Re: [PyMOL] Convert PyMOL isomesh or isosurface to cgo?
Thanks Takanori - that's just what I needed - works brilliantly! : ) I did find that my cgo_line_width setting (1.0) was causing the resultant cgo 'mesh' to appear / draw / raytrace differently to the isomesh counterpart; but I seemed to solve this by setting to -1. The only slight problem I still have is that 'matrix_copy' does not seem to apply a molecule object's matrix to CGOs (or, for that matter to isomeshes). This isn't a huge issue, since for most of what I'm doing I can apply a matrix_copy to a map object, then generate the isomesh, then generate the cgo... It does mean, however, that I am unable to store protein + a number of cgo meshes, with the ability to align the whole ensemble onto another system (which ideally is what I would like to do). I guess I should maybe follow-up with a more specific post on this point. Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. __-- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev___ 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] Mutagenesis and states
Hi Justin, could you fetch just the monomer, mutate it and then construct the assembly with http://pymolwiki.org/index.php/BiologicalUnit/Quat ? Cheers, Thomas On 01/10/2012 08:43 AM, Justin Bailey wrote: > Hello > > I have been working with the pdb file 2C0W. It is a filamentous phage > portion composed of 55 alpha helices, each within their own state. > > I am running into a few problems: > > 1) I'm wanting to add 4 amino acids to the middle of the alpha helix. > I've been practicing my building skills by adding 4 amino acids to the > end alpha helix first. This is where I run into problems - the amino > acids I add to one helix are duplicated to the rest of the 54 helixes in > the other states. When I go to Movies->Show all States, the amino acids > of the other 54 states are all contorted, when I'm looking to have the > alpha helices line up properly like they do in the original file. > > 2) Using the mutagenesis wizard to do a point mutation places the > replacement amino acid way far away from the original amino acid. If I > split the states first, then the mutagenesis works fine, although I'd > rather not do this mutation 55 times. > > Eventually what I want to do is add carbohydrates to these alpha > helices, without having to add them manually to all 55 states. This > goal is looking grim though if I can't get even add or mutate in an > amino acid. I'd rather not split all the states and modify them > individually. > > Maybe I need more knowledge on what is going on when I modify states? > Anyone know to accomplish what I'm setting out to do? > > Justin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ 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
Deal all! I'm intresting about representation of the polarr contacts between ligand and protein 1) Usually I'm ussing Present-> Ligand sites option for that purposes but in my current case I'm working with GFP where tree residues form chromofore group of that protein. So I want to assign that three residues as the ligand and finally find polar contacts between that chromophore and surrounding polar residues. How I could do this assignment? 2) Also I'm looking in possible way to represent Names of residues wich forrm my ligand binding pocket. Always I represent names of residues via Label option. But if I choose Label -> res.names all names will be represented but i want to represent only the names of residues wich form polar contact with ligand. James 2012/1/10 Jason Vertrees > James, > > Please take these questions to the pymol-users list. I'm getting ready > for the PyMOL v1.5 release, so you'll get faster answers there. > > Cheers, > > -- Jason > > On Tue, Jan 10, 2012 at 6:22 AM, James Starlight > wrote: > > Hi Jason > > > > Thank you for help again. > > > > I've also question about representation of the polarr contacts between > > ligand and protein > > > > Usually I'm ussing Present-> Ligand sites option for that purposes but > in my > > current case I'm working with GFP where tree residues form chromofore > group > > of that protein. > > > > So I want to assign that three residues as the ligand and finally find > polar > > contacts between that chromophore and surrounding polar residues. How I > > could do this assignment? > > > > Thanks again > > > > James > > > > > > 2012/1/9 Jason Vertrees > >> > >> Hi James, > >> > >> I see you want chains A and B in one object to become just chain AA, > >> for example, in another object? If so, > >> > >> create newObj, (oldObj1 and chain A) or (oldObj2 and chain B) > >> > >> alter newObj, chain=AA > >> > >> Cheers, > >> > >> -- Jason > >> > >> On Mon, Jan 9, 2012 at 2:26 AM, James Starlight > > >> wrote: > >> > Jason hello! > >> > > >> > I've tried exactly that command with OR operator > >> > > >> > but new object consitsted of 2 different chains like initial > structure ( > >> > this was equal to the simple coppy of the 2g16 to the 2g16new object > >> > without > >> > deleation of initial one). But I want that 2g16new will consist of > only > >> > 1 > >> > chain wich would contait residues from both A and B of initial object. > >> > > >> > James > >> > > >> >> > >> >> Cheers, > >> >> > >> >> -- JAson > >> >> > >> >> On Sun, Jan 8, 2012 at 1:35 AM, James Starlight > >> >> > >> >> wrote: > >> >> > Jason hello! > >> >> > > >> >> > I've tried use Create command to merge 2 chains from one object > into > >> >> > the united chain in new object but failed. > >> >> > > >> >> > create 2g16new, 2g16 and chain A 2g16 and chain B > >> >> > > >> >> > It's because of my new object also consist of 2 chains ( like > >> >> > initial > >> >> > one) but I want to obtain new object only with one chain wich would > >> >> > consist of atoms from both chains of initial object. ( A+B) > >> >> > > >> >> > How I could solve that problem? > >> >> > > >> >> > James > >> >> > > >> >> > 2011/11/27, Jason Vertrees : > >> >> >> James, > >> >> >> > >> >> >> Please look up the 'create' > >> >> >> (http://www.pymolwiki.org/index.php/Create) > >> >> >> comand. > >> >> >> > >> >> >> Cheers, > >> >> >> > >> >> >> -- Jason > >> >> >> > >> >> >> On Sat, Nov 26, 2011 at 6:17 AM, James Starlight > >> >> >> > >> >> >> wrote: > >> >> >>> Dear all! :) > >> >> >>> > >> >> >>> I need to merge two chains in one pdb ( object) into one united > >> >> >>> chain. > >> >> >>> How > >> >> >>> I > >> >> >>> could do it? > >> >> >>> > >> >> >>> Thanks > >> >> >>> > >> >> >>> James > >> >> >>> > >> >> >>> 2011/11/18 Joel Tyndall > >> >> > >> >> James, > >> >> > >> >> > >> >> > >> >> Please post this to the bulletin board. You can try to click on > >> >> the > >> >> word > >> >> (residues usually default) at the bottom right of the viewer. > >> >> > >> >> > >> >> > >> >> Joel > >> >> > >> >> > >> >> > >> >> From: James Starlight [mailto:jmsstarli...