Re: [PyMOL] Symmetry Mates Problem
Hi Humayun, Yes, then you seem to be left with docking as the only option. There are servers for that too, but since you want to do six-body docking, you may need to contact somebody for assistance/guidance. Cheers, Tsjerk On Wed, May 19, 2010 at 1:11 PM, humayun scherrif hum@gmail.com 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 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 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 BSA DGdiss | Formula +-+---+--- 1 | 1 | 6 0 19917.7 5536.3 3.8 | A(2)B(2)C(2) +-+---+--- 2 | 2 | 3 1 10722.9 2004.1 6.2 | ABC +-+---+--- 3 | 3 | 4 2 14004.2 3014.9 0.5 | A(2)B(2) | 4 | 1 3 4217.5 0.0 -0.0 | A +-+---+--- 4 | 5 | 2 4 7506.2 1003.3 7.0 | AB | 6 | 1 3 4217.5 0.0 -0.0 | A +-+---+--- 5 | 7 | 2 5 7443.8 1000.8 6.8 | AB | 8 | 1 6 4282.4 0.0 -0.0 | A +-+---+--- 6 | 9 | 2 7 7556.5 1008.3 2.0 | A(2) | 10 | 1 8 4227.1 0.0 -0.0 | A | 11 | 1 3 4217.5 0.0 -0.0 | A '-'---'--- Waiting for your reply Thanks H On Wed, May 19, 2010 at 4:41 PM, Robert Brynmor Fenwick robert.fenw...@irbbarcelona.org wrote: Also, if you would like to try homology modelling then that could work. However you would need a couple of hexamer strucutres to start with. It would probably take some tinkering with current tools. I would probably use an MD approach to solve this problem. Sorry I don't have a quick fix this is not my current area of expertise. Bryn Sent from my iPod On 19/05/2010, at 09:22, humayun scherrif hum@gmail.com wrote: Thank you Bryn for your reply, But I have already tried all possible symmetries that it generates, but it does not provide a proper
[PyMOL] [Fwd: Re: Symmetry Mates Problem]
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 |A '-'---'--- Waiting for your reply Thanks H On Wed, May 19, 2010 at 4:41 PM, Robert Brynmor Fenwick robert.fenw...@irbbarcelona.org mailto:robert.fenw...@irbbarcelona.org wrote: Also, if you would like to try homology modelling then that could work. However you would need a couple of hexamer strucutres to start with. It would probably take some tinkering with current tools. I would probably use an MD approach
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 |A
Re: [PyMOL] Symmetry Mates Problem
Thank you all and certainly seems llike now I am going to some right direction. I have read some discussion part (page 14) of the paper Maia sent, as stated below, the BSA ( value for my dimer interfaces are ~1000 (as predicted by PISA) which according to the Krissinel paper, is biological relevant. Moreover, the hexameric structure is reported to exist in the same specie on which I am working on. It has been concluded in a number of studies [20, 68, 69, 70] that BSA larger than 600-850°A2 indicates a biologically relevant interface. A lower figure of 400 °A2 was found in Ref. [9] and then used in the Protein Quaternary Structure (PQS) server [5]. The minimal BSA of potentially stable crystal dimers in our dataset is found to be 390 °A2 (PDB entry 1SDX [67]), which agrees with the literature data. However, it follows from Figs. 3B,5A and above considerations that unspecific interactions may prevail at ABSA · 3000°A2, causing substantial changes to the original complexes, and, therefore, dimeric structures with low ABSA may be misrepresented by crystals. On Thu, May 20, 2010 at 1:29 AM, Maia Cherney ch...@ualberta.ca wrote: In his latest paper 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 Krissinel wrote that DGdiss error is 5kcal/mol. I think that DG~5kcal/mol is a gray zone. Then he compares docking results with actual structures, a lot of failures! Is your protein exactly the same as documented or from a different species? My protein has three different oligomeric states from three different species, and the monomers from different species superpose well. Maia humayun scherrif 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 |A '-'---'--- Waiting for your reply Thanks H On Wed, May 19, 2010 at 4:41 PM, Robert Brynmor Fenwick robert.fenw...@irbbarcelona.org mailto:robert.fenw...@irbbarcelona.org wrote: Also, if you would like to try homology modelling then that could work. However you would need a couple of hexamer strucutres to start with. It would probably take some tinkering with current tools. I would probably use an MD approach to solve this problem. Sorry I don't have a quick fix this is not my current area of expertise. Bryn Sent from my iPod On 19/05/2010, at 09:22, humayun scherrif hum@gmail.com mailto:hum@gmail.com wrote: Thank you Bryn for your reply, But I have already tried all possible symmetries that it generates, but it does not provide a proper hexameric assembly. Does it mean this is due to problems in crystal packing ? Is there any alternative way to generate or by homology, which server could be suitable ? Regards
Re: [PyMOL] drawing of objects for illustration
Hi Jason, nice. I didn't know about the pseudoatoms, very cool. nick On Wed, May 19, 2010 at 10:39, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Nicolas, Cool idea. First the witihin operator works on more than just single atoms. So, how about something like this: # fetch a protein fetch 1oky, async=0 # let's target _all_ atoms within 8 Angs of _all_ of # residue 55, not just one atom select target, all within 8 of i. 55 color red, target cmd.center(i. 55) vPos = cmd.get_position() cmd.pseudoatom(identifier,pos= vPos); show_as spheres, identifier cmd.set(sphere_transparency, 0.5, identifier) cmd.set(sphere_scale, 8, identifier) In sum, use pseudoatom for and position it at vPos. Cheers, -- Jason On Wed, May 19, 2010 at 12:22 AM, Nicolas Bock nicolasb...@gmail.com wrote: Hello, I would like to do the following: I have a large protein loaded in pymol. I would like to select all atoms within a radius around a point. I know about select within, however, this command requires the second selection to be an atom. I would prefer if the center of the sphere is not necessarily centered on an atom. Is this possible? In addition I would like to draw the spherical selection region somewhat transparently, so that I can illustrate what I have selected. Is that possible? Thanks already, nick -- ___ 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 Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ 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
