheth" wrote: > Hello, > > I am new to using PyMol. I wanted to see the electrostatic potential map > for a multimeric pro

Re: [PyMOL] Printing Protein Surface residues

2015-05-22 Thread Andreas Warnecke
le to run both lines sequentually, but usually one doesn't care for the heteroatoms. This is just to avoid potential influences by surrounding waters, or other stuff. Cheers, Andreas On Thu, May 21, 2015 at 1:27 PM, Andreas Warnecke < 4ndreas.warne...@gmail.com> wrote: > Hej, &g

Re: [PyMOL] Printing Protein Surface residues

2015-05-21 Thread Andreas Warnecke
rint 'MODEL', 'CHAIN', 'RESN', 'RESI', 'NAME', 'AREA' cmd.iterate('all', 'print model, chain, resn, resi, name, alt, b') Then, in EXCEL you can use the data (sort/filter) to figure out which atoms are most exposed

Re: [PyMOL] Pymol wiki search is not working

2015-02-04 Thread Andreas Warnecke
Hej, While its not perfect I usually end up using google search and adding 'pymol wiki' to the search terms. Works for me. Cheers, Andreas On Feb 4, 2015 2:50 PM, "Matthew Baumgartner" wrote: > Yes, I've been having this problem for a while. > I contacted Jaso

Re: [PyMOL] Phosphoserine

2015-01-30 Thread Andreas Warnecke
Hi Monica, You can check out the plugin PyTMs, which allows you to introduce PTMs into protein models within PyMOL: http://www.pymolwiki.org/index.php/Pytms Let me know should you need any assistance with this plugin. Cheers, Andreas On Fri, Jan 30, 2015 at 4:59 PM, Monica Mittal wrote

Re: [PyMOL] ray trace mode 1 playing up pymol 1.7.4?

2014-12-16 Thread Andreas Warnecke
Hi, This may also be related to the setting: ray_trace_mode Try: set ray_trace_mode, 0 This will deactivate outlines (ray_trace_color) during ray tracing. The wiki page has some examples. Cheers, Andreas On Dec 16, 2014 6:05 PM, "H. Adam Steinberg" wrote: > The thickness, or

Re: [PyMOL] selection of a set of amino acids

2014-12-13 Thread Andreas Warnecke
to simply adjust the coloring command according to the pdb. Hope that helps, Andreas On Dec 13, 2014 4:41 PM, "Alireza Kashani" wrote: > Dear All, > > I would like to colour different regions of a protein in different colour; > say region one, amino acid number 1 to 100 and re

Re: [PyMOL] Goodsell colouring

2014-12-05 Thread Andreas Förster
Hi Jacob, color light_shade1, e. c and (c;a,c,e) color light_shade2, e. c and (c;b,d,f) Replace light_shade1 and light_shade2 with the actual colors you want to use. Andreas On 05/12/2014 12:24, Jacob Lewis wrote: > Hi, > > I am trying to colour a protein which is a hexamer

Re: [PyMOL] Goodsell colouring

2014-12-05 Thread Andreas Warnecke
g and selection algebra for reference. Hope this helps, Andreas On Dec 5, 2014 3:00 PM, "Jacob Lewis" wrote: > Hi, > > I am trying to colour a protein which is a hexamer using the “goodsell” > colouring method where by carbons are a light shade and all other atoms are >

[PyMOL] svn compile error

2014-12-04 Thread Andreas Förster
Dear all, with the latest svn source, I get the following compiler error: layer3/Executive.cpp: In function ‘void ExecutiveFullScreen(PyMOLGlobals*, int)’: layer3/Executive.cpp:13998: error: ‘glutLeaveFullScreen’ was not declared in this scope (RHEL 6.3 64-bit) Andreas

Re: [PyMOL] How to build imedazole by using builder

2014-11-21 Thread Andreas Warnecke
concerning double bonds etc. Cheers, Andreas On Sat, Nov 15, 2014 at 2:32 PM, Osvaldo Martin wrote: > Hi Surya, > > I don't know exactly what problem are you experiencing (I tried to do > something similar without any problem). I guess that maybe the problem is > that when you ar

