[PyMOL] Run pymol from source or compile?

Can one run PyMOL from source (in order to see effects of changes to the source code whenever restarting) or can one only run a compiled version of PyMOL? Are there instructions for running from source? Best regards Martin -- Martin R. Hediger, PhD Mittlere Strasse 65 4056 Basel -

[PyMOL] Current and up to date manual

I found this manual page: http://pymol.sourceforge.net/newman/user/toc.html It says, its ancient and obsolete. Is the wiki the current and up to date manual? Is there a PDF manual anywhere? Many thanks Martin -- Martin R. Hediger, PhD Mit

[PyMOL] What does do_library do?

Hi all I'm trying to understand wizarding better (PyMOL Source code - i think - around 1.7). What does the 'do_library' function do? It seems to be called from every wizard at one point. Thanks, Martin -- Martin R. Hediger, PhD Mittlere Strasse 65 4056 Basel

Re: [PyMOL] Dynamic reloading of plugin

artin, how about: set_key F1, run script.py; function_from_script() Reduces step 3) and 4) to hitting "F1" on the keyboard. Cheers, Thomas On 24 Apr 2016, at 06:36, Martin Hediger wrote: Hi all When working on a PyMOL extension script, my workflow is currently something like this: 1

[PyMOL] Dynamic reloading of plugin

Hi all When working on a PyMOL extension script, my workflow is currently something like this: 1) Start PyMOL 2) Work on script 3) PyMOL> run script.py 4) PyMOL> function_from_script() 5) See if function works, go back to 2) Is it possible to have PyMOL automatically re-run the script everyti

[PyMOL] ccmutate

I found the ccmutate script on the pymol wiki I tried it but I receive a weird error: PyMOL>ccmutate "ALA", resi 112 Traceback (most recent call last): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol/parser.py", line 254, in parse self

Re: [PyMOL] Function signature

m resi 117 or any other more complicated selection syntax without any parentheses. Perhaps I am missing something in your specific requirements? Cheers, Rob On Sun, 2016-04-17 20:18 +0200, Martin Hediger wrote: Dear all In PyMOL, the syntax for eg. zooming in on residue 110 of a protein w

[PyMOL] What does do_library() do?

Hi all I'm trying to understand wizarding better (PyMOL Source code - i think - around 1.7). What does the 'do_library' function do? It seems to be called from every wizard at one point. Thanks, Martin -- Martin R. Hediger, PhD Mittlere Strasse 65 4056 Basel -

[PyMOL] Function signature

Dear all In PyMOL, the syntax for eg. zooming in on residue 110 of a protein would be zoom resi 117 I have a pymol script where I define a function that also zooms in on a residue (it's simple, only to illustrate the point): def zoom_custom(position): cmd.zoom("resi" + " " + str(position)

[PyMOL] What does do_library() do?

Hi all I'm trying to understand wizarding better (PyMOL Source code - i think - around 1.7). What does the 'do_library' function do? It seems to be called from every wizard at one point. Thanks, Martin -- Find and fix

[PyMOL] setting fetch_path fails

Hi all I tried to adjust the 'fetch_path' property such that downloaded PDB files would be saved in os.path.abspath(os.path.join(os.path.curdir, "pdbfiles")) where 'curdir' is $HOME and 'pdbfiles' is within $HOME. However, I get 'fetch-error'. What am I doing wrong? Thanks for help. ---

Re: [PyMOL] Real-time black and white view possible?

, 2014, at 5:10 PM, Martin Hediger mailto:ma@bluewin.ch>> wrote: Hi all I wonder if it's possible to have something like ray_trace_mode, 2 (i.e. black and white with outlines) but in the interactive view. Also, is it possible to have part of the structure in color (say some active

[PyMOL] Real-time black and white view possible?

