Re: [ccp4bb] shape complementarity between protein and DNA surface
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Deepak, the only atom type present in DNA and not in Proteins would be the Phosphorus. You can probably add this to sc_radii.lib yourself with the line ***P* 1.80 the radius stems from http://en.wikipedia.org/wiki/Phosphorus and the link to http://en.wikipedia.org/wiki/Van_der_Waals_radius provides you with the reference. The results will hardly differ if you modify this value within 100%, I guess. Cheers, Tim On 02/07/2012 04:19 AM, Deepak Thankappan Nair wrote: Dear All For calculation of the shape complementarity index using the Sc program between a protein and DNA surface, does anybody have a modified radii.lib file that includes information about DNA atoms? Also, is there any reference that has information regarding the atomic radii of DNA atoms? thanks Deepak - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPMPu1UxlJ7aRr7hoRAhAYAKDHJzkHfEPwcHO99FAV57zOrsYasACgvO/V CtUM1Z8x0NSl0cXK4A4tH0k= =H8Uk -END PGP SIGNATURE-
[ccp4bb] shape complementarity
Hello, After following the discussion on [ccp4bb] shape complementarity between protein and DNA surface, is there someone here able to explain simply what the SC software of CCP4 is calculating? I mean, is there some intuitive/easy to understand explanation of what SC is calculating? I know I should read the corresponding paper, but I'd like someone to enlighten me before so I have better chances of understanding the article. Thanks, Francois.
Re: [ccp4bb] shape complementarity
Hi Francois Here's a one-liner. The major concept behind the Sc coefficient is that it measures the extent to which, on average, the normal vectors between closest-neighbour opposing points within the molecular interface are antiparallel. Sc=1 implies that the surfaces fit exactly, all such vectors are perfectly antiparallel. Heuristically, Sc values of 0.86 are about as good as protein-protein interfaces get (see Nature. 2005 435, pp773-8). Values below 0.65 indicate relatively poor shape complementarity. Use of a normal vector -based metric is considered superior to a distance-based metric, though Sc does have a distance-based weight applied to the normal dot products. Critical to this calculation is that the boundary of the buried molecular interface has to be discarded from the measure, as this region is intrinsically geometrically divergent. Sc is thus computed across only that part of the buried surface that might be expected to be shape complementarity, which makes it somewhat ill-suited to smaller interfaces. All these details are in the JMB paper, which, unfortunately, there is no substitute for reading :-) sincerely Mike Mike Lawrence, PhD Associate Professor and WEHI Fellow Division of Structural Biology Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville Victoria 3052, AUSTRALIA Tel. 61-3-9345-2693 Fax 61-3-9345-2686 Email: lawre...@wehi.edu.au On 08/02/2012, at 12:08 PM, Francois Berenger wrote: Hello, After following the discussion on [ccp4bb] shape complementarity between protein and DNA surface, is there someone here able to explain simply what the SC software of CCP4 is calculating? I mean, is there some intuitive/easy to understand explanation of what SC is calculating? I know I should read the corresponding paper, but I'd like someone to enlighten me before so I have better chances of understanding the article. Thanks, Francois. __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __
Re: [ccp4bb] shape complementarity
On 02/08/2012 12:47 PM, Mike Lawrence wrote: Hi Francois Here's a one-liner. The major concept behind the Sc coefficient is that it measures the extent to which, on average, the normal vectors between closest-neighbour opposing points within the molecular interface are antiparallel. Sc=1 implies that the surfaces fit exactly, all such vectors are perfectly antiparallel. Heuristically, Sc values of 0.86 are about as good as protein-protein interfaces get (see Nature. 2005 435, pp773-8). Values below 0.65 indicate relatively poor shape complementarity. Use of a normal vector -based metric is considered superior to a distance-based metric, though Sc does have a distance-based weight applied to the normal dot products. Critical to this calculation is that the boundary of the buried molecular interface has to be discarded from the measure, as this region is intrinsically geometrically divergent. Sc is thus computed across only that part of the buried surface that might be expected to be shape complementarity, which makes it somewhat ill-suited to smaller interfaces. All these details are in the JMB paper, which, unfortunately, there is no substitute for reading :-) Thanks a lot for this very nice answer. I will definitely read your JMB article. Best regards, Francois.