Re: [PyMOL] set size nb_spheres

2014-11-21 Thread Andreas Warnecke
Cheers, Andreas On Thu, Nov 20, 2014 at 3:41 PM, Matthew Baumgartner wrote: > Hi, > Just to chime in, you might need to call 'sort' and/or 'rebuild' after > using the alter command to see the changes. > Matt Baumgartner > > > On 11/20/2014 08:20 AM, Os

Re: [PyMOL] Fast mmCIF loading in latest Open-Source updates

2014-10-16 Thread Andreas Förster
Hi Thomas, I assume components.cif is the same file that I've just downloaded for LigPlot+. Would it be possible that PyMOL automatically finds this file, say by reading $compcif or some such variable? Thanks. Andreas On 16/10/2014 10:08, Thomas Holder wrote: > Dear all, > &g

[PyMOL] 21th Tcl Conference - Registration & Hotel Reminder

2014-10-14 Thread Andreas Kupries
for a room, call 1-503-796-3851, speak to Mary Kirchner and mention the Tcl Conference to receive the reduced rate. See you in Portland, Andreas Kupries Tcl 2014 Program Chair ActiveState Software Inc. Vancouver,

Re: [PyMOL] CONECT table

2014-10-07 Thread Andreas Warnecke
Oh, and it should be glucoasn, of course. :-P On Oct 8, 2014 1:26 AM, "Andreas Warnecke" <4ndreas.warne...@gmail.com> wrote: > Hi, > > It appears that the following: > Select gluco, bound_to resn NDG > Show sticks, gluco > > does not work. I'm not

Re: [PyMOL] CONECT table

2014-10-07 Thread Andreas Warnecke
ction algebra on the Pymol wiki that may give more inspiration. Hope this gets you started, /Andreas On Oct 7, 2014 10:02 PM, "Markus Heller" wrote: > D'uh. Thanks for pointing this out. > > Follow-up question: I want to show my glycosylated protein as cartoon, > with the

Re: [PyMOL] Testing for incentive vs. open-source in scripts

2014-10-03 Thread Andreas Warnecke
he output and simply not print it. Thanks for pointing this out, Andreas On Fri, Oct 3, 2014 at 3:18 PM, Gianluca Santoni wrote: > I get this output from cmd.get_version > > Open pymol: > > version: 1.7.0.0 (1.700) 1700, Open-Source > > Incentive pymol: > version: 1.7 (1.70

Re: [PyMOL] Testing for incentive vs. open-source in scripts

2014-10-03 Thread Andreas Warnecke
;) # longer command omitted here - error usually printed here sys.stdout = originalstdout # reinstate the output except: pass Thanks for the suggestions, Andreas On Fri, Oct 3, 2014 at 2:59 PM, Gianluca Santoni wrote: > Version number is printed in the startup message, so it has to be

[PyMOL] Testing for incentive vs. open-source in scripts

2014-10-03 Thread Andreas Warnecke
#x27;if' statement instead and avoid the error message. I would welcome suggestions on how to approach this. Thanks, Andreas -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0

[PyMOL] symexp eats chain ID

2014-09-09 Thread Andreas Förster
to chain (null). What's up with this? PyMOL 1.7.3.0 on RHEL 6.3 64-bit installed from cvs 9/9/14. Thanks. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Impe

Re: [PyMOL] drawing arows, CONE cgo doesn't work.

2014-08-25 Thread Andreas Warnecke
3,0],[0,0,3]]) # then we load it into PyMOLcmd.load_cgo(obj,'axes') python end OR you can enter the lines/ copy paste sequentially. If you are interested in arrows/ cones, have a look at the cgo_arrow script: http://www.pymolwiki.org/index.php/Cgo_arrow Hope this helps. Cheers, And

Re: [PyMOL] Hbonds in grid mode

2014-08-21 Thread Andreas Warnecke
Hej, The reason for this happening is that the distances are a separate object. What you are looking for is grid_slot. Simply assign the distance and protein objects to the same slot. http://www.pymolwiki.org/index.php/Grid_mode http://www.pymolwiki.org/index.php/Grid_slot Cheers, Andreas On

Re: [PyMOL] Coloring of helices

2014-08-21 Thread Andreas Warnecke
how sticks, V27 # shows the residue as sticks (including CA) color green, all # base color color red, V27 and not CA # colors the residue red (excluding the CA) Hope this solves the issue. Cheers, Andreas On Fri, Aug 22, 2014 at 12:33 AM, Markus Heller wrote: > Hi all, > > I'