Hi all I wonder if it's possible to have something like ray_trace_mode, 2 (i.e. black and white with outlines) but in the interactive view. Also, is it possible to have part of the structure in color (say some active site amino acids) and the rest in black and white? Thanks for help Martin --

[PyMOL] Ray trace mode 1 outline thickness

Hi guys I wonder if you could help, I'm rendering this image: http://qmviews.blogspot.ch/2014/05/illustrating-protein-structures.html and I wonder if and how I could increase the thickness of the black outlines? Thanks for help Martin --

Re: [PyMOL] pymol does not free-up the RAM when objects are deleted

It's been a problem for a while, check the thread "[PyMOL] Memory not released after load and delete of structure" froom 2012. Martin On 04.04.14 21:54, Thomas Holder wrote: > Hi Osvaldo, > > you are right, I can reproduce this. We'll look into it and let you know when > it has been fixed. >

[PyMOL] Unbond two atoms

Dear PyMOL users Sometimes PyMOL draws bonds between atoms which are not supposed to be connected. I know it is possible to unbond them using "unbond atom1, atom2", however this requires to always select the atoms and rename the selections to "atom1" and "atom2", respectively. It would be great

Re: [PyMOL] sculpt settings

I describe this in a blog post. Maybe it helps you. http://qmviews.blogspot.ch/2012/01/pymol-005-optimizing-only-part-of.html On 24.04.13 19:21, Osvaldo Martin wrote: Where I can find documentation about the exact meaning of all the settings related to the sculpt function? In particular wh

[PyMOL] Show and hide different sets of measurements

Dear PyMOL users Assume I have two objects loaded in a PyMOL session and in each I'm interested in a specific distance. So in both objects I measure this distance and see it displayed in the viewer. Can I somehow configure the measurement such that when I disable the object, also the correspond

[PyMOL] Display style for partial bond

Dear PyMOL Users If you load these coordinates in PyMOL HETATM1 W LIG 1 -1.357 -0.079 0.052 1.00 0.00 W HETATM2 C LIG 1 -0.713 -1.686 1.008 1.00 0.00 C HETATM3 C LIG 1 -0.323 -1.855 -0.270 1.00 0.00 C HETA

[PyMOL] Increase sphere size for heavy element

Hi PyMOL users If I display these coordinates HETATM 38 C LIG 2 1.535 2.288 -4.156 1.00 0.00 C HETATM 39 C LIG 2 2.284 1.535 -3.066 1.00 0.00 C HETATM 40 O LIG 2 3.406 2.362 -2.714 1.00 0.00 O HETATM 41 C

Re: [PyMOL] Write vector graphics of session

r EPS? > > Cheers, > > -- Jason > > On Sat, Jan 12, 2013 at 6:31 AM, Martin Hediger wrote: >> Hi PyMOL users >> Can PyMOL write a vector based picture of a session? Does not require to >> be very "fancy", but vector based would be cool. Something like

[PyMOL] Write vector graphics of session

Hi PyMOL users Can PyMOL write a vector based picture of a session? Does not require to be very "fancy", but vector based would be cool. Something like in the old days with molscript. Best regards Martin -- Master Visua

Re: [PyMOL] Pymol visualization problem

Hi Abida Is it possible that you have multiple states in your PDB file? Try clicking the ">" arrow in the bottom right corner of PyMOL and see if you can display the other protein. If so, you probably need to delete the "MODEL" and "END" from your PDB file. Then all should appear at once. Mar

[PyMOL] unittest for get_coordinate function

Hi PyMOL users I wonder, what is a most meaningful way of programmatically determining that a line of text in an arbitrary file contains atomic coordinates? The context of this question is that I plan to write a program that reads two files containing coordinates and has to perform operations on

Re: [PyMOL] Memory not released after load and delete of structure

hybrid (I can reach >> 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and >> pymol version 1.5.0.3. >> I had to renounce working with Hybrid unless I really need some plug-in. >> >> Gianluigi >> >> >> Da: Jason Vertree

Re: [PyMOL] Memory not released after load and delete of structure

iterating over structures and deleting > them when done? You sure you're not missing a cleanup step somewhere? > (Any chance we can see the script or a stub of it?) > > Cheers, > > -- Jason > > On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger wrote: >> Hi Jason, >

Re: [PyMOL] Memory not released after load and delete of structure

Hi Jason, I'm using PyMOL 1.3. Best regards Martin On 20.12.12 15:53, Jason Vertrees wrote: > Hi Martin, > > Which version of PyMOL are you using? > > Cheers, > > -- Jason > > On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger wrote: >> Dear PyMOL us

[PyMOL] Memory not released after load and delete of structure

Dear PyMOL users In a directory are PDB files of combined size equal to around 3MB. When I load all files into PyMOL, I observe that the required RAM of PyMOL (MacOS X 10.6) increases by roughly this amount. When I delete all objects, the RAM requirement remains the same and when I then reload a

