Re: [ccp4bb] Disulfide bonds
I'd google for "Bart Hazes" and "SSBOND" myself. There is (or was) a server, and the publication is Prot. Eng. 1988, 119, 25 (PMID 3244694). The server seems to be down or has moved. HTH, Fred. > Message du 04/03/12 05:07 > De : "Naveed A Nadvi" > A : CCP4BB@JISCMAIL.AC.UK > Copie à : > Objet : [ccp4bb] Disulfide bonds > > Hello everyone, > > I was wondering if there is any information available regarding the range of > Ca-to-Ca distances between two cysteine residues forming disulfide bonds. Is > there any software available for analysing the PDB for this kind of > information? Some old textbooks suggest a distance of 4.4-6.8 A. I would very > much appreciate any comments or suggestions you may have. > > Regards, > > Naveed > > Faculty of Pharmacy, > The University of Sydney >
Re: [ccp4bb] Disulfide bonds
If you are looking for predicting disulfide bonds, then this may be useful http://lmgtfy.com/?q=predict+disulfide+bonds Cheers, Ed. -- Hurry up, before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] Disulfide bonds
Hi Fred, The SSBOND server has indeed been moved as we have relocated to a new building. SSBOND is still available at the new server address: http://hazeslab.med.ualberta.ca/forms/ssbond.html This was my first ever program,with help from Bauke Dijkstra, and I was pleasantly surprised how many messages I got after the server relocation. SSBOND will soon get some competition for most used service as I am about to release some bioinformatics services. Bart On 12-03-04 02:36 AM, Frederic VELLIEUX wrote: I'd google for "Bart Hazes" and "SSBOND" myself. There is (or was) a server, and the publication is Prot. Eng. 1988, 119, 25 (PMID 3244694). The server seems to be down or has moved. HTH, Fred. Message du 04/03/12 05:07 De : "Naveed A Nadvi" A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Disulfide bonds Hello everyone, I was wondering if there is any information available regarding the range of Ca-to-Ca distances between two cysteine residues forming disulfide bonds. Is there any software available for analysing the PDB for this kind of information? Some old textbooks suggest a distance of 4.4-6.8 A. I would very much appreciate any comments or suggestions you may have. Regards, Naveed Faculty of Pharmacy, The University of Sydney
Re: [ccp4bb] sudden drop in R/Rfree
Hi Rajesh, If you're seeing a lot of extra density coming up in the map in regions where you previously added waters, is it possible that this extra density corresponds to a part of your protein that you previously thought was disordered and is thus missing from the current model? At this resolution you wouldn't expect to see many waters. Also, to the best of my knowledge, the relative weighting of the X-ray and geometry terms in BUSTER is set by the program so as to produce a rmsd in bond lengths equal to a target value. The default value of this is 0.01 Ang (I think) but you can change this using the -r option on the command line. Using a lower value will reduce the weight on the X-ray term and may lower the R/R-free gap. Best wishes, Joe > > > Dear All, > I have a 3.3 A data for a protein whose SG is P6522. Model used was wild > type structure of same protein at 2.3 A. After molecular replacement, > first three rounds of refinement the R/Rf was 26/32.8, 27.1/31.72 % and > 7.35/30.88 % respectively.In the fourth round I refined with TLS and NCS > abd added water and the R/Rf dropped to 19.34/26.46. It has almost 7% > difference. I also see lot of unanswerable density in the map where lot of > waters were placed. Model fits to the map like a low resolution data with > most of side chains don't have best density. > I was not expecting such a sudden drop in the R/Rfree and a difference is > 7.2%. I am wondering if I am in right direction. I am not sure if this > usual for 3.3A data or in general any data if we consider the difference. > I appreciate your valuable suggestions. > ThanksRaj > >
Re: [ccp4bb] sudden drop in R/Rfree
Presumably your data is quite anisotropic, and low resolution, so it is quite likely that a TLS model will give much better description of the B factors than more classical refinement. Modelling solvent at that resolotion will be tricky of course. Elesnor On Mar 4 2012, Joseph Cockburn wrote: Hi Rajesh, If you're seeing a lot of extra density coming up in the map in regions where you previously added waters, is it possible that this extra density corresponds to a part of your protein that you previously thought was disordered and is thus missing from the current model? At this resolution you wouldn't expect to see many waters. Also, to the best of my knowledge, the relative weighting of the X-ray and geometry terms in BUSTER is set by the program so as to produce a rmsd in bond lengths equal to a target value. The default value of this is 0.01 Ang (I think) but you can change this using the -r option on the command