[ccp4bb]
Dear Community, Can you tell me. if we fit some metal in X-ray structure and its geometry and other properties are satisfied but showing some higher B-factor. does it validate to put that metal-ligand.ligand. At one site 2 metals such as K and NA fit, but K shows a higher B-factor, but other parameters such as geometry and other fit better for K instead of NA. So, out of the two ligands at the same site which one would be more favorable to be fit. -- On Thu, Sep 8, 2022 at 6:35 PM smita yadav wrote: > > Dear Community, > Can you tell me. if we fit some metal in X-ray > structure and its geometry and other properties are satisfied but showing > some higher B-factor. does it validate to put that metal-ligand.ligand. At > one site 2 metal such as K and NA fits, but K shows higher > -- > Regards, > Smita Yadav > Ph.D SRF > Regional Centre for biotechnology, > Haryana-121001. > -- Regards, Smita Yadav Ph.D SRF Regional Centre for biotechnology, Haryana-121001. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] CCP4 error in job missing
While Running CCP4 7.0. All the jobs get cleared from the main window and project. How will I get back all the job lists? Thanks in advance for suggestions. SMITA To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] postdoc position
Oklahoma State University-Main Campus: College of Arts & Sciences: Department of Chemistry The Department of Chemistry at Oklahoma State University invites applications for a Postdoctoral Fellow in Protein NMR in Mohanty lab. The PI desires an applicant that can lead an independent project focusing on protein structure-function studies using high-resolution solution NMR, would be able to conduct molecular biology (sub-cloning and mutagenesis) work along with over-expression and purification of recombinant proteins, will provide updates on research progress during weekly group meetings, write scientific manuscripts for peer reviewed journals, disseminate research at national conferences (oral/poster presentations) and assist the PI with various research related work. Minimum qualifications are a PhD in chemistry or biochemistry or biophysics along with familiarity with very good knowledge of protein NMR and 3D structure calculation, and other biophysical and computational techniques. A record of scientific output (peer-reviewed publications) and strong writing and communications skills are also required. For full consideration, please apply at https://apply.interfolio.com/93521 and submit curriculum vitae and contact information by October 15, 2021. Applications will continue to be accepted until the position has been filled. Oklahoma State University, as an equal opportunity employer, complies with all applicable federal and state laws regarding non-discrimination and affirmative action. Oklahoma State University is committed to a policy of equal opportunity for all individuals and does not discriminate based on race, religion, age, sex, color, national origin, marital status, sexual orientation, gender identity/expression, disability, or veteran status with regard to employment, educational programs and activities, and/or admissions. For more information, visit https:///eeo.okstate.edu. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] modelling in coot
Dear Community, I had a problem in correcting cis and tran peptide of structure in coot. how i can resolve it. -- Regards, Smita Yadav Ph.D JRF Regional Centre for biotechnology, Haryana-121001. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Sad News
Yes, this is of course a scam. My husband was almost duped by someone who wrote in the name of a close friend saying that he got mugged in Europe and to send money to return to USA. My husband of course was ready to send for his colleague but just gave a call to his friend to make this not a scam. Of course, it was a scam. Only last night we saved ourselves from another scam. I think it is good share with the group. My son (in high school) found a 2005 BMW X5 on an internet site. The car's blue book price is $26,000 but the asking price by the seller is $2775. Sounds too good to be true. But when my son (who dreams to own a BMW) contacted the owner (Amanda Stone), she replied him immediately saying her son died two months back in an automobile accident hit by a drunk driver while riding his fiancee's car. She simply wants to sell the car so that someone else can use it and she is not interested in making money. She said that she has a deal with e-bay and that the car will be shipped by e-bay to the buyer once the buyer pays the price that will be hold by e-bay. The buyer has 5 days to check the car out and if decides not to buy, the car will be shipped back to e-bay at seller's cost and buyer gets back his money. She sent an invoice that was from e-bay with e-bay logo and exactly looking genuine. She sent car pictures and Vin and my husband checked the car out with car fax. She wanted the money to be sent to a e-bay financial expert through moneygram although she sent name and address of an e-bay expert. That is when my husband called up e-bay just to make sure before he send the moneygram out. That is when e-bay told him this is a scam and that e-bay never asks for moneygram. That all transactions are done on e-bay site only and that e-bay does not get any contract like the one we had. E-bay told us that their logo has/can be copied to make an invoice appears to have come from them. Of course, we went all communications and invoice to e-bay. We lost only $35 for car fax. Lesson: we need to be aware of any advertisements on internet or unsolicited e-mails. Here is a site to read about different scams- http://www.fbi.gov/scams-safety/be_crime_smart Thanks, Smita Vellieux Frederic frederic.velli...