Re: [PyMOL] problems with mutagenesis wizard II

ng the pymol version 1.5 now. Here > the problem did not appear anymore, but the real cause of the problem I > could not find out... > > Carola > > Am Mittwoch, den 07.11.2012, 11:24 +0100 schrieb Martin Hediger: >> Hi Carola >> What did you try? Does it work when you use

Re: [PyMOL] problems with mutagenesis wizard II

Hi Carola What did you try? Does it work when you use these commands right after starting up PyMOL and before you do any of the steps you take: set retain_order, 0 set pdb_retain_ids Martin On 31.10.12 14:03, Carola Sophie Hengstenberg wrote: > Dear all, > > I recently upgraded to Ubuntu

Re: [PyMOL] Select crystal waters inside protein

vant ). >> >> How I could to select such surrounded water ( e.g via some cutoff >> radius relative my protein etc) wich I'd like to remove further ? > > On 04/25/2012 05:34 PM, Martin Hediger wrote: >> In a crystal structure, there are usually a number of relev

[PyMOL] Parallelize mutation script

Dear PyMOL Users I use the following script to prepare small side chain fragment PDB files of mutants in PyMOL: http://pastebin.com/nDTZApHP I use the PyMOL built-in mutagenesis wizard and the sculpting wizard to locally optimize the side chains within the environment of the protein. For large am

[PyMOL] PyMOL Model player

Dear PyMOL Users Is it possible to let the PyMOL model player go back and forward, instead of jumping from the end to the start, once it reached the last loaded model of an object? Thanks for hints. Martin -- Don't let

[PyMOL] Adding hydrogens

Dear PyMOL list I'm adding hydrogens to a crystal structure. Upon saving, however, I realize all hydrogens have been added to the beginning of the PDB file. Can PyMOL be configured such that the hydrogens are placed at the "intuitively appropriate" place in the PDB file? Thanks for any hints. M

Re: [PyMOL] Use arrows to switch between models

Sweet:) I disabled the animate but I can see its applicability in some situations though (makes it pretty impressive). Definitly a must-have from now on, in fact how could I even live without it;) Martin On 20.09.12 19:38, Tsjerk Wassenaar wrote: > Hi :) > > You can also add > > cmd.disab

[PyMOL] Use arrows to switch between models

Dear PyMOL users Is it possible to somehow assign "page up" or "page down" keys to switch from one loaded model to the next one in the PyMOL models list? This would be useful because I often have several similar models listed and in doing so it would be easier and convenient to identify changes

Re: [PyMOL] Very strange problem

Dear Jason Could you point me out to the Python module where the "reader" is implemented? I would be interested in seeing how PyMOL handles this because I recently had to write something similar. Thanks Martin On 23.07.12 18:19, Jason Vertrees wrote: > Hi Malai, > > Thanks for bringing thi

[PyMOL] Verify PDB format

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

[PyMOL] PyMOL MOPAC format

Dear PyMOL users I'm using MOPAC to do quantum chemical calculations of enzymes. I'm wondering if PyMOL could be used to output a PDB file in MOPAC format. An example of this format is here: C( 1 LEU 24) 9.0450 +0 4.9440 +0 19.4560 +0 0.4527 O(

Re: [PyMOL] Dont resequence atoms when saving

ks, Martin On 13.12.10 16:52, Jason Vertrees wrote: > Hi Martin, > > As you've found, the mutagenesis wizard destroys the ordering in some > cases. I'll look into it. > > Cheers, > > -- Jason > > On Tue, Dec 7, 2010 at 11:34 AM, Martin Hediger wrote: >&g

[PyMOL] Select crystal waters inside protein

Dear List In a crystal structure, there are usually a number of relevant crystal waters, as well as water molecules on the surface. In our approach, we model the protein structure within a dielectric continuum, so surface water molecules are not required (to save computer time). However, waters

[PyMOL] PyMOL Selector

Dear PyMOL List What is the segi-identifier? Thanks for your answer. Martin -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure

Re: [PyMOL] Display technical info about objects

do more recording of properties you choose > ># ask PyMOL to now load the file > >cmd.load(fileName,objName) > > Then you could just query obj_info based on object name: > > for obj in cmd.get_names(): >print obj_info[obj] > > Cheers, > > -- Jason &g

