[ccp4bb] quality homology model
Dear Community, I have a question regarding protein model quality for introduction of point mutations which should increase solibity/stability of my protein of interest. I plan to do homology models so that I can check the most promising amino acids. Which quality/resolution of the model do I need? Which parameters would you check (gromos, anolea), and what would you use as cut-off values? At the moment I thought, that it could be interesting to model a homologue of my protein and check the RMSDs with the crystal structure. Maybe you know some good literature, describing this? Thank you Susy
[ccp4bb] Problem of Refinement and density map
Dear all, I have a question regarding the refinement and density map. My protein is 261 amino acids long and crystalize very nicely with very high resolution . There is no multiple spot in the image and diffraction looks amazing. I collected a dataset at 1.38 resolution and the space group is P43, overall Rmerg is 0.02 (most likely the space group is P4122, but then the solvent content is less than 16% for one molecule in the assymmetric unit, that are unlikely), so I processed the image in P4 (36% solvent) and run molecular replacement with a model that have 42 sequence identity. I got a solution in P43 that are good enough in some part but in the map there are many gap at even lower sigma level. I tried to refine and Rfree stacked at 36 along with Rwork, which is 33. I also checked the degradation patteren of the protein in the crystal and it looks not degraded and full length protein crystalize. Is there anybody can suggest me anything that I can try? Regards, Md. Munan ShaikPhD Student Department of Biotehnology School of Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com munan.sh...@unipd.it
Re: [ccp4bb] Problem of Refinement and density map
Have you checked for twinning? Look at the plots after scala.. Eleanor On 02/07/2011 10:49 AM, Md. Munan Shaik wrote: Dear all, I have a question regarding the refinement and density map. My protein is 261 amino acids long and crystalize very nicely with very high resolution . There is no multiple spot in the image and diffraction looks amazing. I collected a dataset at 1.38 resolution and the space group is P43, overall Rmerg is 0.02 (most likely the space group is P4122, but then the solvent content is less than 16% for one molecule in the assymmetric unit, that are unlikely), so I processed the image in P4 (36% solvent) and run molecular replacement with a model that have 42 sequence identity. I got a solution in P43 that are good enough in some part but in the map there are many gap at even lower sigma level. I tried to refine and Rfree stacked at 36 along with Rwork, which is 33. I also checked the degradation patteren of the protein in the crystal and it looks not degraded and full length protein crystalize. Is there anybody can suggest me anything that I can try? Regards, Md. Munan ShaikPhD Student Department of Biotehnology School of Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com munan.sh...@unipd.it
Re: [ccp4bb] Problem of Refinement and density map
Also try lower symmetry space groups. 36% solvent, while not unheard of, is on a high end. On Mon, 2011-02-07 at 02:49 -0800, Md. Munan Shaik wrote: Dear all, I have a question regarding the refinement and density map. My protein is 261 amino acids long and crystalize very nicely with very high resolution . There is no multiple spot in the image and diffraction looks amazing. I collected a dataset at 1.38 resolution and the space group is P43, overall Rmerg is 0.02 (most likely the space group is P4122, but then the solvent content is less than 16% for one molecule in the assymmetric unit, that are unlikely), so I processed the image in P4 (36% solvent) and run molecular replacement with a model that have 42 sequence identity. I got a solution in P43 that are good enough in some part but in the map there are many gap at even lower sigma level. I tried to refine and Rfree stacked at 36 along with Rwork, which is 33. I also checked the degradation patteren of the protein in the crystal and it looks not degraded and full length protein crystalize. Is there anybody can suggest me anything that I can try? Regards, Md. Munan Shaik PhD Student Department of Biotehnology School of Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com munan.sh...@unipd.it -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] exo and endo conformation
Hi there i have modeled a ribavirin molecule in one of the structures that i solved at 2.5A recently. omit map confirms the presence of ligand but the map itself is not very clear.there is some positive density in fo-fc map around the ribose ring, that disappears at 3.2sigma level. I wonder whether it is possible that the ribose ring has exo(2' and 3') and endo(2' and 3') conformation in the model. from where can i get the coordinates of these conformations of ribavirin. or how can i draw this using sketcher in ccp4. can anyone please send me the smileys of these two conformations. any other suggestions are also welcome. regards and thanks in advance, -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
