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/
Re: [ccp4bb] phenix refinement about cis-proline
Dear Niegel,
May be Shijun had to cancel his registration to the PhenixBB as I had to do
since 2015 due to "too many bounces" whatever the email address I used,
professional, yahoo or gmail ?... Has this been fixed at some point ?
All the best,Philippe
Philippe BENAS, Ph.D.
Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ ,
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
De : Nigel Moriarty <nwmoria...@lbl.gov>
À : CCP4BB@JISCMAIL.AC.UK
Envoyé le : Vendredi 2 mars 2018 8h25
Objet : Re: [ccp4bb] phenix refinement about cis-proline
Shijun
You can ask all the questions you like about Phenix on PhenixBB. However, to
answer your question, you can set all peptides to trans using
apply_all_trans=True
or more specific control using
apply_cis_trans_specification { cis_trans_mod = cis *trans
residue_selection = None }
to any number of peptides.
Cheers
Nigel
---Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence
Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Thu, Mar 1, 2018 at 10:58 PM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:
Dear all I am refining a structure which has cis-Pro and trans-Pro, the
tans-Pro is gone when I set the "threshold degrees for cis-peptide " from
default 45 to 65, but still has cis-Pro. While no significant change when I set
it to 15. My question is how to set in phenix refinement to clear the Pro
residues in cis- or trans- conformations.Best Regards shijun
Re: [ccp4bb] phenix refinement about cis-proline
Shijun
You can ask all the questions you like about Phenix on PhenixBB. However,
to answer your question, you can set all peptides to trans using
apply_all_trans=True
or more specific control using
apply_cis_trans_specification {
cis_trans_mod = cis *trans
residue_selection = None
}
to any number of peptides.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Thu, Mar 1, 2018 at 10:58 PM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:
> Dear all
>
>I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro
> is gone when I set the "threshold degrees for cis-peptide " from default 45
> to 65, but still has cis-Pro. While no significant change when I set it to
> 15. My question is how to set in phenix refinement to clear the Pro
> residues in cis- or trans- conformations.
>
> Best Regards
>
> shijun
>
[ccp4bb] phenix refinement about cis-proline
Dear all I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro is gone when I set the "threshold degrees for cis-peptide " from default 45 to 65, but still has cis-Pro. While no significant change when I set it to 15. My question is how to set in phenix refinement to clear the Pro residues in cis- or trans- conformations. Best Regards shijun
Re: [ccp4bb] Phenix refinement
Change ad to and in selection. Sent from Jack's iPad On Nov 26, 2014, at 7:16 AM, Almudena Ponce Salvatierra maps.fa...@gmail.com wrote: Dear all, I am refining my structure with Phenix refine and I get the following error message just before starting: no atom selected, name CA ad chain A and resname CA and resseq 1. I knew how to fix it once but I think I have forgotten now. Anyway, the only difference between the output model that came from the previous Phenix refine run and this one (the input for the new run) is that I removed a Calcium ion (this used to be chain A). So, if there is no chain A anymore, why does this appear? I have no clue. Any suggestions that will enable the continuation of this refinement will be more than welcome. Thanks a lot in advance. Best wishes, Almudena. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
Re: [ccp4bb] Phenix refinement
FYI, there is a phenix BB for phenix questions. Sent from Jack's iPad On Nov 26, 2014, at 7:16 AM, Almudena Ponce Salvatierra maps.fa...@gmail.com wrote: Dear all, I am refining my structure with Phenix refine and I get the following error message just before starting: no atom selected, name CA ad chain A and resname CA and resseq 1. I knew how to fix it once but I think I have forgotten now. Anyway, the only difference between the output model that came from the previous Phenix refine run and this one (the input for the new run) is that I removed a Calcium ion (this used to be chain A). So, if there is no chain A anymore, why does this appear? I have no clue. Any suggestions that will enable the continuation of this refinement will be more than welcome. Thanks a lot in advance. Best wishes, Almudena. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
Re: [ccp4bb] Phenix refinement
Hi Almudena, I am refining my structure with Phenix refine and I get the following error message just before starting: no atom selected, name CA ad chain A and resname CA and resseq 1. this is due to atom selection syntax error that you provided: after CA must be and not ad . I knew how to fix it once but I think I have forgotten now. Anyway, the only difference between the output model that came from the previous Phenix refine run and this one (the input for the new run) is that I removed a Calcium ion (this used to be chain A). So, if there is no chain A anymore, why does this appear? I have no clue. Any suggestions that will enable the continuation of this refinement will be more than welcome. I would do refinement run afresh. Perhaps you have some settings specific to that atom that got carried our to the next refinement run.. It's difficult to guess without more information. Pavel P.S.: there is Phenix mailing list for Phenix-specific questions.