[ccp4bb] shape complementarity between protein and DNA surface
Dear All For calculation of the shape complementarity index using the Sc program between a protein and DNA surface, does anybody have a modified radii.lib file that includes information about DNA atoms? Also, is there any reference that has information regarding the atomic radii of DNA atoms? thanks Deepak
[ccp4bb] shape complementarity
Dear All, Greetings! Can anybody tell me a method to quantitate shape complementarity between two surfaces? Sc program in CCP4 is not running properly. thanks and regards Deepak
Re: [ccp4bb] shape complementarity
Deepak Thankappan Nair wrote: ~~~ Can anybody tell me a method to quantitate shape complementarity between two surfaces? Sc program in CCP4 is not running properly. thanks and regards Deepak I think SC is THE way to calculate it. If not working in the current release, we should get it fixed. Can you be more specific? For me using ccp4-6.2.0 it runs and gives apparently reasonable output: Mean normal product:surface 2 to surface 1 = 0.419 Median normal product: surface 2 to surface 1 = 0.411 Summary of results: D(A-B) D(B-A) D(A-B)+D(B-A)/2 Mean 1.1681.0571.113 Median 1.1161.0001.058 S(A-B) S(B-A) S(A-B)+S(B-A)/2 Mean 0.3890.4190.404 Median 0.3550.4110.383 Shape complementarity statistic Sc =0.383 _
Re: [ccp4bb] shape complementarity
Deepak Thankappan Nair wrote: Dear Dr. Berry thanks for the mail. maybe the syntax that I provide is not correct. i assume you have to write MOLECULE1 CHAIN A to define the first surface but i get the following error: MOLECULE1 CHAIN A No molecule number given BFONT COLOR=#FF!--SUMMARY_BEGIN-- SC: Syntax: MOLECULEn SC: Syntax: MOLECULEn I think you don't put the in n - just the number. here is an example that runs: sc xyzin temp.pdb eof MOLecule 1 zone C 20 C 379 MOLecule 2 zone R 74 R 196 eof Good luck! eab there are no examples on the ccp4 website any light on this would be very valuable, regards deepak On 2/6/12, Edward A. Berryber...@upstate.edu wrote: Deepak Thankappan Nair wrote: ~~~ Can anybody tell me a method to quantitate shape complementarity between two surfaces? Sc program in CCP4 is not running properly. thanks and regards Deepak I think SC is THE way to calculate it. If not working in the current release, we should get it fixed. Can you be more specific? For me using ccp4-6.2.0 it runs and gives apparently reasonable output: Mean normal product:surface 2 to surface 1 = 0.419 Median normal product: surface 2 to surface 1 = 0.411 Summary of results: D(A-B) D(B-A) D(A-B)+D(B-A)/2 Mean 1.1681.0571.113 Median 1.1161.0001.058 S(A-B) S(B-A) S(A-B)+S(B-A)/2 Mean 0.3890.4190.404 Median 0.3550.4110.383 Shape complementarity statistic Sc =0.383 _
[ccp4bb] shape complementarity using NMR structures
Hello Everyone, I am trying to calculate shape complementarity of NMR structure (1U89) using CCP4 Sc. I get following error $WARNING: NO CRYST CARDS READ$ BFONT COLOR=#FF!--SUMMARY_BEGIN-- $TEXT:Warning: $$ comment $$ WARNING: NO CRYST CARDS READ FROM XYZIN $$ !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- $TEXT:Warning: $$ comment $$ WARNING: NO SCALE CARDS READ FROM XYZIN $$ !--SUMMARY_END--/FONT/B Any advice is highly appreciated. Thanks in advance. Regards, Yogesha
Re: [ccp4bb] shape complementarity using NMR structures
Thanks Boaz. I tried that too. But error was same. What worked is removal of all models except 1 model and removal of all waters. Thanks Yogesha From: Boaz Shaanan [bshaa...@exchange.bgu.ac.il] Sent: Thursday, April 07, 2011 5:44 PM To: Sollepura Yogesha Subject: RE: shape complementarity using NMR structures Hi, I guess you have to provide a dummy unit cell and identity matrix (which NMR structures obviously don't have) in order to make SC happy. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sollepura Yogesha [yoge...@scripps.edu] Sent: Friday, April 08, 2011 12:06 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] shape complementarity using NMR structures Hello Everyone, I am trying to calculate shape complementarity of NMR structure (1U89) using CCP4 Sc. I get following error $WARNING: NO CRYST CARDS READ$ BFONT COLOR=#FF!--SUMMARY_BEGIN-- $TEXT:Warning: $$ comment $$ WARNING: NO CRYST CARDS READ FROM XYZIN $$ !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- $TEXT:Warning: $$ comment $$ WARNING: NO SCALE CARDS READ FROM XYZIN $$ !--SUMMARY_END--/FONT/B Any advice is highly appreciated. Thanks in advance. Regards, Yogesha
