[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

[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

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 <ma@bluewin.ch> wrote: Hi all When working on a PyMOL extension script, my workflow is currently somethin

[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

Re: [PyMOL] Function signature

i 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 <ma@bluewin.ch> wrote: Dear all In PyMOL, the syntax for eg. zooming in on resid

[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" + " " +

[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

[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.

[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

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

, 2014, at 5:10 PM, Martin Hediger ma@bluewin.ch 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

[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.

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

[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

[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

Re: [PyMOL] Write vector graphics of session

On Sat, Jan 12, 2013 at 6:31 AM, Martin Hediger ma@bluewin.ch 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 in the old days with molscript. Best regards Martin

[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 Visual

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. Martin

[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

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

). 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 Vertrees jason.vertr...@schrodinger.com A: Martin Hediger ma@bluewin.ch Cc: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net

[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

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 ma@bluewin.ch wrote: Dear PyMOL users In a directory are PDB files

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

? 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 ma@bluewin.ch wrote: Hi Jason, I'm using PyMOL 1.3. Best regards Martin On 20.12.12 15:53, Jason Vertrees

Re: [PyMOL] problems with mutagenesis wizard II

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 these commands right after starting up PyMOL

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

05:34 PM, Martin Hediger wrote: 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

[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

[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.

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

[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

[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

Re: [PyMOL] Dont resequence atoms when saving

Dear Pymol users We are trying to generate a number of mutated structures using the mutagenesis wizard. However, after mutating a position and saving to a new PDB file, the mutated residue ends up being mixed into the coordinate lines of the first residue. Some two coordinate lines are

[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,

[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

Most helpful, thats exactly the solution I was looking for. Thanks a lot Martin On 17.01.12 16:01, Jason Vertrees wrote: Hi Martin, PyMOL does not keep track of which files the objects were loaded from. If you wanted, you could wrap the load command in with your own load command that

[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

[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

Re: [PyMOL] RMSD between two structures

[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, Martin Hediger wrote: Dear List. When aligning two structures using the PyMOL align command, one gets a final RMS value indicating some kind

[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

[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

Re: [PyMOL] creating PDB structure

If you are in the PyMOL Viewer and in Edit mode, you can hit ALT+{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

[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. #

Re: [PyMOL] Expose PyMOL API

, Thomas Martin Hediger wrote, On 11/22/11 13:14: Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8. me @ ~/PROG_TEST $ python Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55) [GCC 4.0.1 (Apple Inc. build 5493)] on darwin Type help, copyright, credits or license for more

[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

[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 only an

Re: [PyMOL] Script for Torsion angles

Great page. Good to know. Thanks all for the feedback. Martin Am 06.09.11 16:17, schrieb Robert Immormino: Martin, If you end up wanting to do this a lot then it might be worth looking into Dangle ( http://kinemage.biochem.duke.edu/software/dangle.php ). This is one of the tools from

[PyMOL] Configuration of Player

Dear List Is it possible to run the PyMOL-Player in a way such that it does not skip to the first frame once it reaches the end, but rather that it goes back and forward? I.e. if running over the models/frames in a multi frame file, it goes from 1-10 and then from 10-1. Kind regards. Martin

Re: [PyMOL] Run script synchronized

) 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 PyMOL fetches the next protein

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

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

1577-8944752 2011/8/22 Martin Hediger ma@bluewin.ch mailto:ma@bluewin.ch 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

[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] 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

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

I see, so if i get this right, every protein structure has at least one biological unit, sometimes it just conincides with the asymmetric unit. So it would be save to write .pdb1 in any case. Cool, thanks for pointing this out to me. Martin On 03.05.11 22:22, li...@cowsandmilk.net wrote:

[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] Get Protein Dimension

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 returns the dimensions of the selection. Is it complicated to make this function available from within an ordinary Pythonscript

[PyMOL] Display coordinate vectors

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 authentic gaming

Re: [PyMOL] Display coordinate vectors

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 display something like coordinate vectors in PyMOL? I.e. arrows in the 3d view space

[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

Re: [PyMOL] Dont resequence atoms when saving

hey, just wanted to ask if you could find something on why the mutagenesis wizard is destroying the ordering of atoms? Is this perhaps fixed in the latest versions? Then a download would make sense. Thanks, Martin Am 13.12.10 16:52, schrieb Jason Vertrees: Hi Martin, As you've found,