@gmail.com] > >> >> Sent: Thursday, 17 November 2011 7:52 a.m. > >> >> > >> >> To: Joel Tyndall > >> >> Subject: Re: [PyMOL] Editing of the pdb structure > >> >> > >> >> > >> >> > >> >> Another question about working with the structure. > >> >> > >> >> > >> >> I have structure of the fulerene molecule wich consist of 60 > >> >> carbon > >> >> atoms > >> >> > >> >> I switch to the Sequence mode-> Atoms and try to select > individual > >> >> carbon > >> >> atoms ( e.g I want to find where this atom situated in my > >> >> molecule). > >> >> But > >> >> instead of selection of the individual carbons the whole > molecule > >> >> was > >> >> selected. How I can work wi
Re: [PyMOL] Editing of the pdb structure
On Tuesday 10,January,2012 09:43 PM, James Starlight wrote: > Deal all! > > I'm intresting about representation of the polarr contacts between > ligand and protein > > 1) Usually I'm ussing Present-> Ligand sites option for that purposes > but in my current case I'm working with GFP where tree residues form > chromofore group of that protein. > > So I want to assign that three residues as the ligand and finally find > polar contacts between that chromophore and surrounding polar residues. > How I could do this assignment? > > 2) Also I'm looking in possible way to represent Names of residues wich > forrm my ligand binding pocket. Always I represent names of residues via > Label option. But if I choose Label -> res.names all names will be > represented but i want to represent only the names of residues wich form > polar contact with ligand. > > James Sorry a bit off-list-topic. the Ligplot+ can do this pretty well. http://www.ebi.ac.uk/thornton-srv/software/LigPlus/ -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ 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] Having problems using clean function
Hi, I have the same problem. But instead of "Unable to validate freemol.mengine" it's "Unable to import freemol.mengine module" followed by "This pymol build appears to not include full modeling capabilities." The message would take a long time to appear and pymol seems frozen if it is loaded with a very large complex. Best, Quyen On Tue, Jan 10, 2012 at 1:05 PM, Jonathan Saboury wrote: > I used to have pymol installed and when I built a complex molecule, > morphine for example, it would be very messy with overlap. So I pressed > cleana dn it made it into its correct structure. > > Now, I installed pymol in the very same way, using pymol precompiled for > windows here: http://www.lfd.uci.edu/~gohlke/pythonlibs/ > and tried all combinations with the correct python type, python 2.5-2.7 32 > and 64 bit. > > For some reason I cannot use clean anymore, which is a vital function for > me. When I press it it says "Error: Unable to validate freemol.mengine". > > For SOME molecules if I use sculpt it works almost the same, but not for > all. Why am I having this problem? Thanks for the help! I extremely > appreciate pymol and teh support I am getting now. > > PS Would be great to get a user supported forum up, would ease the pain > and make it simpler to get information/support. Tried searching for one but > couldn't find any, only found this email address. Was expecting one since > this is such a great program with so many people using it. > > > -- > Write once. Port to many. > Get the SDK and tools to simplify cross-platform app development. Create > new or port existing apps to sell to consumers worldwide. Explore the > Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join > http://p.sf.net/sfu/intel-appdev > ___ > 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 > -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev___ 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] PyMol 1.4 not running on Ubuntu Linux 11.10
Hi folks, I just upgraded my Ubuntu Linux installation to 11.10. Of course, this removes obsolete versions of applications. So I had to reinstall PyMol. The Ubuntu Linux 11.10 manifest states that PyMol 1.4.1 is the supported version, and a package file is available. So, I downloaded and (supposedly) installed PyMol 1.4.1 -- first through Ubuntu Software Center, and then through Synaptic Package Manager when Software Center failed (I didn't expect it to to make a difference, but I tried anyway). The way in which PyMol is failing is very simple. When I click on the PyMol icon to start the application, nothing happens. There were no error messages visible in the GUI during the installation, nor when attempting to start the application. So next I tried to run PyMol from a terminal prompt, and here I saw errors: 23:29:55 -> pymol Traceback (most recent call last): File "", line 1, in ImportError: No module named pymol /usr/local/bin/python2.7: No module named pymol This tells me that there's an executable file on my system path named pymol.py, which starts. Then pymol.py tries to import a module, also named pymol (why is the name "pymol" used twice?), which fails. I'm a bit baffled at this behavior, especially as it comes from a standard package file. Any help you might offer is appreciated. -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox___ 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
