Re: [PyMOL] symmetry mates
Sometimes it is easier to see the overall structure when looking at a single unit cell rather than the symmetry mates within a certain distance. You might want to try the supercell http://www.pymolwiki.org/index.php/Supercell script. Otherwise I tend to generate symmetry mates multiple times and then hide or delete the ones that don't match the expected biological assembly. -Spencer On Fri, Aug 15, 2014 at 9:26 AM, sunyeping sunyep...@aliyun.com wrote: Dear pymol users, I want to operate a structure whose crystal structure has one molecule in one asymmetry unit. I try to display its polymer. I loaded the structure and used generate command in the pymol GUI interface: Ageneratesymmetry mates4A, and then many copies of this molecure appeared but in a quite disoder pattern. According to the paper that published this structure, it is a polymer arranged in a linear pattern. Could you tell me how can I display this linear polymer? Thanks in advance. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- ___ 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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ 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] symmetry mates
Dear pymol users, I want to operate a structure whose crystal structure has one molecule in one asymmetry unit. I try to display its polymer. I loaded the structure and used generate command in the pymol GUI interface: Ageneratesymmetry mates4A, and then many copies of this molecure appeared but in a quite disoder pattern. According to the paper that published this structure, it is a polymer arranged in a linear pattern. Could you tell me how can I display this linear polymer? Thanks in advance. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- ___ 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] symmetry mates
Hi Yeping Sun, A linear polymer is likely to apparent when you look at a large number of symmetry mates. Looking at lots of symmetry mates in cartoon view is quite intensive and can be slow unless you have a powerful graphics card - if you show the first molecule as 'ribbon' and then generated symmetry mates it can lead to a better viewing experience. If you tell me the pdb code I can have a look. Kind regards, Amar On Aug 15, 2014 8:28 AM, sunyeping sunyep...@aliyun.com wrote: Dear pymol users, I want to operate a structure whose crystal structure has one molecule in one asymmetry unit. I try to display its polymer. I loaded the structure and used generate command in the pymol GUI interface: Ageneratesymmetry mates4A, and then many copies of this molecure appeared but in a quite disoder pattern. According to the paper that published this structure, it is a polymer arranged in a linear pattern. Could you tell me how can I display this linear polymer? Thanks in advance. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- ___ 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] 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
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
[PyMOL] Pymol Symmetry Mates Naming
Hi,all, I am encountering a problem with symmetry mates generated by pymol. It seems that the naming system in pymol and ccp4-supported ACT program are not consistent. I have tested several pdbs in P4212 space group and attempted to figure out the relationship between these two, but failed. I appreciate it if you could hint me out. Some comparisons are listed below. ACT:NSYM ( number of symmetry operation) followed by number of translations of one unit cell along x,y,z. PYMOL: the first two digits are the symmetry operation. The next six digits correspond to the relative integral unit cell translation xxyyzz. I figured that the symmetry operation( the first two digits in pymol) is off by 1 compared to the first digit in ACT, but have no idea how the last six digits relates to the ACT 1em7.pdb pymolACT 0100 21-10 0200 3220 0300 4010 0500 6000 0501 6001 --- 1RH4.PDB pymol ACT 00-1100-1 03004000 010020-10 --- 178l.pdb 0100 21-10 0001 1001 03-1 401-1 07-1 8110 0700 8111 0300 4010 Sincerely Fang Sheng -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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] Pymol Symmetry Mates Naming
Fang, There is no relationship between ACT and PyMOL, so one wouldn't necessarily expect them to match in terms of how they name the resulting objects. However, I suspect there may also be a difference of intent: Based on a quick glance at PyMOL source code, PyMOL appears to convey a relative cell translation (based on centers of geometries), whereas ACT may be returning the computation formula. In other words, PyMOL attempts to inform the user as to whether the generated symmetry-related atom selection is within the same cell as the query selection or in one of the adjacent cells (in a translational sense). Thus in PyMOL, the (overall) nearest mates (with respect to the center of geometry) will usually have a translation of 00 00 00, and most of the time, nearby mates will vary +1 or -1 along a single translation. I'm guessing ACT simply provides the symmetry operator and the effective translation applied to generate the nearby mate. That's useful for recomputing the mate later on, but it doesn't tell the user anything about proximity. PyMOL's approach is unhelpful for recomputing a mate, but one can tell from the object name alone which objects are likely to have the most extensive contacts and how they relate in a relative sense (with respect to cell translations away from the query selection). Perhaps PyMOL could provide ACT-like naming through an optional setting? Cheers, Warren -Original Message- From: fangsh...@mbi.ucla.edu [mailto:fangsh...@mbi.ucla.edu] Sent: Thu 9/17/2009 4:52 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol Symmetry Mates Naming Hi,all, I am encountering a problem with symmetry mates generated by pymol. It seems that the naming system in pymol and ccp4-supported ACT program are not consistent. I have tested several pdbs in P4212 space group and attempted to figure out the relationship between these two, but failed. I appreciate it if you could hint me out. Some comparisons are listed below. ACT:NSYM ( number of symmetry operation) followed by number of translations of one unit cell along x,y,z. PYMOL: the first two digits are the symmetry operation. The next six digits correspond to the relative integral unit cell translation xxyyzz. I figured that the symmetry operation( the first two digits in pymol) is off by 1 compared to the first digit in ACT, but have no idea how the last six digits relates to the ACT 1em7.pdb pymolACT 0100 21-10 0200 3220 0300 4010 0500 6000 0501 6001 --- 1RH4.PDB pymol ACT 00-1100-1 03004000 010020-10 --- 178l.pdb 0100 21-10 0001 1001 03-1 401-1 07-1 8110 0700 8111 0300 4010 Sincerely Fang Sheng -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf ___ 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 -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ 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
