[PyMOL] MacPymol + Missing Features (APBS?)
Dear all, I had the incentive version installed for a while (v1.7 beta2) and I was surprised to see that in the [A] menu, under 'generate' there was an option to generate an electrostatic map with apbs. Unfortunately my laptop HD died, and when I reinstalled everything today this option is missing, although there is an apbs executable under MacPyMOL.app/.../ext/bin. Is there something I'm missing or was this an experimental feature that didn't make the cut? Cheers, João -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] MacPymol + Missing Features (APBS?)
Hi Thomas, Thank you very much, that was exactly it. After a while I lost track of what I had installed.. Cheers, João 2014-02-13 20:59 GMT+01:00 Thomas Holder thomas.hol...@schrodinger.com: Hi João, I guess you had the psico module installed, which indeed adds an APBS option to the A generate menu. http://pymolwiki.org/index.php/psico Cheers, Thomas João Rodrigues wrote, On 02/13/14 14:44: Dear all, I had the incentive version installed for a while (v1.7 beta2) and I was surprised to see that in the [A] menu, under 'generate' there was an option to generate an electrostatic map with apbs. Unfortunately my laptop HD died, and when I reinstalled everything today this option is missing, although there is an apbs executable under MacPyMOL.app/.../ext/bin. Is there something I'm missing or was this an experimental feature that didn't make the cut? Cheers, João -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] accurate way to change/process b-factor in PDB
Hi Afonso, PyMOL allows for Python scripting so in principle you could do something like: import math alter structure, b=math.log(b, 10) Just make sure not to have 0.0 bfactors in there! Cheers, João 2013/7/4 Afonso Duarte afonsomdua...@gmail.com Dear All, I have a pdb file composed by several chains where the b-factor column was replaced by a physical property of the proteins. I am now trying to color according to b-factor and to obtain a better representation of the properties described. i.e. I am interested in calculating the log of the b-factor and place that value in the b-factor column. I tried to export this column form the pdb, process it and then import it back, but due to the presence of different chains the b-factors got messed up. Would it be possible to do this kind of math operation directly in Pymol? Best Afonso -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to avoid the protonation of a particular atom
Hi, Protonate everyone, deprotonate that particular atom Cheers, João 2013/4/1 gdus...@cbm.uam.es Hello, I'm working with a receptor that has a catalytic Zn and i have to protonate everything except this atom. I have proved everything to avoid this protonation (put Zn2+ on the pdb, change the protonation with builder...etc) without success. Could you please tell me how to do this? I'm using PyMOL 1.4.1 in Linux. Thank you very much. Best regards, Gema. -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Zoom + Fading simultaneously in movie
Hi all, I'm trying to make a short movie here and I came across something I can't find on the internet how to do it.. I want to zoom in a region of the protein (done easily) and at the same time fade its surface (also easily done on its own, thanks Tsjerk). Is this possible or we cannot have two actions in the same frame? Sorry for the limited jargon for movie making! Best, João -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Using cmd.png with ray=False still ray traces the image
Thanks for the tips all of you. As I told Jason, the renderer option was the billionth thing I tried to make it work.. all default settings didn't. So it comes down to what Thomas said: if running in batch mode, there is no opengl window to capture from and PyMOL will always fall back to ray tracing, since it is the only way to obtain a figure in this mode. So, in a script, I shouldn't use ray. I should just use png directly and allow it to ray. It worked. Cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 18 de Abril de 2012 09:38, Thomas Holder spel...@users.sourceforge.net escreveu: Hi João, Pete Jason, I think pml vs. py or 1.4 vs. 1.5 will make no difference. But I see two other things here: 1) renderer=2 is a dry-run according to the documentation, so it will not actually render a image. 2) if running in batch mode, there is no opengl window to capture from and PyMOL will always fall back to ray tracing, since it is the only way to obtain a figure in this mode. Cheers, Thomas Pete Meyer wrote, On 04/18/12 01:00: It may be worth trying pymol 1.4 (instead of 1.5) - although this shouldn't make a difference, it might provide some more information (you also mentioned that you've got a large scene - depending on composition 1.4 may use less memory than 1.5). You may also want to try using a pml script vs python (start pymol with -q -c your_raytrace_script.pml arguments) and see if that helps, or at least breaks in different ways. Pete João Rodrigues wrote: Hi Jason, I've tried a lot of stuff, thus the renderer=2.. (i installed povray and tried to use it). With the default option the result is the same. cmd.png(default_name+'.png', width, height, dpi, ray=0) Doing what you wrote still causes the renderer to kick in.. I'm a bit out of ideas.. Cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 17 de Abril de 2012 22:33, Jason Vertrees jason.vertrees@schrodinger.