Re: [ccp4bb] Phenix refinement
Thank you all very much for your replies. However I am sorry this ad was a typing mistake of mine while transcribing the message. I have signed up for the phenixbb mailing list. And I will look up at the restraints that may still be there for this atom that I removed. Thanks again, best wishes, ALmudena 2014-11-26 15:58 GMT+00:00 Pavel Afonine pafon...@gmail.com: Hi Almudena, I am refining my structure with Phenix refine and I get the following error message just before starting: no atom selected, name CA ad chain A and resname CA and resseq 1. this is due to atom selection syntax error that you provided: after CA must be and not ad . I knew how to fix it once but I think I have forgotten now. Anyway, the only difference between the output model that came from the previous Phenix refine run and this one (the input for the new run) is that I removed a Calcium ion (this used to be chain A). So, if there is no chain A anymore, why does this appear? I have no clue. Any suggestions that will enable the continuation of this refinement will be more than welcome. I would do refinement run afresh. Perhaps you have some settings specific to that atom that got carried our to the next refinement run.. It's difficult to guess without more information. Pavel P.S.: there is Phenix mailing list for Phenix-specific questions. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
Re: [ccp4bb] Phenix refinement
Your .eff file must be explicitly referencing the Ca that you removed. Since it doesn't exist, phenix stops. Search your .eff file for the string name CA and chain A and resname CA and resseq 1 (maybe a geometry.edit) and remove the reference. I think the CCP4 bylines specifically encourage discussion of software other than ccp4, and i think this should be the case even if a discussion list exists for that software. Not everyone doing crystallography wants to sign up for 10 different mailing lists and get bombarded by the sometimes voluminous mail (CCP4, phenix, pymol, coot, xplor, sharp, solve, PDBL, sci.techniques.xtallography, bionet.xtallography, bionet.molbio.proteins, bionet.structural-nmr, bionet.molec-model, bionet.software.x-plor ) On 11/26/2014 11:09 AM, Almudena Ponce Salvatierra wrote: Thank you all very much for your replies. However I am sorry this ad was a typing mistake of mine while transcribing the message. I have signed up for the phenixbb mailing list. And I will look up at the restraints that may still be there for this atom that I removed. Thanks again, best wishes, ALmudena 2014-11-26 15:58 GMT+00:00 Pavel Afonine pafon...@gmail.com mailto:pafon...@gmail.com: Hi Almudena, I am refining my structure with Phenix refine and I get the following error message just before starting: no atom selected, name CA ad chain A and resname CA and resseq 1. this is due to atom selection syntax error that you provided: after CA must be and not ad . I knew how to fix it once but I think I have forgotten now. Anyway, the only difference between the output model that came from the previous Phenix refine run and this one (the input for the new run) is that I removed a Calcium ion (this used to be chain A). So, if there is no chain A anymore, why does this appear? I have no clue. Any suggestions that will enable the continuation of this refinement will be more than welcome. I would do refinement run afresh. Perhaps you have some settings specific to that atom that got carried our to the next refinement run.. It's difficult to guess without more information. Pavel P.S.: there is Phenix mailing list for Phenix-specific questions. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
[ccp4bb] Phenix refinement with modified amino acids
Dear all, I'm refining a structure with three modified amino, ccp4 code: CY3, DTR, and MPT respectively. However I don't know how to give phenix.refine the adequate libraries as to obtain the correct geometry for three amino acids. I tried to add the cif libraries downloaded from ccp4 to the command, but it doesn't seem to work. Thanks in advance for your help,
Re: [ccp4bb] phenix refinement peptide bond poor geometry
