Re: [ccp4bb] To Trim or Not to To Trim
Hi Phil, I don't think that this is model cosmetics, but I certainly didn't claim that this isn't controversial. That's why we're having this discussion again and again after all. Have you tried to model a disordered Arg with 10 (why only 10?) alternate rotamers? Did it refine to something sensible? If so, then I would agree that this would be better. I haven't tried it, but I suspect they would all converge more or less on top of each other. (If anyone wants to give it a try, please let me know what happened!) I still maintain that modeling a disordered Arg as an Arg with a single rotamer with high B-factors is more correct than modeling it as an Ala or setting its side chain occupancy to zero, because it is not an Ala, and its side chain atoms are not absent. (Yes, I see Harry's point, but let's assume you've collected your data carefully and don't have such serious radiation damage that you've lost arginine side chains. If that was the case, you'd be missing a whole lot of other side chains too.) I do not claim that such a model accurately reflects where the Arg really is, I only claim that it's the best we can do (at present). Hence why we need to educate users. And absolutely, none of the current solutions is ideal, that's also why we're having this discussion again and again. It seems no one has found a better solution yet. /Julia On 3/10/23, 17:15, "Phil Jeffrey" mailto:pjeff...@princeton.edu>> wrote: On 3/10/23 4:05 AM, Julia Griese wrote: > Hi all, > > My impression has been that the most common approach these days is to > “let the B-factors take care of it”, but I might be wrong. Maybe it’s > time to run another poll? > > Personally, I call any other approach R-factor cosmetics. The goal in > model building is not to achieve the lowest possible R-factors, it’s to > build the most physically meaningful, most likely to be correct, model. And I could call your approach "model cosmetics". If you can't see the side-chain, you don't know where it is and you probably don't even know where the centroid of the distribution is. Only in the case of very short side-chains with few rotamers can you make a reasonable volume approximation to where the side-chain is and "let the B-factors" smear out the density to cover a range of the projected conformations. For longer side-chains, if you put it in a single conformation, you are very likely NOT coming close to correctly modeling the actual distribution of the conformations. So let's circle back on "most likely to be correct model" and ask what we *actually* know about where the atoms are. Put your disordered Arg in with 10 alternate conformations, each with a refined relative occupancy, and then let the B-factors smear that lot out, and that's your better model. Phil Jeffrey Princeton VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy 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] To Trim or Not to To Trim
Surely not if the locations of those other atoms are strongly supported by density? And surely you would always select a rotamer that does not clash with its surroundings? On 3/10/23, 17:32, "CCP4 bulletin board on behalf of Goldman, Adrian" mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of adrian.gold...@helsinki.fi <mailto:adrian.gold...@helsinki.fi>> wrote: Maybe simplest just to trim it back. I do worry that the presence of a wrong conformation will lead to inaccurate vdw clashes that could negatively affect other atoms. Sent from my iPhone > On 10 Mar 2023, at 18:25, Phil Jeffrey <mailto:pjeff...@princeton.edu>> wrote: > > On 3/10/23 4:05 AM, Julia Griese wrote: >> Hi all, >> My impression has been that the most common approach these days is to “let >> the B-factors take care of it”, but I might be wrong. Maybe it’s time to run >> another poll? >> Personally, I call any other approach R-factor cosmetics. The goal in model >> building is not to achieve the lowest possible R-factors, it’s to build the >> most physically meaningful, most likely to be correct, model. > > And I could call your approach "model cosmetics". > > If you can't see the side-chain, you don't know where it is and you probably > don't even know where the centroid of the distribution is. Only in the case > of very short side-chains with few rotamers can you make a reasonable volume > approximation to where the side-chain is and "let the B-factors" smear out > the density to cover a range of the projected conformations. > > For longer side-chains, if you put it in a single conformation, you are very > likely NOT coming close to correctly modeling the actual distribution of the > conformations. So let's circle back on "most likely to be correct model" and > ask what we *actually* know about where the atoms are. > > Put your disordered Arg in with 10 alternate conformations, each with a > refined relative occupancy, and then let the B-factors smear that lot out, > and that's your better model. > > Phil Jeffrey > Princeton > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BBA=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/ > <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 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BBA=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/ <https://www.jiscmail.ac.uk/policyandsecurity/> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy 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] To Trim or Not to To Trim