[PyMOL] 2nd Call For Papers, 21th Annual Tcl/Tk Conference 2014

2014-08-12 Thread Andreas Kupries
eral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Brian Griffin Mentor GraphicsSite/Facilities Chair Arjen MarkusDeltares Cyndy Lilagan Nat. Museum of Health & Medicine, Chicago Donal Fellows

Re: [PyMOL] Fwd: color by RMSF or RMSD

2014-07-23 Thread Andreas Warnecke
olwiki.org/index.php/Split_states Hope this helps out. Cheers, Andreas On Wed, Jul 23, 2014 at 1:09 PM, Nidhi Jatana wrote: > > Dear Sir/Madam > I have generated five models for a protein and I wanted to check how the > models align to each other and color them by RMSD/RMSF. I wanted to

Re: [PyMOL] directing output of "print"

2014-07-23 Thread Andreas Warnecke
alt, b))') f=open('report.txt','w') for x in stored.b_load: f.write(x+"\n") f.close() python end # The report is comma separated and good for EXCEL import. Hope this helps you out. Cheers, Andreas On Wed, Jul 23, 2014 at 12:48 PM, Harry Mark Greenblat

Re: [PyMOL] Faster installation of plugins during development

2014-07-18 Thread Andreas Warnecke
file. So be sure to backup your script should you decide to remove scripts or paths that were added to the Plugin Manager. Hope this will relieve some of the frustration. Cheers, Andreas On Fri, Jul 18, 2014 at 5:41 PM, Matthew Baumgartner wrote: > Hi, > So i am working on a pymol p

Re: [PyMOL] Iterating through states of a topology object (trajectories) and writing out a distance

2014-07-17 Thread Andreas Warnecke
dis, numarray[i])) # format using %f syntax, %.3f gives you 3 digits f.close() If you want to go through the states of the object you can use a loop: for state in range(1, cmd.count_states('topo')+1): cmd.set('state', state, 'topo') # and so on Hope this

[PyMOL] Fwd: Re: How to show atom index or atom serial when clicking on an atom?

2014-07-13 Thread Andreas Warnecke
-- Forwarded message -- From: "Andreas Warnecke" <4ndreas.warne...@gmail.com> Date: Jul 14, 2014 1:03 AM Subject: Re: [PyMOL] How to show atom index or atom serial when clicking on an atom? To: "Jose Borreguero" Cc: minor amendment, changin the iterate

Re: [PyMOL] How to show atom index or atom serial when clicking on an atom?

2014-07-13 Thread Andreas Warnecke
get_resi_macro_name\n#")) python end print get_macro_name('resi 1 and name CA') # example Hope this helps, Andreas On Mon, Jul 14, 2014 at 12:28 AM, Jose Borreguero wrote: > Dear pymol users, > > When I click in an atom (mouse-

Re: [PyMOL] Aligning multiple residue sets in two or more proteins

2014-07-02 Thread Andreas Warnecke
Hi Monica, I haven't tested, but maybe you could try: align PDB1 and (resi 80-120 or resi 160-220), PDB2 and (resi 80-120 or resi 160-220) I.e. expanding the selection to both streches. Running sequential alignments will replace existing ones. How this may help. /Andreas On Jul 2, 2014 1:

Re: [PyMOL] side chain helper glycine

2014-06-23 Thread Andreas Warnecke
w the cartoon plus non-main chain atoms. Hope that works, /Andreas On Mon, Jun 23, 2014 at 8:13 PM, Christian Roth < christian.r...@bbz.uni-leipzig.de> wrote: > Hi there, > > I used the side chain helper option to create a binding site in the > protein. However I want i

Re: [PyMOL] Set fullscreen and grid mode in batch script

2014-06-19 Thread Andreas Warnecke
nd line option '-e' should make pymol start in fullscreen this will probably not work with '-c', but you can open your script from another shortcut. http://www.pymolwiki.org/index.php/Command_Line_Options Hope this helps, /Andreas On Thu, Jun 19, 2014 at 5:33 AM, J.R. W w