Re: [PyMOL] Adding Hydrogens

to manually cycle the valences. On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger ma@bluewin.ch 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, meaning is it possible to set

[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

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 last

Re: [PyMOL] Selecting ASP and GLU

yeah, its true. We should work out a tutorial for this kind of things. Something where there is only one line of instruction and one line of command, like: 1) Download a file fetch pdb1.pdb 2) Select all ASP or GLU residues: select acids, resn ASP+GLU 3) Suggestions? Am 02.03.11 22:36,

[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

[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

Re: [PyMOL] Plugin Tutorial

Ok, good to know. I was using the code as shown on the tutorials page, and since I have only limited experience with the zlib module, I was not exactly sure about what it's doing in the first place. I am still wondering though if it is possible to avoid the reinstallment of the plugin whenever

[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

Re: [PyMOL] Start PyMOL session in web browser

be 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 a PyMOL viewer through

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

of an atom. cheers, Hongbo Zhu On 11/01/2010 10:02 AM, Martin Hediger wrote: Hi Tsjerk, I am still wondering about how the numbering is done. Given a PDB file looking like this (some random molecule): HETATM 1 C LIG 1 -4.242 2.555 -0.814 1.00 0.00 C HETATM 2 C LIG 1 -2.736 2.361 -0.665 1.00

[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 be

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

Thanks Tsjerk (on both occasions). As a matter of fact, I'm kind of making a living out of writing a Python script once in a while, so thats no worry ;) What I was trying to get at was that I was trying to understand how certain PyMOL scripts work, and naturally from that become able to improve

[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

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

. For a given mutant, I need a PDB file for every available rotamer. I guess thats the simplest way of putting it. How can I achieve that? Thanks for hints. Martin Am 12.09.10 00:08, schrieb Martin Hediger: Hi all I want to do some scripted mutations on a range of residues. Say I

[PyMOL] Mutagenesis How many rotamers per amino acid

Hi all I want to do some scripted mutations on a range of residues. Say I want to mutate residue 189 to every rotamer of [Asp, His, Glu, Thr, Lys] available in the PyMOL internal rotamer library. I'm seeing that PyMOL issues cmd.get_wizard().do_state(i) to select rotamer 'i' for a mutation.

[PyMOL] Wizard Measurement

Dear All I'm trying to write a littel function that allows for a short cut to invoke the wizard measurement. The idea is, that instead of having to open the GUI menueMeasurement or typing wizard measurement, I would like to be able to just type mes and have the measurement tool-box

[PyMOL] Specific Expansion of selection

Dear All I am trying to cut out a subset of a protein structure. I am selecting an active site atom and expanding by residue with radius 12 Angstrom around that atom. Is there a way of doing the following: If the edge of the selection ends with a carbonyl of a peptide bond, keep it included.

[PyMOL] Writing Hbond list

Dear all I am using the script of Robert Campell to collect hydrogen bonds and the essential part looks like this: [collect pairs in hb by cmd.find_pairs] for pairs in hb: cmd.iterate(%s and index %s % (pairs[0][0], pairs[0][1]), 'print %1s/%3s`%s/%-4s % (chain,

[PyMOL] as sticks set up

Hi all Is there a way to have the command as sticks show sticks and only polar hydrogens? Right now it shows all hydrogens and it would be nice if I could set it to leave out non polar hydrogens. Thanks for any suggestions. Martin

Re: [PyMOL] How does PyMol add hydrogen atoms?

That would be really interesting to know. If there is no connectivity data provided, then my only guess is that it has some really precise bond length data to compare to. -- This SF.net email is sponsored by Make an

[PyMOL] PyMol Connectivity Data

Dear all I am confused about the requirement of providing connectivity data in a pdb file to properly render a protein with PyMol. Right now, I am displaying a pdb file not containing any connectivity data but still the protein seems perfectly valid. My question is: how does PyMol know how to

[PyMOL] Align different Structures

Hi all, My problem is: I have two structures, A and B. Both are part of a protein and contain residues from the active site. A is a subset of B in a sense that B is contains residues even further from the active site (generated by the expand command). I ran a QM calculation on the active site