Re: [ccp4bb] Problem of Refinement and density map
Although there might be space group and twining trouble from the sound of it, running ARP/wARP starting from your molrep solution, at that resolution should really do whatever can be done and reduce R/RFree while building the vast majority of the model. If Rfree stays high, start looking at sg possibilities and twining. A. PS In general I would suggest to download and install arp/warp but a quick try for new users can always be through the web interface http://cluster.embl-hamburg.de/ARPwARP/remote-http.html On Feb 7, 2011, at 11:49, Md. Munan Shaik wrote: Dear all, I have a question regarding the refinement and density map. My protein is 261 amino acids long and crystalize very nicely with very high resolution . There is no multiple spot in the image and diffraction looks amazing. I collected a dataset at 1.38 resolution and the space group is P43, overall Rmerg is 0.02 (most likely the space group is P4122, but then the solvent content is less than 16% for one molecule in the assymmetric unit, that are unlikely), so I processed the image in P4 (36% solvent) and run molecular replacement with a model that have 42 sequence identity. I got a solution in P43 that are good enough in some part but in the map there are many gap at even lower sigma level. I tried to refine and Rfree stacked at 36 along with Rwork, which is 33. I also checked the degradation patteren of the protein in the crystal and it looks not degraded and full length protein crystalize. Is there anybody can suggest me anything that I can try? Regards, Md. Munan Shaik PhD Student Department of Biotehnology School of Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com munan.sh...@unipd.it P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
[ccp4bb] Preliminary X-ray studies
Just out of curiosity does any one still use, or know of anyone else who still uses X-ray photography to screen cell parameters and data quality prior to data collection, for either macromolecular or small molecule studies? Rex Palmer Birkbeck College
Re: [ccp4bb] Problem of Refinement and density map
Have you tried both the P43 and P41 space groups? I ask because you said you got a solution in P43 but the likely space group is P4122. If the likely space group is really P4122 (and not P4322), the corresponding space group is P41, not P43. Sue On Feb 7, 2011, at 3:49 AM, Md. Munan Shaik wrote: Dear all, I have a question regarding the refinement and density map. My protein is 261 amino acids long and crystalize very nicely with very high resolution . There is no multiple spot in the image and diffraction looks amazing. I collected a dataset at 1.38 resolution and the space group is P43, overall Rmerg is 0.02 (most likely the space group is P4122, but then the solvent content is less than 16% for one molecule in the assymmetric unit, that are unlikely), so I processed the image in P4 (36% solvent) and run molecular replacement with a model that have 42 sequence identity. I got a solution in P43 that are good enough in some part but in the map there are many gap at even lower sigma level. I tried to refine and Rfree stacked at 36 along with Rwork, which is 33. I also checked the degradation patteren of the protein in the crystal and it looks not degraded and full length protein crystalize. Is there anybody can suggest me anything that I can try? Regards, Md. Munan Shaik PhD Student Department of Biotehnology School of Bioscience and Biotechnology via G. Colombo 03 Padova 35131, Italy Mobile: 00393275671896 E-mail: munanbt2...@yahoo.com munan.sh...@unipd.it Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray
[ccp4bb] FW: 21st July 2011 Barkla Blundell Celebratory Symposium
IMPORTANT: Registration is free but participation requires registration by sending an email to Mrs Angela Dell, d...@liverpool.ac.uk. barkla_blundell_symposium_21July.pdf Description: barkla_blundell_symposium_21July.pdf
[ccp4bb] how to install cns1.3 to mac (10.6) by fink
Hi all, I installed fink 64 bit on my mac osx 10.6. I want to install cns by fink. I found only cns 1.3 is suitable for osx 10.6. Can someone help me to install this program? Thanks. Lisa
Re: [ccp4bb] how to install cns1.3 to mac (10.6) by fink
1. Go to the following URL: http://cns-online.org/v1.3/ http://cns-online.org/v1.3/2. Click the Installation link on the left-hand side. 3. Follow the provided instructions for your operating system and/or shell environment. On Mon, Feb 7, 2011 at 6:12 PM, LISA science...@gmail.com wrote: Hi all, I installed fink 64 bit on my mac osx 10.6. I want to install cns by fink. I found only cns 1.3 is suitable for osx 10.6. Can someone help me to install this program? Thanks. Lisa -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov
[ccp4bb] coot command cannot be located in phenix
Hi all, I installed phenix1.7 on my mac osx 10.6. But I cannot open coot in this phenix.When I press coot, it said coot command cannot be located. How to fix this problem? Thank. Lisa