I'd like to thank you all, the problem is resolved. Apparently, in the pdb file, the carbonyl oxygen should be listed right after the carbonyl carbon not after the side chain atoms! M ** Mohd A. Salameh, Ph.D. Mayo Clinic Cancer Center Griffin Cancer Research building,Rm 331 4500 San Pablo Rd Jacksonville, FL 32224 Tel: (904) 953-0046 Fax: (904) 953-0277 salameh.m...@mayo.edu ** From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Salameh, Mohd A., Ph.D. Sent: Friday, December 18, 2009 5:32 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] phenix refinement peptide bond poor geometry Dear all, I'm about to deposit a structure into the protein data bank and I'm encountering a disturbing problem, I have a protein site where the peptide bond is not properly linked, the distance of C-N bond is 2.23 Angstrom, I tried to restrain that site by modifying my def file but the problem persist after refinement. I wonder if anybody can help resolving this problem. Thanks and happy holidays! Mohd ** Mohd A. Salameh, Ph.D. Mayo Clinic Cancer Center Griffin Cancer Research building,Rm 331 4500 San Pablo Rd Jacksonville, FL 32224 Tel: (904) 953-0046 Fax: (904) 953-0277 salameh.m...@mayo.edu **
[ccp4bb] phenix refinement peptide bond poor geometry
Dear all, I'm about to deposit a structure into the protein data bank and I'm encountering a disturbing problem, I have a protein site where the peptide bond is not properly linked, the distance of C-N bond is 2.23 Angstrom, I tried to restrain that site by modifying my def file but the problem persist after refinement. I wonder if anybody can help resolving this problem. Thanks and happy holidays! Mohd ** Mohd A. Salameh, Ph.D. Mayo Clinic Cancer Center Griffin Cancer Research building,Rm 331 4500 San Pablo Rd Jacksonville, FL 32224 Tel: (904) 953-0046 Fax: (904) 953-0277 salameh.m...@mayo.edu **
Re: [ccp4bb] phenix refinement peptide bond poor geometry
Hi Mohd, - if it is a regular peptide bond then they are linked automatically and this problem should never happen, otherwise there must be something not right with your input PDB file. - check in .geo file if this particular bond is restrained; If you send me (and not to the whole bb) the PDB file, or at its fragment containing this and a couple of adjacent residues, then I probably tell more about what the problem is. Pavel. PS There is a PHENIX bulletin board: http://www.phenix-online.org/ On 12/18/09 2:31 PM, Salameh, Mohd A., Ph.D. wrote: Dear all, I'm about to deposit a structure into the protein data bank and I'm encountering a disturbing problem, I have a protein site where the peptide bond is not properly linked, the distance of C-N bond is 2.23 Angstrom, I tried to restrain that site by modifying my def file but the problem persist after refinement. I wonder if anybody can help resolving this problem. Thanks and happy holidays! Mohd ** *Mohd A. Salameh, Ph.D.* Mayo Clinic Cancer Center Griffin Cancer Research building,Rm 331 4500 San Pablo Rd Jacksonville, FL 32224 Tel: (904) 953-0046 Fax: (904) 953-0277 salameh.m...@mayo.edu
[ccp4bb] phenix refinement --set cif for sugar links
Dear folks:
I am currently using Phenix to refine a structure that has many
carbohydrate chains on it.
I created the cif file according to an old message from Dr.Ralf W like
the following:
refinement.pdb_interpretation {
apply_cif_link {
data_link = NAG-ASN
residue_selection_1 = chain A and resname NAG and resid 900
residue_selection_2 = chain A and resname ASN and resid 329
}
apply_cif_link {
data_link = NAG-NAG-b-D
residue_selection_1 = chain A and resname NAG and resid 901
residue_selection_2 = chain A and resname NAG and resid 900
}
apply_cif_link {
data_link = NAG-MAN-b-D
residue_selection_1 = chain A and resname MAN and resid 902
residue_selection_2 = chain A and resname NAG and resid 901
}
}
However, there was an error: Missing CIF link : data_link_NAG-NAG-b-D
please check for spelling errors or specify the file name with the link as an
additional argument.
How can I fix this problem? Thanks a lot and have a nice holiday season.
Jerry
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