**com jason.vertr...@schrodinger.com mailto:jason.vertrees@**schrodinger.comjason.vertr...@schrodinger.com escreveu: João, I'm not sure why this is giving you problems. Why do you have renderer=2? Why not the default? Are you counting primitives? If so, I suggest: cmd.set(ray_default_renderer**, 2) # snapshot cmd.png(myFile, width=w, height=h, dpi=d, ray=0) # this will ray trace cmd.png(myFile, width=w, height=h, dpi=d, ray=1) Cheers, -- Jason On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues anar...@gmail.com mailto:anar**y...@gmail.com anar...@gmail.com wrote: Same result Jason, i also tried =false... No dia 17 de Abr de 2012 20:45, Jason Vertrees jason.vertrees@schrodinger.**com jason.vertr...@schrodinger.com mailto:jason.vertrees@**schrodinger.comjason.vertr...@schrodinger.com escreveu: Hi João, What about cmd.png(default_name+'.png', dpi=300, ray=0) Cheers, -- Jason On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues anar...@gmail.com mailto:anar**y...@gmail.com anar...@gmail.com wrote: Hello all, I'm using Pymol v1.5 (from fink, so open source version) to trace large scene that I have. To that end, I'm avoiding having PyMOL open and I wrote a small python script to do the rendering for me. All goes well, except this last part (don't mind the obvious variable names): cmd.ray(width, height, renderer=2) cmd.png(default_name+'.png', dpi=300, ray=False) This actually renders my scene twice. I've tried cmd.do and it does the same.. am I missing something or is this not supposed to happen? Thanks and cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com**mailto:Jason.Vertrees@** schrodinger.com jason.vertr...@schrodinger.com (o) +1 (603) 374-7120tel:%2B1%20%28603%29%20374-**7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com**mailto:Jason.Vertrees@** schrodinger.com jason.vertr...@schrodinger.com (o) +1 (603) 374-7120tel:%2B1%20%28603%29%20374-**7120 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Using cmd.png with ray=False still ray traces the image
Hello all, I'm using Pymol v1.5 (from fink, so open source version) to trace large scene that I have. To that end, I'm avoiding having PyMOL open and I wrote a small python script to do the rendering for me. All goes well, except this last part (don't mind the obvious variable names): cmd.ray(width, height, renderer=2) goog_409444192cmd.png(default_name+'.png', dpi=300, ray=False) This actually renders my scene *twice. *I've tried cmd.do and it does the same.. am I missing something or is this not supposed to happen? Thanks and cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Using cmd.png with ray=False still ray traces the image
Same result Jason, i also tried =false... No dia 17 de Abr de 2012 20:45, Jason Vertrees jason.vertr...@schrodinger.com escreveu: Hi João, What about cmd.png(default_name+'.png', dpi=300, ray=0) Cheers, -- Jason On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues anar...@gmail.com wrote: Hello all, I'm using Pymol v1.5 (from fink, so open source version) to trace large scene that I have. To that end, I'm avoiding having PyMOL open and I wrote a small python script to do the rendering for me. All goes well, except this last part (don't mind the obvious variable names): cmd.ray(width, height, renderer=2) cmd.png(default_name+'.png', dpi=300, ray=False) This actually renders my scene twice. I've tried cmd.do and it does the same.. am I missing something or is this not supposed to happen? Thanks and cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Using cmd.png with ray=False still ray traces the image
Hi Jason, I've tried a lot of stuff, thus the renderer=2.. (i installed povray and tried to use it). With the default option the result is the same. cmd.png(default_name+'.png', width, height, dpi, ray=0) Doing what you wrote still causes the renderer to kick in.. I'm a bit out of ideas.. Cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 17 de Abril de 2012 22:33, Jason Vertrees jason.vertr...@schrodinger.com escreveu: João, I'm not sure why this is giving you problems. Why do you have renderer=2? Why not the default? Are you counting primitives? If so, I suggest: cmd.set(ray_default_renderer, 2) # snapshot cmd.png(myFile, width=w, height=h, dpi=d, ray=0) # this will ray trace cmd.png(myFile, width=w, height=h, dpi=d, ray=1) Cheers, -- Jason On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues anar...@gmail.com wrote: Same result Jason, i also tried =false... No dia 17 de Abr de 2012 20:45, Jason Vertrees jason.vertr...@schrodinger.com escreveu: Hi João, What about cmd.png(default_name+'.png', dpi=300, ray=0) Cheers, -- Jason On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues anar...@gmail.com wrote: Hello all, I'm using Pymol v1.5 (from fink, so open source version) to trace large scene that I have. To that end, I'm avoiding having PyMOL open and I wrote a small python script to do the rendering for me. All goes well, except this last part (don't mind the obvious variable names): cmd.ray(width, height, renderer=2) cmd.png(default_name+'.png', dpi=300, ray=False) This actually renders my scene twice. I've tried cmd.do and it does the same.. am I missing something or is this not supposed to happen? Thanks and cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to select whole residues around an object?