Re: [PyMOL] command question RE printing out distances to text file

2014-06-17 Thread Andreas Warnecke
name CB','chain A and resi 17 and name CB') dst2=cmd.distance('chain B and resi 297 and name CB','chain A and resi 18 and name CB') dst3=cmd.distance('chain B and resi 297 and name CB','chain A and resi 19 and name CB') # and then for writing t

Re: [PyMOL] command question RE printing out distances to text file

2014-06-17 Thread Andreas Warnecke
.write("%8.3f\n"%dst2) f.write("%8.3f\n"%dst3) inserting these blocks in your script hopefully will do the trick. Cheers, Andreas On Tue, Jun 17, 2014 at 8:21 PM, Lapolla, Suzanne M (HSC) < suzanne-lapo...@ouhsc.edu> wrote: > Another follow up question to this.

[PyMOL] 1st Call For Papers, 21th Annual Tcl/Tk Conference 2014

2014-05-01 Thread Andreas Kupries
events in general, subscribe to the tcl-announce list. See: http://code.activestate.com/lists/tcl-announce to subscribe to the tcl-announce mailing list. Conference Committee Clif Flynt Noumena Corp General Chair, Website Admin Andreas Kupries ActiveState So

[PyMOL] pymol svn

2014-04-30 Thread Andreas Förster
Dear all, trying to update PyMOL with the usual svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol I get an "svn: Network connection closed unexpectedly" error. This is on two different computers/OSs. Has anything changed? Thanks. Andreas -- Andre

Re: [PyMOL] Ligand - binding

2013-11-14 Thread Andreas Förster
t you know the structure of your protein. If you don't have that, Phyre can quickly show if (and how much) your protein is similar to known creatine binding proteins. Best. Andreas On 14/11/2013 10:40, Michel Bielecki wrote: > Hey guys, > > I was wondering if someone could give

[PyMOL] cylindrical helices

2013-11-01 Thread Andreas Förster
helices, and in perpendicular orientations. Best regards. Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial

[PyMOL] John Ousterhout Featured Speaker at Tcl New & Proven User Conference in New Orleans (Tcl'2013)

2013-08-18 Thread Andreas Kupries
Founder of Tool Command Language to talk about Tcl Past, Present & Future Ann Arbor, MI -- August 16, 2013 -- The Tcl/Tk User Association, which is celebrating over 20 years of innovation using the Tool Command Language (Tcl), confirmed today that John Ousterhout will be a Featured Speaker at the

[PyMOL] Hotel Room Rate Reminder - 20th Annual Tcl/Tk Conference (Tcl'2013)

2013-08-13 Thread Andreas Kupries
that page. Our schedule can be found at http://www.tcl.tk/community/tcl2013/schedule.html Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Gerald Lester

[PyMOL] Registration Open for 19th Annual Tcl/Tk Conference (Tcl'2012)

2013-08-06 Thread Andreas Kupries
edule.html Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Nat. Museum of Health & Medicine, Chicago Site/Fa

[PyMOL] pymol fails to compile

2013-07-23 Thread Andreas Förster
Dear all, following up on my previous post, pymol-v1.6.0.0.tar.bz2 from http://sourceforge.net/projects/pymol/ compiles just fine on my machine. It's the most recent source from svn that doesn't. Andreas -- Andreas Förster Crystallization and Xra

[PyMOL] pymol fails to compile

2013-07-23 Thread Andreas Förster
Dear all, I'm installing PyMOL from svn on a RHEL 6.2 machine. This has always worked. Today, I get an "command 'gcc' failed with exit status 1" error (see below). Any suggestions? Is there something amiss with the source? Thanks. Andreas gcc -pthread -fno-str

[PyMOL] 3rd Call For Papers, 20th Annual Tcl/Tk Conference 2013

2013-06-05 Thread Andreas Kupries
See: http://code.activestate.com/lists/tcl-announce to subscribe to the tcl-announce mailing list. Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Gerald Lester

Re: [PyMOL] Show and hide different sets of measurements

2013-05-03 Thread Andreas Förster
Use the group command: group nameOfGroup, object1 distance1 (disclaimer: I haven't tried this) Andreas On 03/05/2013 1:20, Martin Hediger wrote: > Dear PyMOL users > > Assume I have two objects loaded in a PyMOL session and in each I'm > interested in a specifi

