Re: [ccp4bb] [External] Re: [ccp4bb] phenix refinement for bent DNA
Dear Dhiraj, you may want to check our web service dnatco.datmos.org where you can also generate 3D constraints for refinement in Phenix. Best regards, Bohdan, bs.structbio.org On 2021-03-30 3:52, Srivastava, Dhiraj wrote: 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 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
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/
[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/