line. Using a lower value will reduce the weight on the X-ray term and may lower the R/R-free gap. Best wishes, Joe Dear All, I have a 3.3 A data for a protein whose SG is P6522. Model used was wild type structure of same protein at 2.3 A. After molecular replacement, first three rounds of refinement the R/Rf was 26/32.8, 27.1/31.72 % and 7.35/30.88 % respectively.In the fourth round I refined with TLS and NCS abd added water and the R/Rf dropped to 19.34/26.46. It has almost 7% difference. I also see lot of unanswerable density in the map where lot of waters were placed. Model fits to the map like a low resolution data with most of side chains don't have best density. I was not expecting such a sudden drop in the R/Rfree and a difference is 7.2%. I am wondering if I am in right direction. I am not sure if this usual for 3.3A data or in general any data if we consider the difference. I appreciate your valuable suggestions. ThanksRaj -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] twin refinement in refmac
Is this twinning or several crystals indexed according to different conventions? You usually see evidence of twinning for each crystal if it is really there.. Trigonal data can be indexed as h,k,l k,h,-k -h,-k,l or -k,-h,-l of course so you have a 75% chance of getting the 2nd crystal on a different convention than the first.. POINTLESS checks for this if you give it pairs of input files and does a good job in selecting the same indexing convention - providing of course the twinning isnt present. I would be suspicious because a) I have been convinced by having more than 2 twin domains b) when there is twinning the data analysis on each crystal seperately shows it up. Eleanor - On Mar 2 2012, wtempel wrote: Dear CCp4ers, A good morning to everyone. Today, I have a structure that I initially refined in space group P6522, 1mol/asu. Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; / > 3 2.61-2.55A: Rsym=39.6%, / > 10 50.00-6.13: Rsym=6.4% Some mild anisotropy in the resolution limits is apparent on the diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in the other. Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A resolution, with some difference density for loops that cannot be interpreted with reasonable geometry. Rsym is very similar for data scaled in P3, in all resolution shells. Xtriage does not suggest merohedral twinning. Nevertheless, I extended my free flags in sftools from P6522 to P32 and cad'd them to amplitudes merged in spacegroup P32. Correspondingly, I expanded my model to a homotetramer and ran Refmac with amplitude based twinning. (Would this be a reasonable input to twin refinement?) From the output coordinates: REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS :4 REMARK 3 TWIN DOMAIN :1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.269 REMARK 3 TWIN DOMAIN :2 REMARK 3 TWIN OPERATOR : -K, -H, -L REMARK 3 TWIN FRACTION : 0.171 REMARK 3 TWIN DOMAIN :3 REMARK 3 TWIN OPERATOR : K, H, -L REMARK 3 TWIN FRACTION : 0.258 REMARK 3 TWIN DOMAIN :4 REMARK 3 TWIN OPERATOR : -H, -K, L REMARK 3 TWIN FRACTION : 0.302 Does this establish twinning versus underestimated symmetry? And what do I need to know about my free-R? Did refmac assign a new flag? Whereas the output file's flags are all 1s and 0s, the input file had 0 ... 19. During the first run, Rfree dropped to <28%. But on a subsequent run, Rfree was stuck >30% when I used the initial job's output MTZ. Many thanks in advance for your helpful comments. Wolfram Tempel -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] Disulfide bonds
I wonder if it's not in the output of pisa from ccp4mg. On 03/05/2012 12:30 AM, Bart Hazes wrote: Hi Fred, The SSBOND server has indeed been moved as we have relocated to a new building. SSBOND is still available at the new server address: http://hazeslab.med.ualberta.ca/forms/ssbond.html This was my first ever program,with help from Bauke Dijkstra, and I was pleasantly surprised how many messages I got after the server relocation. SSBOND will soon get some competition for most used service as I am about to release some bioinformatics services. Bart On 12-03-04 02:36 AM, Frederic VELLIEUX wrote: I'd google for "Bart Hazes" and "SSBOND" myself. There is (or was) a server, and the publication is Prot. Eng. 1988, 119, 25 (PMID 3244694). The server seems to be down or has moved. HTH, Fred. Message du 04/03/12 05:07 De : "Naveed A Nadvi" A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Disulfide bonds Hello everyone, I was wondering if there is any information available regarding the range of Ca-to-Ca distances between two cysteine residues forming disulfide bonds. Is there any software available for analysing the PDB for this kind of information? Some old textbooks suggest a distance of 4.4-6.8 A. I would very much appreciate any comments or suggestions you may have. Regards, Naveed Faculty of Pharmacy, The University of Sydney