[PyMOL] 2nd Call For Papers, 20th Annual Tcl/Tk Conference 2013

2013-04-09 Thread Andreas Kupries
ounce list. See: http://code.activestate.com/lists/tcl-announce to subscribe to the tcl-announce mailing list. Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Ger

Re: [PyMOL] Splitting a PDB file into its constituent chains, and making multiple (smaller) PDB files

2013-04-04 Thread Andreas Förster
Hi Anasuya, load 1a55.pdb create 1a55_P, 1a55 and c. P create 1a55_Q, 1a55 and c. Q create 1a55_R, 1a55 and c. R save 1a55_P.pdb, 1a55_P save 1a55_Q.pdb, 1a55_Q save 1a55_R.pdb, 1a55_R Andreas On 04/04/2013 11:19, Anasuya Dighe wrote: > Hello, > > I wanted to know if its possible in

[PyMOL] 1st Call For Papers, 19th Annual Tcl/Tk Conference 2012

2013-02-04 Thread Andreas Kupries
Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Gerald Lester KnG Consulting, LLC Site/Facilities Chair Arjen MarkusDeltares Brian Griffin Mentor Graphics Cyn

Re: [PyMOL] apbs2 plugin failure

2013-01-22 Thread Andreas Förster
Did I say thanks? It seems I was using an older version of the plugin. The one downloaded just now works fine. Thanks! Andreas On 10/01/2013 9:18, Troels Emtekær Linnet wrote: > Hi Andreas. > > The line: > /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py > &

[PyMOL] apbs2 plugin failure

2013-01-03 Thread Andreas Förster
renced before assignment When I chose "User PyMOL generated PQR and PyMOL generated Hydrogens and termini" or "User PyMOL generated PQR and existing hydrogens and termini", I can set the grid, run APBS and visualize the result just fine. I'm happy with that, but maybe som

[PyMOL] Hotel Room Rate Reminder - 19th Annual Tcl/Tk Conference (Tcl'2012)

2012-10-15 Thread Andreas Kupries
Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Nat. Museum of Health & Medicine, Chicago Site/Facilities Chair Arjen MarkusDeltares Bria

[PyMOL] Registration Open for 19th Annual Tcl/Tk Conference (Tcl'2012)

2012-09-10 Thread Andreas Kupries
community/tcl2012/schedule.html Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Nat. Museum of Health & Medicine

[PyMOL] 3rd Call For Papers, 19th Annual Tcl/Tk Conference 2012

2012-08-07 Thread Andreas Kupries
-announce mailing list. Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Nat. Museum of Health & Medicine

[PyMOL] 2nd Call For Papers, 19th Annual Tcl/Tk Conference 2012

2012-05-30 Thread Andreas Kupries
e tcl-announce list. See: http://code.activestate.com/lists/tcl-announce to subscribe to the tcl-announce mailing list. Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Softwar

[PyMOL] 1st Call For Papers, 19th Annual Tcl/Tk Conference 2012

2012-04-02 Thread Andreas Kupries
e tcl-announce mailing list. Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Nat. Museum of Health & Medicine

Re: [PyMOL] Isstall on CentOS 6

2012-02-24 Thread Andreas Förster
Hi Yuri, I'd say yes. It runs under RHEL 6.2. In contrast to what was officially said, there is no requirement for python 2.7. Version 2.6.6 works fine. Andreas On 24/02/2012 4:12, Yuri wrote: > Hello everyone, > Does the latest free Pymolv1.5.0.1 from sourceforge run

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-05 Thread Andreas Förster
show their age. Andreas On 05/12/2011 1:50, grantaka36 wrote: > Hi, Marius, Troels and David, > > I appreciate very much for guiding, tried in three ways but no success > currently. > > - I also think some difference on distributions (CentOS 5 here,) trapped at >> f

Re: [PyMOL] Visualise molecules to scale?