[PyMOL] Display technical info about objects

Dear List I'm frequently loading a number of objects into PyMOL which formally have the same name, but are different in structure. Sometimes it can become a bit difficult to keep track of which object is what. Is there a way to display technical information about a loaded object? Say, the file p

[PyMOL] Context sensitive mutation wizard

Dear PyMOL List I'm frequently using the PyMOL mutagenesis wizard. Consider the mutation of tryptophan to phenylalanin. If the sidechain is mutated from W to F, its reasonable to assume that the plane of the phenyl moiety of F would/should/could/might lie in the same plane as the indol part of t

Re: [PyMOL] RMSD between two structures

t; > x = cmd.align('foo', 'bar', transform=0) > print 'RMSD:', x[0] > > About the "some kind of refinement": There are arguments "cutoff" and > "cycles" that control this behaviour. > > Cheers, > Thomas > >

[PyMOL] Get number of residues in model

Dear List How can I compute the numbers of residues in a model? Martin -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threat

Re: [PyMOL] RMSD between two structures

27;foo', 'bar', transform=0) > print 'RMSD:', x[0] > > About the "some kind of refinement": There are arguments "cutoff" and > "cycles" that control this behaviour. > > Cheers, > Thomas > > On 11/11/2011 02:46 PM,

[PyMOL] Question Iterate

In this example below (from Thomas), the method 'iterate' is used. The function saves every amino acid of a structure to a separate file. First of all, I'm not sure of how to understand the docs: " "iterate" iterates over an expression within a temporary namespace for each atom." What does tem

Re: [PyMOL] creating PDB structure

If you are in the PyMOL Viewer and in Edit mode, you can hit +<{a,g,d,e,...}> to build up a linear polypeptide, where the single letters correspond to the amino acide identifiers. Is this useful to you? Am 23.11.11 11:43, schrieb James Starlight: Dear PyMol Users! I wounder to know ab

Re: [PyMOL] Expose PyMOL API

This would imply that you cannot use MacPyMOL like in the >> "Launching_From_a_Script" examples. Maybe someone of the MacPyMOL users >> knows more? >> >> Cheers, >>Thomas >> >> Martin Hediger wrote, On 11/22/11 13:14: >>> Thanks

[PyMOL] Expose PyMOL API

Dear PyMOL List It comes up once in a while, is it possible to use PyMOL features from outside of PyMOL? An example, the below is a script (inspired by Thomas Holder) which saves down to disk all amino acids of a protein structure into separate PDB files. # *

[PyMOL] RMSD between two structures

Dear List. When aligning two structures using the PyMOL align command, one gets a final RMS value indicating some kind of "convergence" i would say. Can I somehow access the function for calculating this value directly from the pymol prompt without aligning? Thanks for hints Martin ---

[PyMOL] PQR Display in PyMOL

Dear List I have the below model of three charged atoms (as a PQR file). ATOM 1C ASP A 0.0 0.010.0 -2.0 4.0 ATOM 2C ASP A 0.0 0.0 0.0 -2.0 4.0 ATOM 3C ASP A 0.0 0.0 -10.02.0 4.0 The last two numbe

[PyMOL] Saving Issue

Dear List When I try to save an object as a PDB (after editing it slightly with the PyMOL edit mode, i.e. adjusting a dihedral angle), the "Save Molecule" dialog asks to save "all", "global" or "objects current" state. When saving with the last two, I get no coordinates in the generated file onl

Re: [PyMOL] Script for Torsion angles

ne of the tools from the Richardson Lab which allows quick > output of various bond length, angle, torsion and plane measurements. > > -bob > > On Fri, Sep 2, 2011 at 5:48 AM, Martin Hediger wrote: >> Dear List >> Does anyone have a script to calculate torsion angles lying a

[PyMOL] Script for Torsion angles

Dear List Does anyone have a script to calculate torsion angles lying around? Ideally, i would like to be able to enter x1, x2, x3, x4 and get the (smaller) angle between the two normals of the planes defined by x1, x2, x3 and x2, x3, x4, respectively. For some odd reason the measurment wizard i

[PyMOL] Configuration of Player

10-1. Kind regards. Martin Hediger -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shi

Re: [PyMOL] Run script synchronized

E shell=False) propkap.stdout.read() Martin Hediger On 28.08.11 19:24, Troels Emtekær Linnet wrote: Thanks Jason. But still no luck... So, I changed it to a python script. It was important that the ending of the file is .py :-) But, I can see from the list of objects, that P

Re: [PyMOL] Run script synchronized

you may want to check out the Popen class from the subprocess module... hth Martin On 23.08.11 10:48, Troels Emtekær Linnet wrote: Hi. If one writes a pymol script, and calls an external function, the pymol script continues its operation before waiting for the "success" of the external functi

Re: [PyMOL] Interacting with Mutagenesis wizard in command line.