Hi all, My impression has been that the most common approach these days is to “let the B-factors take care of it”, but I might be wrong. Maybe it’s time to run another poll? Personally, I call any other approach R-factor cosmetics. The goal in model building is not to achieve the lowest possible R-factors, it’s to build the most physically meaningful, most likely to be correct, model. So if you know that the side chain is part of the protein, you should model it the best way you can. If it’s there, just disordered, then the most correct way to model it is to let it have high B-factors. Most molecular graphics programs don’t flag zero-occupancy atoms, so the user might never notice. Truncation of a side chain, unless there is evidence that it really physically isn’t there, is also misleading, in my opinion. I don’t believe that it is more helpful to the non-expert user than high B-factors either. If people who are not structural biologists themselves don’t know how to use a structure, then we need to educate them better. It is very straightforward these days to look at electron density in the PDB viewer. It used to be difficult, but nowadays there’s no excuse for not checking the electron density. The PDB validation flags RSRZ outliers. You can easily colour a structure by B-factors. It doesn’t take that much effort to teach students how to validate structures. The main point you need to get across is that it is necessary to do so. And this needs to be done not only in courses aimed at prospective experimental structural biologists, of course, but whenever students use structures in any way. This is just the opinion of someone who feels very strongly about teaching structure validation and rejoices when students’ reply to the question “What was the most important thing you learned today?” is: “Don’t blindly trust anything.” Cheers /Julia -- Dr. Julia Griese Associate Professor (Docent) Principal Investigator Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ From: CCP4 bulletin board on behalf of Bernhard Lechtenberg <968307750321-dmarc-requ...@jiscmail.ac.uk> Reply-To: Bernhard Lechtenberg Date: Friday, March 10, 2023 at 05:07 To: "CCP4BB@JISCMAIL.AC.UK" Subject: Re: [ccp4bb] To Trim or Not to To Trim I found the poll I wrote about earlier. This actually is way older than I had expected (2011). You can see the poll results (which was run by Ed Pozharski) and discussion at the time here in the CCP4BB archive: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20268.html In brief, the results of 240 respondents were: Delete the atoms 43% Let refinement take care of it by inflating B-factors41% Set occupancy to zero12% Other 4% Bernhard From: CCP4 bulletin board on behalf of Debanu Das Date: Friday, 10 March 2023 at 2:56 pm To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] To Trim or Not to To Trim We dealt with this in-depth during structural genomics days when we deposited over 1500 novel, high-quality, experimentally-phased structures into the PDB. Think it’s prudent to trim/truncate side chains without reliable density. Non-structural biologists using PDB structures without expert help can err in any of these scenarios: misinterpreting most common/random rotamer, zero occupancy atoms, B-factors, etc. What is the value of populating the PDB, which is a structural model repository, with such information that is not there, i.e., reliable structural model? Any trained crystallographer/structural biologist can easily add in side chain information if needed for modeling/computational chemistry reasons. Best regards, Debanu On Thu, Mar 9, 2023 at 6:50 PM Jurgen Bosch mailto:jxb...@case.edu>> wrote: I’d say no trimming to side chains for the following reason: There are non-structural biologists using PDB files and if atoms are missing they don’t know what to do. A better approach is where no side chain density allows support of placement, pick the most common rotamer and set the occupancy to zero for those atoms lacking density support. More work for you but more accurate in my opinion. Jürgen ___ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University Cleveland, OH 44106 https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC On Mar 9, 2023, at 9:45 PM, Bernhard Lechtenberg <968307750321-dmarc-requ...@jiscmail.ac.uk<mailto:968307750321-dmarc-requ...@jiscmail.ac.uk>> wrote: Hi Rhys, I am also all for leaving side chains and letting the B-factors deal with the weak/absent density. I don’t think th
