Re: [ccp4bb] phenix refinement for bent DNA
On 30/03/2021 02:52, Srivastava, Dhiraj wrote: I am sorry about phenix related question. But since the question was refinement related I thought it will be ok to ask on ccp4bb. For the record, it's not wrong, it just that questions about Phenix are more likely to get accurate and timely responses on the phenixbb. Paul. 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/
Re: [ccp4bb] [External] Re: [ccp4bb] phenix refinement for bent DNA
Thank you everyone for the help. I am sorry about phenix related question. But since the question was refinement related I thought it will be ok to ask on ccp4bb. Thank you Dhiraj From: Oleg Sobolev Sent: Monday, March 29, 2021 6:18 PM To: Srivastava, Dhiraj Cc: CCP4BB@jiscmail.ac.uk Subject: [External] Re: [ccp4bb] phenix refinement for bent DNA Hi Dhiraj, I have structure with bent DNA. I am trying to refine the structure using phenix. do I need to turn off the DNA secondary structure restraints during refinement? Application of secondary structure restraints depends on the quality of the experimental data. The most basic parameter to consider would be a resolution. For lower-resolution SS restraints might help to keep a reasonable geometry of the structure. The bent DNA should also work fine with SS since they are restraining base pairs and stacking pairs which normally don't distort too much. P.S. There is a separate bulletin board for Phenix-specific questions: http://www.phenix-online.org/mailman/listinfo/phenixbb Best regards, Oleg Sobolev. Thank you Dhiraj To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 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/
Re: [ccp4bb] phenix refinement for bent DNA
Hi Dhiraj, I have structure with bent DNA. I am trying to refine the structure > using phenix. do I need to turn off the DNA secondary structure restraints > during refinement? > Application of secondary structure restraints depends on the quality of the experimental data. The most basic parameter to consider would be a resolution. For lower-resolution SS restraints might help to keep a reasonable geometry of the structure. The bent DNA should also work fine with SS since they are restraining base pairs and stacking pairs which normally don't distort too much. P.S. There is a separate bulletin board for Phenix-specific questions: http://www.phenix-online.org/mailman/listinfo/phenixbb Best regards, Oleg Sobolev. > Thank you > Dhiraj > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > 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/
Re: [ccp4bb] phenix refinement for bent DNA
Hi Dhiraj, I have structure with bent DNA. I am trying to refine the structure > using phenix. do I need to turn off the DNA secondary structure restraints > during refinement? > probably not, unless you have reasons to do so otherwise. P.S.: There is a Phenix mailing list for Phenix specific questions. This is CCP4 mailing list! 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/
Re: [ccp4bb] refmac twin refinement vs resolution limit
Well - I am not sure whether this has anything to do with twin refinement but resolution limits are often a bit iffy. First the low resolution discrepancy. The Free R is generated to a lower and higher resolution than any observation. The FreeR set is meant to be complete for any possible index regardless of whether there IS an observation or not. (There are good reasons for this - if your data set is very incomplete it is better to have "reflections" included in map calculations with values DFc rather than omitting them altogether - ie effectively using them with intensity set to zero.) But it does look a bit bizarre in the printed limits.. I dont think it matters - the number of observations is not changed. However for twin refinement things are a bit more complicated. Every "reflection" is actually a sum of two (or more) overlapping observations, I (h k l) and I(h(twin) k(twin) l(twin) ) and I really do not know what REFMAC will do if one of the pair is not observed.. And there are even more complicated scenarios if your twin is non-merahedral! Eleanor On Mon, 29 Mar 2021 at 08:21, Yuji Kado wrote: > When I use refmac restrained refinement with intensity based twin > refinement, > resolution limit has been changed from 71.4519- 1.9996 to 47.392-1.986. > > From Log file, before refinement, Scaling and SigmaA resln: 71.4519 > 1.9996, seems to be correct. > But in the middle of log file, around Fom and SigmaA vs resolution, > Resolution limits are from 47.392 to 1.986. > > Output mtz file also shows different resolution range 71.46-1.925. > Amplitude based twin refinement is also failed. > Even if I input resolution range at Refinement parameters in refmac, the > problem still occurs. > > I also read someone's similar problem, but it has been solved because of > the update of refmac. > What should I do to correspond with resolution range between the output of > aimless and refmac restrained refinement? > > regards, > Yuji > > > > 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/ > 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] Call for candidate for PhD position