3, 2 RE<http://maps.google.dk/> 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/8/22 Martin Hediger mailto:ma@bluewin.ch>> Hi Troels It's indeed possible. The wizards are available through the cmd module. # Initialize load yourProtein cmd.wiza

Re: [PyMOL] Interacting with Mutagenesis wizard in command line.

Hi Troels It's indeed possible. The wizards are available through the cmd module. # Initialize load yourProtein cmd.wizard("mutagenesis") cmd.do("refresh_wizard") # To get an overview over the wizard API: for i in dir(cmd.get_wizard(): print i # lets mutate residue 104 to GLN cmd.get_wizard().s

Re: [PyMOL] Saving each residue to file

quot;, "byres _tmp") > python end > delete _justca _tmp > > Hope that helps. > > Cheers, > Thomas > > On 08/15/2011 09:14 AM, Martin Hediger wrote: >> Dear List >> I was wondering if there could be a way of having every residue of a >> protei

[PyMOL] Saving each residue to file

Dear List I was wondering if there could be a way of having every residue of a protein structure being saved to a separate file. How could this be done? I believe the 'iterate' method might be useful in combination with the 'byres' identifier, but I havent figured out how to combine them in the

[PyMOL] PyMOL Sculpting Wizard

Dear List Is there any other information about the force field of the sculpting wizard available other than what is on the wiki? Kind regards Martin -- BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA The must-a

[PyMOL] Generating Image of Periodic System

Dear List I am trying to prepare a figure. I have a protein structure, enclosed by a rectangular box. Is it possible to copy/translate the enboxed structure for a given amount of times? This would end up as something as an illustration of a system with periodic boundaries. I attached a figure o

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

: > http://www.rcsb.org/pdb/files/1avd.pdb1 > > The key is adding 1 to the suffix. Sometimes there is more than one > biological unit, in which case, there is a pdb2, pdb3, etc. > > -David > > On May 3, 2011, at 4:00 PM, Martin Hediger wrote: > >> Dear all >>

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

; >> The key is adding 1 to the suffix. Sometimes there is more than one >> biological unit, in which case, there is a pdb2, pdb3, etc. >> >> -David >> >> On May 3, 2011, at 4:00 PM, Martin Hediger wrote: >> >>> Dear all >>> I woul

[PyMOL] Downloading the biological assembly from the PDB

Dear all I would like to ask how it is possible to download the coordinate file for the biological assembly of a protein structure from the PDB. Naturally, this is not a question directly related to PyMOL, but I thought I'll be reaching at least a couple of Biochemists/Chrystallographers who kno

Re: [PyMOL] Get Protein Dimension

eds to be tuned if you need only the first MODEL or > only the first alternate position etc. > > cheers,hongbo > > On 04/26/2011 01:40 PM, Martin Hediger wrote: >> Dear all >> >> I found that PyMOL offer the cmd.get_extent('protein') function, which >>

[PyMOL] Get Protein Dimension

Dear all I found that PyMOL offer the cmd.get_extent('protein') function, which returns the dimensions of the selection. Is it complicated to make this function available from within an ordinary Pythonscript? Thanks for hints. Martin ---

Re: [PyMOL] Display coordinate vectors

.py > > hope it helps, > hongbo > > On 04/08/2011 04:29 PM, Martin Hediger wrote: >> Dear all >> I'm sure this question was answered before, but I could not find >> anything related to it in neither the mail list nor on the Wiki. >> Is it possible to disp

[PyMOL] Display coordinate vectors

]? I would like to illustrate the alignment of the principal axes of a protein with the coordinate system. Kind regards and thank you for answers. Martin Hediger -- Xperia(TM) PLAY It's a major breakthrough. An authen

[PyMOL] Logging the sculpt wizard

Dear List I'm trying to automate the following sequence of steps in a PyMOL python script: 1. Start the mutagenesis wizard 2. Mutate a reside according to an input from the script (some integer to specify the id) 3. "Apply" and close the mutagenesis wizard 4. Start the Sculpt Wizard 5. Fix all co

