Re: [PyMOL] [Fwd: Re: Symmetry Mates Problem]
But maybe you can have a try: HADDOCK seems to give good results, once you have defined the symmetry of your complex... See: Mol. Cell. Proteomics 2010 'Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multi-body docking server' Karaca E. et al. Cheers, Annalisa - Annalisa Bordogna PhD. Student Università degli Studi di Milano - Bicocca Milano (Italy) 2010/5/19 Maia Cherney ch...@ualberta.ca Docking is very non-reliable. E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. J. Comp. Chem., in press; published on-line 6 May 2009; DOI 10.1002/jcc.21303 Maia humayun scherrif wrote: Hello, Thank you for detailed explanation, surely it is helping me to sort out the possibilities. As per your query a) There are many references that the protein is a Hexamer, but I am considering, because the domain which I have got structure, interacts with other proteins to make a biological complex, their interaction could be important for biological hexamerization of the whole complex ( those interacting proteins also exist as hexamer in complex with my protein ) b) I coudnt find any hexameric homologue (although there are some good homologue structures but they mostly exist as dimer or monomer) c) the structure is not yet been solved and not reported as yet. So according your reply, does that mean the only possibility left is docking ? because others are not working for me at all. Thank you again for suggestions. On Wed, May 19, 2010 at 6:31 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Humayun, Crystallograpic symmetries are often not of much help to construct biologically relevant complexes. Do you have (a) a reference of the hexameric structure, or (b) of a hexameric homologue, or (c) is it only known to form hexamers and is the structure still unsolved? In case of (a), the structure is likely to have a recipe to build the biological unit (possibly as REMARK 350 in the PDB file). In case of (b), you can try to fit copies of the structure onto each chain of the homologue, being aware that that will give you a crude approximation as starting point for further work. And in case of (c), you might want to consider doing some docking. Hope it helps, Tsjerk On Wed, May 19, 2010 at 10:26 AM, humayun scherrif hum@gmail.com mailto:hum@gmail.com wrote: Thank you all for the replies. The protein itself makes hexamer which is well documented and proved structural evidence from other cytoplasmic domains ( my structure is also a domain). I have run PISA, but the online PISA server didnt give me output like standalone PISA in CCP4 (result is mentioned below). Online PISA results show that there are not significant dimer interfaces and thus the trimer structure is because of only crystal packing result For homology modeling I didnt get any proper homologs which have hexameric assembly (I@ Bryn: I cant send you PDB id since its not submitted yet) Analysis of protein interfaces suggests that the following quaternary structures are stable in solution (I wonder the DGdiss is positive value, is it significant to make Hexamer assembly because I couldnt find any help to find out about the allowed values) .-.---.--- Set | No | Size Id ASA BSADGdiss | Formula +-+---+--- 1 | 1 | 60 19917.75536.3 3.8 | A(2)B(2)C(2) +-+---+--- 2 | 2 | 31 10722.92004.1 6.2 | ABC +-+---+--- 3 | 3 | 42 14004.23014.9 0.5 | A(2)B(2) | 4 | 134217.5 0.0 -0.0 | A +-+---+--- 4 | 5 | 247506.21003.3 7.0 |AB | 6 | 134217.5 0.0-0.0 |A +-+---+--- 5 | 7 | 257443.81000.8 6.8 | AB | 8 | 164282.4 0.0 -0.0 | A +-+---+--- 6 | 9 | 277556.51008.3 2.0 | A(2) | 10 | 184227.1 0.0 -0.0 |A | 11 | 134217.5 0.0 -0.0
Re: [PyMOL] hi
I'm afraid not. You should use docking programs ( http://en.wikipedia.org/wiki/Macromolecular_docking). Cheers, Annalisa 2010/2/24 mohan raj mohanrajdec2...@gmail.com hi all: i am a new to pymol. could some one tell me more about the programs involved in ligand interaction. could i do protein protein interaction simulateions using pymol??? -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] Exporting a selection to file
Hi! Try with: select selection name, name of the object to which the selection belongs w. 5 of other object select other selection name, br. selection name save name.pdb, other selection name The first command select the atoms at 5 Angstroms from other object; the second select the whole residues to which the atoms selected belong; the third saves the complete selection. Hope it helps! Annalisa Annalisa Bordogna PhD. Student DISAT - Università degli Studi di Milano Bicocca Milano Italy 2009/3/31 Luca Varani luca.var...@irb.unisi.ch Hello, is it possible to generate a list of all residues within 5A of another (or whatever you need) and then save this list to a file/clipboard? Thanks a lot for the help, Luca -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] weird visualization of a peptide structure
Hi Andrew, thank you for your answer: now I have a clue! I knew that the structure is a NMR model, but what I didn't understand was that some atoms were repeated (with different coordinates). Now I have pruned my structure file and I can see a much more acceptable structure. Thank you very much, Annalisa 2008/12/19 Andrew Purkiss-Trew a.purk...@mail.cryst.bbk.ac.uk Hi Annalisa, Is the original coordinate file an NMR structure? It looks to me like there are several copies of each atom, which is consistent with the pdb file resulting from an NMR refinement. These will usually have several different models of the peptide, all consistent with the NMR data. You will need to extract just one set of coordinates and look at those. Which set of coordinates to use depends on the software used to generate the pdb, but look for the first or the 'best' model, the pdb header should tell you which is best. Hope this helps at bit Andrew Purkiss-Trew On Thu, 2008-12-18 at 15:40 +0100, annalisa bordogna wrote: Hi all, I have a little problem with the visualization of a peptide conformation: as you can see from the picture I enclose, the structure appears as if every atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to visualize a correct structure? Thank you very much for your help. Best regards, Annalisa --- Annalisa Bordogna Ph.D. Student Università degli Studi di Milano - Bicocca Milano, IT -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] weird visualization of a peptide structure
Hi all, I have a little problem with the visualization of a peptide conformation: as you can see from the picture I enclose, the structure appears as if every atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to visualize a correct structure? Thank you very much for your help. Best regards, Annalisa --- Annalisa Bordogna Ph.D. Student Università degli Studi di Milano - Bicocca Milano, IT attachment: weird_peptide.png