@ibs.fr 2/28/2012 7:01 AM From: regnicat@, reply to: regniica@... Somehow I don't believe someone in such a situation would write to ccp4bb instead of calling the family back home. Using Skype since there is apparently internet access ! And I rather view with my mind's eye someone sitting in an internet cafe in (say) Lagos, or the Paris suburbs or Kingston or... Fred Catherine Regni wrote: I'm writing this with tears in my eyes,my family and I came over here to Madrid,Spain for a short vacation. unfortunately,we were mugged at the park of the hotel where we stayed,all cash and credit card were stolen off us but luckily for us we still have our passports with us. We've been to the Embassy and the Police here but they're not helping issues at all and our flight leaves in few hours from now but we're having problems settling the hotel bills and the hotel manager won't let us leave until we settle the bills. Well I really need your financial assistance..Please, Let me know if you can help us out? Am freaked out at the Moment. Catherine Regni.. Catherine Regni, Ph.D.
Re: [ccp4bb] Insoluble ligand?
Hi Ritcha, Did you try Methanol or Ethanol to see if your ligand dissolve in these solvents? You should try these solvents first before adding any detergents. Good luck. Smita Mohanty Chaudhary, Ritcha chaudha...@missouri.edu 9/16/2011 11:04 AM Hi All I have a ligand that is dissolved in 100% DMSO. The ligand crashes out even when diluted to 20% final DMSO concentration in the protein buffer. I have heard of people using detergents such as n octyl Beta D glucoside to keep the ligand solubilized at lower DMSO concentrations. Can someone give me pointers in this direction? Any suggestions, references etc. Thanks much Ritcha
Re: [ccp4bb] nmr question
NMR people do collect NMR data beyond 40 deg C. Many membrane protein structures are determined at 55-60 deg .C (the membrane proteins may not be very large but in micelles -combined weight is large). When the protein is stable and the 1H-15N-HSQC (fingerprint region) does not change with temp (meaning temp has no effect on the protein), one can go higher temp. Yes, it certainly helps reducing line width and if you combine TROSY based experiments, the resolution increases dramatically. Smita Mohanty Roopa Thapar rtha...@hwi.buffalo.edu 7/1/2011 11:47 AM ‘NMR people’ do use thermophilic proteins but I have never heard of anyone boiling samples :) By increasing temperature I meant going to around 37-40 deg C. On 7/1/11 12:26 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: ...they are stable enough that one can raise the temperature to increase the correlation time. I wonder whether NMR people have tried using hyperthermophile proteins to be able to essentially boil the sample to decrease the rotational correlation time constant? There is even an organism I read about in a Science brevia paper whose peak doubling time is at autoclave temperatures... JPK
[ccp4bb] Postdoctoral Research Associate Position Available
Postdoctoral Research Associate Department of Chemistry and Biochemistry Auburn University Auburn, AL 36849-5312 Project Description: The postdoctoral research associate position is available in the laboratory of Professor Smita Mohanty. The project involves structure-function studies of membrane proteins. The laboratory has made very good progress in the overexpression, purification and optimizing crystallization conditions for a 80 kDa membrane protein. The successful candidate will join a multi-disciplinary research team that includes NMR Spectroscopists as well. This position represents an excellent opportunity for a young postdoctoral scientist to develop his/her expertise, broaden his/her experience and interact with scientists from around the world. Qualifications A Ph.D. completed within the last 5 years in physics, biophysics, physical chemistry or structural biology is required. Previous experience in protein crystallography is required. The candidate should be self-motivated, interpersonal communication skills and ability to interact effectively and work productively in a team. How to Apply: Qualified applicants may apply directly to Professor Smita Mohanty at moha...@auburn.edu This appointment is open to all qualified U.S. and non-U.S. citizens without regard to race, color, age, religion, sex, national origin, physical or mental disability, or status as a Vietnam-era veteran or disabled veteran. Please contact Prof. Mohanty for any questions about this position.