Dear all, We are looking for a highly motivated student to be candidate for a PhD position in the field of glycobiology and situated at the interface between bacterial genetics and structural biology. The student will be hosted in two Marseille laboratories, located in proximity of the beautiful Calanque Natural resort. A full description of the call can be found in the attachment. Please feel free to spread the information. Thank you in advance for your time, With best wishes, Gerlind -- Gerlind Sulzenbacher Architecture et Fonction des Macromolécules Biologiques UMR7257 CNRS, Aix-Marseille Université Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel +33 491 82 55 66 Fax +33 491 26 67 20 E-mail: gerlind.sulzenbac...@univ-amu.fr 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/ PhD-call-glycobiology-Marseille.docx Description: MS-Word 2007 document
[ccp4bb] phenix refinement for bent DNA
Hi I have structure with bent DNA. I am trying to refine the structure using phenix. do I need to turn off the DNA secondary structure restraints during refinement? Thank you Dhiraj 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] Job opportunities at Astex Pharmaceuticals, Cambridge, UK
Dear all, We have a number of positions available in our Molecular Sciences group at Astex Pharmaceuticals, Cambridge UK to help us continue to develop and expand our cryoEM and structural biology capabilities. Further details of these and other roles can be found at https://astx.com/our-people-and-culture/current-uk-openings/ Informal inquiries are welcome (pamela.willi...@astx.com). Kind regards Pamela 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] PhD position at ICTER in Warsaw, Poland (MCBO/35/2021)
Dear all In the Integrated Structural Biology laboratory at The International Center for Translational Eye Research (ICTER) in Warsaw, Poland, one PhD position is available for highly motivated biologists, biochemists, or structural biologists, for 32 months (maximum planned period of contract: 31/12/2023). The position involves cloning, protein production, purification, characterization, and structural elucidation of proteins from the visual cycle. For details and how to apply until 18 th April, see: [ https://www.fnp.org.pl/en/oferta_pracy/phd-student-15/ | https://www.fnp.org.pl/en/oferta_pracy/phd-student-15/ ] Feel free to spread this information at your institutes and to interested colleagues. And please do not hesitate to contact me if you have any questions. To apply, please send the requested documents to [ mailto:icter_j...@ichf.edu.pl | icter_j...@ichf.edu.pl ] with the title MCBO 35/2021. Thank you and have a great day, Humberto [ http://www.icter.pl/ | www.icter.pl ] The controller of your personal data is the International Centre for Translational Eye Research with its registered office in Warsaw, NIP: 108002 (ICTER). ICTER will process your data for the purpose of carrying out scientific and research activities, providing services and contact with the Institute, on the basis of a contract (in connection with the performance of the contract or in order to take action on your request before the contract is concluded – Article 6, paragraph 1, letter b) of GDPR), the legitimate interest of the Institute (Article 6, paragraph 1, letter f) of the GDPR) and legal provisions (Article 6, paragraph 1, letter c) of the GDPR) - depending on the circumstances. You have the right to: request access to your data, receive a copy of it; rectify (correct) it; delete it; limit its processing; transfer it; lodge a complaint to the supervisory body; withdraw your consent for processing at any time (withdrawal of consent does not affect the lawfulness of the processing carried out prior to its withdrawal) or to lodge an objection to data processing. More information is available on the Institute's website. [ https://www.icter.pl/blob/ICTER_GICR.pdf | https://www.icter.pl/blob/ICTER_GICR.pdf ] 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] refmac twin refinement vs resolution limit
When I use refmac restrained refinement with intensity based twin refinement, resolution limit has been changed from 71.4519- 1.9996 to 47.392-1.986. From Log file, before refinement, Scaling and SigmaA resln: 71.4519 1.9996, seems to be correct. But in the middle of log file, around Fom and SigmaA vs resolution, Resolution limits are from 47.392 to 1.986. Output mtz file also shows different resolution range 71.46-1.925. Amplitude based twin refinement is also failed. Even if I input resolution range at Refinement parameters in refmac, the problem still occurs. I also read someone's similar problem, but it has been solved because of the update of refmac. What should I do to correspond with resolution range between the output of aimless and refmac restrained refinement? regards, Yuji 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/