[ccp4bb] Shape complementarity for nucleic acids
Hi! I am trying to calculate shape complementarity using SC in CCP4 for nucleic acids. SC stopped with an error no radius found for atoms of nucleic acid residues. I can edit in the radii for those atoms in sc_radii.lib, but am wondering what would the recommended radii be, especially for phosphorus? Thanks. -Sam
[ccp4bb] shape complementarity
Hello everybody, I recently tried to feed the shape complementarity program (sc) with GRASP surface files for visualisation. Sc is supposed to output modified surface files, again, in GRASP format. However, the program terminated without producing a file, or, sometimes, writing truncated ones. The GRASP files passed the compatibility check of sc. I tested two different pdb files with the according GRASP surface files (made with Chimera). The first run ended with: At line 2825 of file /usr/local/xtal/ccp4-6.1.13/src/sc_/sc.f Fortran runtime error: End of file In the second run, I removed all hydrogen atoms before I calculated the surface files. Sc showed the following error: Header information from grasp file 1 format=2 Keywords=vertices,normals,triangles Properties= Decoding property list Updated property list is:,gproperty Number of vertices=76375 Number of triangles= 54697 Size of grid= 65 Midpoint 91.033806 91.542160 89.700684 vertices read accessibles read BFONT COLOR=#FF!--SUMMARY_BEGIN-- SC: read error in s/r read_real_line SC: read error in s/r read_real_line Times: User: 8.3s System:0.4s Elapsed: 0:09 /pre /html !--SUMMARY_END--/FONT/B I can't make head or tail of it, maybe someone else can. Thanks in advance for any information and advice Reiner
Re: [ccp4bb] shape complementarity
Hi Reiner I haven't seen this problem before; if you send me all the relevant files I will try to check it out. It may relate to the fact that the GRASP files were made with Chimera. sincerely Mike Lawrence Hello everybody, I recently tried to feed the shape complementarity program (sc) with GRASP surface files for visualisation. Sc is supposed to output modified surface files, again, in GRASP format. However, the program terminated without producing a file, or, sometimes, writing truncated ones. The GRASP files passed the compatibility check of sc. I tested two different pdb files with the according GRASP surface files (made with Chimera). The first run ended with: At line 2825 of file /usr/local/xtal/ccp4-6.1.13/src/sc_/sc.f Fortran runtime error: End of file In the second run, I removed all hydrogen atoms before I calculated the surface files. Sc showed the following error: Header information from grasp file 1 format=2 Keywords=vertices,normals,triangles Properties= Decoding property list Updated property list is:,gproperty Number of vertices=76375 Number of triangles= 54697 Size of grid= 65 Midpoint 91.033806 91.542160 89.700684 vertices read accessibles read BFONT COLOR=#FF!--SUMMARY_BEGIN-- SC: read error in s/r read_real_line SC: read error in s/r read_real_line Times: User: 8.3s System:0.4s Elapsed: 0:09 /pre /html !--SUMMARY_END--/FONT/B I can't make head or tail of it, maybe someone else can. Thanks in advance for any information and advice Reiner __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __
[ccp4bb] shape complementarity
Dear All, Could someone please suggest me program(s) to get the shape complementarity index for a protein complex structure of mine? Many thanks -- Amit Sharma, Ph.D. Research Associate, Department of Biology, University of York, YO10 5DD UK
Re: [ccp4bb] shape complementarity
amit sharma wrote: Dear All, Could someone please suggest me program(s) to get the shape complementarity index for a protein complex structure of mine? Many thanks sc, by Michael Lawrence: http://www.ccp4.ac.uk/dist/html/sc.html (included in ccp4 distro)
Re: [ccp4bb] shape complementarity calculations