2011-10-20 Thread Andreas Förster
Hi Daniel, grid_mode is your friend to display different molecules side by side and to scale. set grid_mode, on Andreas On 20/10/2011 9:51, Daniel Lundin wrote: > Hi, > > I'm quite new to Pymol, but have searched and found nothing on how to > visualise and draw a mole

Re: [PyMOL] distance bug

2011-09-29 Thread Andreas Förster
Ah, indeed, the latest revision 3969 has a correctly working distance command. Thanks Jason. Andreas On 29/09/2011 3:08, Jason Vertrees wrote: > Hi Andreas, > > It was a bug with the invalidation system. I just pushed a fix to source > forge. > > Thanks for bringing thi

Re: [PyMOL] Mutagenesis script

2011-09-03 Thread Andreas Förster
Dear Rozaimi, I'm sure people would bother to read your script and reply to your question if you told us what your trying to achieve and what "not working properly" looks like. Otherwise your wasting your time. Andreas On 02/09/2011 4:58, Rozaimi Razali wrote: > Can some

[PyMOL] 3rd Call For Papers, 18th Annual Tcl/Tk Conference 2011

2011-08-05 Thread Andreas Kupries
l/ to subscribe to the tcl-announce mailing list. Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Iomas Research, LLC Brian Griffin M

Re: [PyMOL] PYMOL MOVIE

2011-07-10 Thread Andreas Förster
(pymol -qc script.py). This will be much quicker. Assemble the png files into a movie with Quicktime Pro or Adobe Premier or mencoder (see PyMOL Wiki). Andreas On 10/07/2011 6:18, Babban Mia wrote: > Thanks a lot Andrea and Michael > > So this would align/super impose all the other p

Re: [PyMOL] PYMOL MOVIE

2011-07-10 Thread Andreas Förster
one structure onto another. Hope that helps. Andreas On 10/07/2011 12:05, Babban Mia wrote: > Hello Everyone > > I have got a doubt relating to making PYMOL MOVIE. > I have like 10,000 PDBs named x_1.pdb .x_23.pdb and so on > > I want to make a movie which essentially

Re: [PyMOL] Delete frames in movie

2011-07-10 Thread Andreas Förster
Mac, which also has its own movie editor that comes with the breathtaking marketing praise of any Apple product. Andreas On 09/07/2011 9:32, Matthias Schmidt wrote: > Hi, > > I made a nice movie and it's fine and I would just like to delete a > part of it or to insert some fr

[PyMOL] 2nd Call For Papers, 18th Annual Tcl/Tk Conference 2011

2011-06-17 Thread Andreas Kupries
ounce list. See: http://aspn.activestate.com/ASPN/Mail/ to subscribe to the tcl-announce mailing list. Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan

Re: [PyMOL] problems cloring sticks

2011-06-09 Thread Andreas Spitzmüller
new version, though ;) Before, I was using pymol 1.2r1 from the Ubuntu repository and I always had the coloring problem. So, thank you very much for solving it! Andreas Am 09.06.2011, 09:58 Uhr, schrieb Gianluigi Caltabiano : > With Ubuntu 10.04 LTS - Lucid Lynx and Pymol 1.4.1 it seems

Re: [PyMOL] problems cloring sticks

2011-06-05 Thread Andreas Spitzmüller
bug. I know that this is for sure not convenient, but still it is possible to make figures for publication or presentation slides. Just try the 'ray' command to see if this yields correct coloring for you, too. Regards, Andreas Am 05.06.2011, 08:29 Uhr, schrieb Ariel Talavera :

[PyMOL] installation from cvs fails

2011-05-12 Thread Andreas Förster
y build [some compiling, then error message] In file included from layer0/Block.c:19: layer0/os_gl.h:30:20: error: GL/glew.h: No such file or directory error: command 'gcc' failed with exit status 1 Is that an issue with the source, with my computer, or potentially with both (upgrade to 1

[PyMOL] 1st Call For Papers, 18th Annual Tcl/Tk Conference 2011

2011-04-11 Thread Andreas Kupries
Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Iomas Research, LLC Brian Griffin Mentor Graphics Ron Fox NSCL/FRIB Michigan State University Arjen MarkusDeltares Mike Doyle

[PyMOL] Newline character in labels

2011-03-29 Thread Andreas Spitzmüller
36.2 However, I cannot get the line break into the label! Is there any possibility? I tried things like \n or unicode encoding u"\u000a" in combination with a unicode font (label_font_id 15). But I couldn't manage to get the label on two lines. Thanks for any hints! Andreas PS: P

Re: [PyMOL] Pymol no longer fetches from pdb

2011-03-22 Thread Andreas Prlic
Hi Roger, Just to clarify, for the FTP protocol the correct prefix is ftp://ftp.wwpdb.org/ and NOT http://ftp ... Hope that makes sense, Andreas On Tue, Mar 22, 2011 at 9:54 AM, Jason Vertrees wrote: > Great, thanks, David.  Just ensuring the problems been isolated. > &g

Re: [PyMOL] Pymol no longer fetches from pdb

2011-03-22 Thread Andreas Prlic
Hi Jason, Can you clarify what URL is being used to download the files from RCSB PDB? I don't think that there was any change regarding those last year. Andreas On Tue, Mar 22, 2011 at 9:02 AM, Jason Vertrees wrote: > Hi Roger, > >> Has anyone else noticed that Pymol (v 1.