Re: [PyMOL] Dont resequence atoms when saving

've found, the mutagenesis wizard destroys the ordering in some > cases. I'll look into it. > > Cheers, > > -- Jason > > On Tue, Dec 7, 2010 at 11:34 AM, Martin Hediger wrote: >> Good day >> I use PyMOL to introduce mutations into a structure. It occu

Re: [PyMOL] Adding Hydrogens

name of the residue, so you have to manually cycle the valences. On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger <mailto:ma@bluewin.ch>> wrote: Dear All I would like to ask if the PyMOL function to add hydrogens to an entire protein also has options, meanin

[PyMOL] Adding Hydrogens

Dear All I would like to ask if the PyMOL function to add hydrogens to an entire protein also has options, meaning is it possible to set the protonation state of individual residues specifically? Like in a list or something? h_add, His202:+1 or so? And, it can be relevant at what atom a residue g

Re: [PyMOL] Selecting ASP and GLU

t;> or, if you need parentheses, >>>> >>>> select ((resn GLU) or (resn ASP)) >>>> >>>> >>>> Maybe this will help: >>>> >>>> # fetch a test protein >>>> >>>> fetch 1rsy, async=0 &

Re: [PyMOL] Selecting ASP and GLU

or resn GLU) >> >> >> While the boolean 'and' works, the following will fail to select and >> color any atoms: >> >> color tv_red, (resn ASP and resn GLU) >> >> because there will be no _single atom_ in both an ASP and a GLU. The >> b

Re: [PyMOL] R: Re: Re: labeling by a pseudoatom

Dear all thanks for the feedback. Indeed, after thinking for a second its totally clear why 'select identifyer, (resn asp and resn glu)' returns { }. So, speaking of syntax, '+' is OR and '&' is AND? Thanks again Martin Am 02.03.11 01:35, schrieb rv...@libero.it: > Hi Jason, > sorry for la

[PyMOL] Selecting ASP and GLU

Dear all What is the selection syntax to select all GLU and ASP residues within an object? I'm trying it the way its written on the wiki: remove resn hoh# remove water h_add # add hydrogens as surface color grey90 color slate, resn lys # lysines in light blue color pal

Re: [PyMOL] Plugin Tutorial

t; > zlib.decompress(pdbFile.read()[22:], zlib.MAX_WBITS) > > Downloading in compressed form is much more efficient. But otherwise I > don't think it should give you trouble doing it like that. > > Cheers, > > Tsjerk > > On Wed, Feb 9, 2011 at 1:43 PM, Martin Hediger wrot

[PyMOL] Plugin Tutorial

Dear all I was just working through the Plugin tutorial http://www.pymolwiki.org/index.php/Plugins_Tutorial Writing the plugin from the tutorial as is shown, I happen to receive a gzip error (from the Python Shell): zlib.decompress(pdbFile.read()[22:], -zlib.MAX_WBITS) Traceback (most recent

Re: [PyMOL] Start PyMOL session in web browser

I was thinking of something like a browser plug-in, just as it is available for PowerPoint. We'll see, where it goes. Am 19.12.10 17:06, schrieb Rich: > On 19-12-2010 10:27, Martin Hediger wrote: >> Of course, Jmol is very poweful and I am using it as well for many things. &

Re: [PyMOL] Start PyMOL session in web browser

particularyl helpful. Anyway, the questions remains, how one could run a PyMOL session through a web browser. I will be looking at the input from the previous postings. Am 19.12.10 14:11, schrieb Rich: > On 19-12-2010 7:37, Martin Hediger wrote: >> Dear all >> Is it possible to start

[PyMOL] Start PyMOL session in web browser

Dear all Is it possible to start a PyMOL viewer through a web browser? What I mean by this is, is it possible to view a protein over the internet where the viewing features are provided by some "limited" PyMOL server? The only thing able to do that right now is Jmol, but i think its very inconv

[PyMOL] Orienting protein on surface

Dear all Let protein P be of C1 symmetry, so no symmetry elements. It can be approximated by a cube C, where every face of C has its own value, say 1 to 6. Lets assume, the positive x-direction is coming out of the computer screen, the plane of the screen is the yz plane, the lower left corner