Use byres(). select neighbours, byres( chain A w. 4A of chain B) Cheers, João -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] atom structure
Hi, You can set something like this: set sphere_scale, 0.2 set stick_radius, 0.15 show spheres show sticks I usually use lines for the bonds though. Best, João -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Editing of the pdb structure
Dear James, As someone has told you already, Pymol is a visualization tool, not a modelling suite. I guess you would be better off using something like AMBERTOOLS or MODELLER, depending on what you want to model, or any other real simulation/modelling package otherwise your results are very weak... My opinion only. João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 27 de Janeiro de 2012 09:50, James Starlight jmsstarli...@gmail.comescreveu: Arne, Thomas Thanks alot. Bond works finw I'd like just to ask what about geometry optimisation of the new structure E.g I want create 5memb imidazole ring where the 2 adj atoms are apart from 1.5 A from each other. When I've create new bond by bond command new ring look like 6memb ( like benzol) because of long distance between adj atoms. How I could optimise geometry of the new mollecule? Have pymol some built-in functions like conformational search be means of monte carlo or energy minimisation ? James 2012/1/27 Thomas Holder spel...@users.sourceforge.net On 01/27/2012 09:11 AM, James Starlight wrote: Dear PyMol users! I need to create NEW covalent bond between two adjacent atoms. How this could be done in PyMOl? you could have guessed it: http://pymolwiki.org/index.**php/Bondhttp://pymolwiki.org/index.php/Bond :-) The atoms must both be within the same object. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Create a dimer from predicted monomer
Hello Karen, Predicting protein complexes structures is docking. Pymol should not be used for this. I would advise you to look at docking software that allows for symmetrical molecules, such as HADDOCK (http://haddocking.org/) or SymmDock (http://bioinfo3d.cs.tau.ac.il/SymmDock/). Best, João [...] Rodrigues 2011/11/8 Cell Cycle cellc...@gmail.com Hi, A fragment of my protein is predicted by I-TASSER to be similar to a homodimer module. But the predicted pdb file (named copy) is only a monomer. Can I generate a dimer using pymol? I tried symexp sym, copy, copy, 2.5, which would work for other known pdb file, but got the error message no symmetry loaded. Can anyone tell me how to create a dimer from my predcited monomer? Thanks, Karen -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] (HB) dotted line with out distance number
Hey Leila, The distance is a Label, so if you hide the labels for the distance object is should disappear. Regards, João -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How does PyMol add hydrogen atoms?
Hey Jason! Thanks for the reply, no problem at all with the delay :) I got my hands around the code and I *think* I got it to add hydrogens to a protein (including checking that random effect). My only question is, how PyMol determines which atoms lack hydrogens. I checked the hetatm.py and protein.py files and they seems to compare the structure with a pre-defined database of bonds for each residue. However, this works for proteins only right? How does it work for methane? How does it recognize that is lacks 4 atoms? If you can point me to the file where that part is described, that would be amazing! I've lost two weeks trying to figure it out already and I can't... Best! João -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How does PyMol add hydrogen atoms?
Hey Jason, Thanks! I'd traced add_H to that function before but my knowledge of C is rudimentary so I was quite overwhelmed. Yet, I think I managed to understand a bit better what's going on, but correct me if I'm wrong. It seems PyMol looks for neighbours first, derives a bonding network from that, and then calculates valences. Thanks a lot for the help! And good luck with the new city! João -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] How does PyMol add hydrogen atoms?
Hello all, I've been looking at Pymol's code for sometime time now and yet the algorithm for addition of hydrogen atoms to molecules in Pymol is not clear to me.. I've traced the h_add function to OMOP_AddHydrogens in layer2/Executive.c: op.code = OMOP_AddHydrogens;/* 4 passes completes the job */ I'd argue this 4 passes to complete the job requirement is related with the algorithm in chempy/place.py that iterates over a need list of lists. need = [ [], [], [], [] ] This list of lists hold info for heavy atoms that lack 1, 2, 3, or 4 atoms. This seems quite logical. But then the H atoms added have names like H01, H02, etc, when they were correctly identified in chempy/proteins.py and have their names in protein_amber.py and protein_residues.py. My main questions are: are there different treatments for proteins when it comes to H-addition? How are H-s added to say, Methane? (given a single C). Best! João [...] Rodrigues @ http://doeidoei.wordpress.org -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
