autobuild : MSE's keep coming back - phenixbb - phenix-online.org

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autobuild : MSE's keep coming back

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Re: [phenixbb] Something that came...

Lepore, Bryan

15 Sep 2010 15 Sep '10

8:41 p.m.

i used "semet=False" the .pdb has MET the .seq has M the output models, however, keep getting MSE's in them, complete with selenium. am i missing something? -bryan

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Tom Terwilliger

15 Sep 15 Sep

10:15 p.m.

Hi Bryan, I'm sorry about that. Can you tell me, are you using a recent version? If so, is this rebuild_in_place or not? Thanks! -Tom T On Sep 15, 2010, at 2:41 PM, Lepore, Bryan wrote:

i used "semet=False" the .pdb has MET the .seq has M

the output models, however, keep getting MSE's in them, complete with selenium.

am i missing something?

-bryan _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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r n

16 Sep 16 Sep

2:53 p.m.

New subject: autosol ?

Dear Tom I have collected Cu anomalous peak data (low resolution with high redundancy). Also I do have model and tried to do difference fourrier using Phenix.automr and phenix.autosol. Phenix found three sites with significant peak height 10, 9 , 8, rest of them 4.0. But all the three sites are close to methionine ? any explanation will be appreciated. Also I do have some unusual, I tried molecular replacement with phaser and phenix.automr. Phaser found the dimer with correlation TZ 9.0 and 14, but phenix.automr , failed to find the model. It is very low resolution data. Thanks ram

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Sylvia Fanucchi

2:59 p.m.

New subject: Postdoctoral positions available

SARChI POSTDOCTORAL FELLOWSHIPS IN PROTEIN BIOCHEMISTRY AND STRUCTURAL BIOLOGY AT THE UNIVERSITY OF THE WITWATERSRAND SOUTH AFRICA Postdoctoral positions in protein biochemistry and structural biology are available for suitably qualified PhD graduates to pursue research into improving our understanding of the relationship between protein structure and function - one of the foremost challenges in post-genomic biology. To this end, our research interests are consolidated into two main areas: (1) the stability, dynamics and folding mechanisms of multidomain and oligomeric proteins, and, (2) the structural and energetic foundations of molecular recognition between proteins and other molecules such as drugs, proteins and membranes. Proteins under investigation are of relevance to human health and include proteins involved in molecular toxicology, oxidative stress, cancer, apoptosis and HIV/AIDS. Excellent in-house facilities are available for protein expression, purification and crystallisation as well as for state-of-the-art biophysical techniques such as protein crystallography, UV/Vis, CD and fluorescence spectroscopy, isothermal titration calorimetry, and stopped-flow kinetics. Successful candidates should have a PhD degree in biochemistry, molecular biology, chemistry or crystallography. Good communication (written and verbal) and interpersonal skills, and computer literacy are absolute requirements. Interested applicants should send a letter of motivation, CV, PhD synopsis, certified copy of PhD degree, and a list of three references with their email addresses to: Prof Heini Dirr, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa. E-mail [email protected]. <html><p><font face = "verdana" size = "0.8" color = "navy">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.</font></p></html>

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Charles Allerston

3:59 p.m.

New subject: Postdoctoral positions available

You mean . . . we could work together? <sighs> :) charlie

...
...
"Sylvia Fanucchi" 9/16/2010 3:59 pm >>> SARChI POSTDOCTORAL FELLOWSHIPS IN PROTEIN BIOCHEMISTRY AND STRUCTURAL BIOLOGY AT THE UNIVERSITY OF THE WITWATERSRAND SOUTH AFRICA