Re: [PyMOL] Dont resequence atoms when saving

PROT H Can this be explained somehow? Thanks for your answers. Martin On 09.11.10 13:26, Jason Vertrees wrote: > Hi Martin, > > set retain_order > set pdb_retain_ids > > Cheers, > > -- Jason > > On Tue, Nov 9, 2010 at 4:30 AM, Martin Hediger wrote: >&

[PyMOL] Increase number of digits in Measurement

Dear all Is it possible to increase the number of digits displayed when measuring the distance between two atoms? Thanks Martin -- The Next 800 Companies to Lead America's Growth: New Video Whitepaper David G. Thomson

[PyMOL] Dont resequence atoms when saving

Dear all It occured to me that PyMOL is resequencing a structure when saving. I am trying to interpolate between two structures where it is critical to have identical sequence in both structures. Is it possible submit a -option to the save command? Thanks for your help Martin -

Re: [PyMOL] Fwd: What is the difference between Atom ID and Index

d of indices. " > > > I suppose you should use>>RANK<<, if you like to "find a way to get the > 'linenumber-dependent' index of an atom". > > cheers, > Hongbo Zhu > > > On 11/01/2010 10:02 AM, Martin Hediger wrote: >> Hi Tsjerk,

Re: [PyMOL] Fwd: What is the difference between Atom ID and Index

an atom. Thanks for your help so far. Martin On 31.10.10 18:31, Tsjerk Wassenaar wrote: Hi Martin, So it seems I was right :D ID is an atomic property, read from the PDB file, whereas index is an 'internal' identifier. Following Jasons comments, ID is not changed upon addition

Re: [PyMOL] Fwd: What is the difference between Atom ID and Index

;6-9") > label *, "%s-%s" % (index,ID) > > Cheers, > > -- Jason > > > > > On Mon, Oct 25, 2010 at 6:49 AM, Tsjerk Wassenaar wrote: >> Never get used to that only-reply-to-sender policy... >> >> >> -- Forwarded mess

Re: [PyMOL] Fwd: What is the difference between Atom ID and Index

Wassenaar wrote: > Never get used to that only-reply-to-sender policy... > > > -- Forwarded message -- > From: Tsjerk Wassenaar > Date: Mon, Oct 25, 2010 at 12:30 PM > Subject: Re: [PyMOL] What is the difference between Atom ID and Index > To: Martin Hedige

[PyMOL] What is the difference between Atom ID and Index

Dear All I'm trying to figure out for myself, what the two labels 'Label > Atom Identifiers > ID' and 'Label > Atom Identifiers > index' mean, or what the respective difference between the two is. For sure, the numerical value is very different when I show the labels in a structure. ID seems to

[PyMOL] Question about Iterate and Edit-Mode

Dear All I am trying to get behind the way 'iterate' works, since I see it quite frequently in PyMOL scripts. The example in the help page is a bit limited in the sense that I cant explain to myself what actually is happening. Say, if I were to write the functionality of 'iterate' using a for-lo

Re: [PyMOL] Mutagenesis How many rotamers per amino acid

resume the UI > cmd.set("suspend_updates",0) > > # write coords > cmd.sculpt_iterate("myProtein") > > #quit sculpting > cmd.unset("sculpting") > > > Load a small protein and call it "myProtein". Then, copy/paste the > above code

Re: [PyMOL] Mutagenesis How many rotamers per amino acid

d.set("sculpting_cycles",100) > > # resume the UI > cmd.set("suspend_updates",0) > > # write coords > cmd.sculpt_iterate("myProtein") > > #quit sculpting > cmd.unset("sculpting") > > > Load a small protein and call it &quo

Re: [PyMOL] Mutagenesis How many rotamers per amino acid

/PMW are very easy to develop with. Good luck! > > Cheers, > > -- Jason > > On Sat, Sep 18, 2010 at 6:48 PM, Martin Hediger wrote: >> This is great. Thanks a lot. >> I am wondering, are there any scripts/ plugins for PyMOL out there that >> facilitate the g

Re: [PyMOL] Mutagenesis How many rotamers per amino acid

_wizard().do_select("("+res+")") >cmd.frame(i) > cmd.get_wizard().apply() >cmd.save("state" + str(i) + ".pdb", cpy) >cmd.delete(cpy) >cmd.create(cpy,org) > > # end the python block > python end > > # quit the wizard &g

  1   2   >