Hi Vaheh, Below is a reply I made to the BB in 2007 after a similar enquiry. I expect the program should still work the same, although I haven't used it in recent releases. You have to run it from line command, as there is no interface for it in CCP4i. If you are running under Windows, as I do, you have to start a DOS prompt window and run it from there. You might even need to specify the full path of the binary executable. You also need to specify the output log file, and you can either type your input directly or put it in a text file. I hope this helps. Pierre p.s. I echo Ed Berry's exhortation: If you have been running MD on your interacting molecules, the SC parameter is probably meaningless. But I am prepared for surprises. * Start of previous Reply *** The SC manual URL http://www.ccp4.ac.uk/dist/html/sc.html does contain all the information you need, but I agree it takes some deciphering. The basic parameters are the selections of two 'molecules' whose interface you want to study. For that purpose, the script or line input is really minimal, such as: molecule 1 zone C 3 C 5 molecule 2 chain D chain E end Here molecule 1 is a number of residues in chain C (zone), and molecule 2 is all of chains D and E. You can include and exclude other atoms in each 'molecule' selection. The instruction 'end' tells the program to start calculating. You can modify the program defaults by adding other instructions for 'dot density', 'probe radius' and others, but I usually run it with all the hard wired defaults. These parameters are largely equivalent to their counterparts in AREAIMOL to determine how accurately you want the interfaces to be calculated. Good Luck. ** End of previous reply *** ** Dr. Pierre Rizkallah, Senior Lecturer in Structural Biology, School of Medicine, Academic Avenue, Heath Park, Cardiff CF14 4XN email: rizkall...@cf.ac.uk phone + 44 29 2074 2248 Oganesyan, Vaheh oganesy...@medimmune.com 03/03/09 10:28 PM Colleagues, Would some one kindly suggest software that calculates shape complementarity of two interacting proteins based on co-crystal structure? I've seen number of reports with sc parameter included but none of those mention how it was done. Among non-runnable programs in CCP4 there is the sc program that indeed does not run. Thanks in advance. ___ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
[ccp4bb] shape complementarity calculations
Colleagues, Would some one kindly suggest software that calculates shape complementarity of two interacting proteins based on co-crystal structure? I've seen number of reports with sc parameter included but none of those mention how it was done. Among non-runnable programs in CCP4 there is the sc program that indeed does not run. Thanks in advance. ___ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] shape complementarity calculations
Actually sc is part of the ccp4 package. (more $CDOC/sc.doc) The reference describing the procedure is: 1. Michael C. Lawrence and Peter M. Colman J. Mol. Biol., 234, p946 - p950 (1993) As you say, it calculates shape complimentarity of the surfaces as they are docked in the structure. So before you attribute changes in sc to conformational changes, be sure the surfaces haven't moved wrt each other! Cheers, Ed Oganesyan, Vaheh wrote: Colleagues, Would some one kindly suggest software that calculates shape complementarity of two interacting proteins based on co-crystal structure? I've seen number of reports with sc parameter included but none of those mention how it was done. Among non-runnable programs in CCP4 there is the sc program that indeed does not run. Thanks in advance. ___ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] shape complementarity calculations - oops!
Oganesyan, Vaheh wrote: Among non-runnable programs in CCP4 there is the sc program that indeed does not run. Sorry, I didn't see the rest of your post. I had sc running and producing meaningful results back in 2006-2007, I can check which version etc. Ed
Re: [ccp4bb] shape complementarity calculations
Hi Vaheh I have not had anyone report problems with sc of late. If you send me the relevant files or output I can check it out for you. sincerely Mike Lawrence, PhD WEHI Principal Research Fellow Division of Structural Biology Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville Victoria 3052, AUSTRALIA Tel. 61-3-9345-2693 Fax 61-3-9345-2686 Email: lawre...@wehi.edu.au On 04/03/2009, at 9:17 AM, Oganesyan, Vaheh wrote: Colleagues, Would some one kindly suggest software that calculates shape complementarity of two interacting proteins based on co-crystal structure? I've seen number of reports with sc parameter included but none of those mention how it was done. Among non-runnable programs in CCP4 there is the sc program that indeed does not run. Thanks in advance. ___ Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. Mike Lawrence, PhD WEHI Principal Research Fellow Division of Structural Biology Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville Victoria 3052, AUSTRALIA Tel. 61-3-9345-2693 Fax 61-3-9345-2686 Email: lawre...@wehi.edu.au