Re: [PyMOL] No PowerPC / Universal builds of 1.3?

2011-02-11 Thread Andreas Förster
Dear Francis, PPC was actually phased out in 2005. Here's Apple's original announcement: http://www.apple.com/pr/library/2005/jun/06intel.html Andreas On 11/02/2011 5:52, Francis E Reyes wrote: > Hi all, > > > Has PPC been phased out? (or has been for a long

Re: [PyMOL] viewing axis

2010-09-30 Thread Andreas Förster
When I type 'axes' into the search window at the PyMOL wiki, I get the following ONE hit: http://pymolwiki.org/index.php/Axes Try it! It might just be what you're looking for. Andreas On 30/09/2010 10:28, Chandan Choudhury wrote: > Dear PyMOL users, > Is it possible t

[PyMOL] Register For The 17th Annual Tcl/Tk Conference 2010

2010-09-09 Thread Andreas Kupries
ommittee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Iomas Research, LLC Facilities Coordination Brian Griffin Mentor Graphics Ron Fox

Re: [PyMOL] Fetch Command

2010-08-06 Thread Andreas Forster
Fetching different biological units is cool. But can I query the pdb through PyMOL to see what biological units are associated with a pdb? (Could look it up directly, but I like one-stop shopping.) Thanks. Andreas On Fri, Aug 6, 2010 at 4:14 PM, Jason Vertrees wrote: > Hi David, > &g

[PyMOL] 3rd Call For Papers, 17th Annual Tcl/Tk Conference 2010

2010-07-20 Thread Andreas Kupries
nsights he had for “Seven Brides for Seven Brothers”, we knew we would have a great show for the holidays. Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lil

[PyMOL] 2 Call For Papers, 17th Annual Tcl/Tk Conference 2010

2010-06-28 Thread Andreas Kupries
neral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Iomas Research, LLC Facilities Coordination Brian Griffin Mentor Graphics Ron Fox NSCL/FRIB Michigan State University Arjen Markus

[PyMOL] spheres representation

2010-06-16 Thread Andreas Förster
em will go away, but I'm curious if anyone else sees that too. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://w

Re: [PyMOL] Pymol 64-bits MacOSX

2010-04-09 Thread Andreas Förster
/index.php/64-bit_Fink_for_10.6 Andreas On 09/04/2010 4:22, Lucas Santos wrote: > Hi there, > > I have been facing some memory problems with macpymol 32-bits lately. When I > try to ray a couple of big images my pymol crashes (malloc error), issue that > could be easily fixed just by

[PyMOL] 1st Call For Papers, 17th Annual Tcl/Tk Conference 2010

2010-03-22 Thread Andreas Kupries
CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Cyndy Lilagan Iomas Research, LLC Facilities Coordination Brian Griffin Mentor Graphics Ron Fox NSCL/FRIB Michigan State University

Re: [PyMOL] Showing electric field lines

2010-02-15 Thread Andreas Förster
ys 'Could not find pymol-generated.dx so searching for pymol-generated-PE0.dx.') The field lines can be visualized as described by Michael. Andreas On 15/02/2010 10:42, Alan wrote: > Dear Michael, > > I am using Pymol 1.2r3pre and APBS 1.2, all installed via FINK in my Mac >

Re: [PyMOL] superimpose option

2009-12-08 Thread Andreas Prlic
Just to quickly add... probably the easiest way to run CE at the present might be through the new protein comparison tool at RCSB-PDB web site: http://www.rcsb.org/pdb/workbench/workbench.do Andreas On Tue, Dec 8, 2009 at 8:12 AM, Michael Zimmermann wrote: > Dr. Vertrees, thank you for

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