Postdoctoral positions in protein biochemistry and structural biology are available for suitably qualified PhD graduates to pursue research into improving our understanding of the relationship between protein structure and function - one of the foremost challenges in post-genomic biology. To this end, our research interests are consolidated into two main areas: (1) the stability, dynamics and folding mechanisms of multidomain and oligomeric proteins, and, (2) the structural and energetic foundations of molecular recognition between proteins and other molecules such as drugs, proteins and membranes. Proteins under investigation are of relevance to human health and include proteins involved in molecular toxicology, oxidative stress, cancer, apoptosis and HIV/AIDS. Excellent in-house facilities are available for protein expression, purification and crystallisation as well as for state-of-the-art biophysical techniques such as protein crystallography, UV/Vis, CD and fluorescence spectroscopy, isothermal titration calorimetry, and stopped-flow kinetics. Successful candidates should have a PhD degree in biochemistry, molecular biology, chemistry or crystallography. Good communication (written and verbal) and interpersonal skills, and computer literacy are absolute requirements. Interested applicants should send a letter of motivation, CV, PhD synopsis, certified copy of PhD degree, and a list of three references with their email addresses to: Prof Heini Dirr, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa. E-mail [email protected]. <html><p><font face = "verdana" size = "0.8" color = "navy">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.</font></p></html>

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Sylvia Fanucchi

17 Sep 17 Sep

9:42 a.m.

New subject: Spam:Re: Postdoctoral positions available

You and me baby!! ;) -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Charles Allerston Sent: Thursday, September 16, 2010 5:59 PM To: PHENIX user mailing list Subject: Spam:Re: [phenixbb] Postdoctoral positions available You mean . . . we could work together? <sighs> :) charlie

...
...
"Sylvia Fanucchi" 9/16/2010 3:59 pm >>> SARChI POSTDOCTORAL FELLOWSHIPS IN PROTEIN BIOCHEMISTRY AND STRUCTURAL BIOLOGY AT THE UNIVERSITY OF THE WITWATERSRAND SOUTH AFRICA

Postdoctoral positions in protein biochemistry and structural biology are available for suitably qualified PhD graduates to pursue research into improving our understanding of the relationship between protein structure and function - one of the foremost challenges in post-genomic biology. To this end, our research interests are consolidated into two main areas: (1) the stability, dynamics and folding mechanisms of multidomain and oligomeric proteins, and, (2) the structural and energetic foundations of molecular recognition between proteins and other molecules such as drugs, proteins and membranes. Proteins under investigation are of relevance to human health and include proteins involved in molecular toxicology, oxidative stress, cancer, apoptosis and HIV/AIDS. Excellent in-house facilities are available for protein expression, purification and crystallisation as well as for state-of-the-art biophysical techniques such as protein crystallography, UV/Vis, CD and fluorescence spectroscopy, isothermal titration calorimetry, and stopped-flow kinetics. Successful candidates should have a PhD degree in biochemistry, molecular biology, chemistry or crystallography. Good communication (written and verbal) and interpersonal skills, and computer literacy are absolute requirements. Interested applicants should send a letter of motivation, CV, PhD synopsis, certified copy of PhD degree, and a list of three references with their email addresses to: Prof Heini Dirr, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa. E-mail [email protected]. <html><p><font face = "verdana" size = "0.8" color = "navy">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.</font></p></html> _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb <html><p><font face = "verdana" size = "0.8" color = "navy">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.</font></p></html>

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Tom Terwilliger

16 Sep 16 Sep

4:41 p.m.

New subject: autosol ?

Hi Ram, I don't have a good answer to your questions; perhaps others will. Here are some thoughts:

I have collected Cu anomalous peak data (low resolution with high redundancy). Also I do have model and tried to do difference fourrier using Phenix.automr and phenix.autosol.

Phenix found three sites with significant peak height 10, 9 , 8, rest of them 4.0. But all the three sites are close to methionine ?

I think you placed your model with phenix.automr (or below with phaser) and then used autosol with input_partpdb_file=your_model.pdb to identify sites, is that right? Now the sites you got with peak heights of 10,9,8 sigma sound reasonably high, yes. Are they right where SD of methionine is located, or some distance away such as 4-5 A? Where do you expect the Cu to be located?

Also I do have some unusual, I tried molecular replacement with phaser and phenix.automr. Phaser found the dimer with correlation TZ 9.0 and 14, but phenix.automr , failed to find the model. It is very low resolution data.

If you are using phenix for phaser and phenix.automr, then the difference is probably just the parameters used in your phaser run vs your automr run; perhaps the allowed number of clashes is different or the RMSD input is different? All the best, Tom T

Thanks ram

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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participants (5)

Charles Allerston
Lepore, Bryan
r n
Sylvia Fanucchi
Tom Terwilliger