Re: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
Oh, I hadn’t thought of trying that, that works! Obviously it would still be great if this issue was fixed (I guess it’s MacOS rather than PyMOL that’s to blame here), but this is a decent workaround. Thanks! /Julia -- Dr. Julia Griese Assistant Professor/Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ From: CCP4 bulletin board on behalf of Nicholas Clark Reply-To: Nicholas Clark Date: Monday, February 6, 2023 at 12:46 To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2 -- Forwarded message - From: Nicholas Clark mailto:ndcla...@buffalo.edu>> Date: Mon, Feb 6, 2023 at 6:44 AM Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2 To: Julia Griese mailto:julia.gri...@icm.uu.se>> Julia, I have the same issue with PyMOL. After it opens the blank session, if you return to the file explorer and try to reopen the file it will open the session correctly. Seems what you’re trying to open gets “lost” while loading PyMOL. Best, Nick Clark On Mon, Feb 6, 2023 at 5:38 AM Julia Griese mailto:julia.gri...@icm.uu.se>> wrote: Hi all, I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my computer’s nagging) and am now encountering some issues with Coot and PyMOL. The issues persist after updating to version 13.2. Regarding Coot version 0.9.8.7<http://0.9.8.7>: The rotate/translate zone function does not work properly. Everything works when using the slider bars in the dialog, and translating with the mouse works, but rotating with the mouse does not work. The region to be rotated disappears from view. I can make do with the slider bars, but feel that I have much better fine control and it’s much faster when using the mouse to rotate. Has anyone else encountered this problem and knows of a workaround? (I’m aware of the workaround for the main window disappearing when you delete items.) Regarding PyMOL version 2.5.4 (had the same issue with 2.4.1): When I try to open any kind of file that is set to open in PyMOL by default (pdb or cif coordinates, pse), PyMOL opens, but to an empty session. I can only open PyMOL files through the File Open dialog, having to navigate through the entire folder structure first, which obviously takes much longer. Has anyone else encountered this issue and knows how to fix it? Best, Julia -- Dr. Julia Griese Assistant Professor/Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se<mailto:julia.gri...@icm.uu.se> phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.icm.uu.se%2Fstructural-biology%2Fgriese-lab%2F=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C20d5eb5f89124f88131408db082e3833%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638112766972241444%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=8bFzv1MlDG9wxZdBaPgnYX%2BkF%2BrK7TKr%2FGivROK3hXE%3D=0> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C20d5eb5f89124f88131408db082e3833%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638112766972241444%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=4GAZj1fdgo%2FO7UnQFPgkfnefTajRC%2FTR4TZM2S1ZEd0%3D=0> -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 Cell: 716-830-1908 -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 Cell: 716-830-1908 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 CAUTION: Do not click on links or open attachments u
[ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
Hi all, I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my computer’s nagging) and am now encountering some issues with Coot and PyMOL. The issues persist after updating to version 13.2. Regarding Coot version 0.9.8.7: The rotate/translate zone function does not work properly. Everything works when using the slider bars in the dialog, and translating with the mouse works, but rotating with the mouse does not work. The region to be rotated disappears from view. I can make do with the slider bars, but feel that I have much better fine control and it’s much faster when using the mouse to rotate. Has anyone else encountered this problem and knows of a workaround? (I’m aware of the workaround for the main window disappearing when you delete items.) Regarding PyMOL version 2.5.4 (had the same issue with 2.4.1): When I try to open any kind of file that is set to open in PyMOL by default (pdb or cif coordinates, pse), PyMOL opens, but to an empty session. I can only open PyMOL files through the File Open dialog, having to navigate through the entire folder structure first, which obviously takes much longer. Has anyone else encountered this issue and knows how to fix it? Best, Julia -- Dr. Julia Griese Assistant Professor/Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy 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] PDBeMotif and like methods
Hi Andy, I’ve used PINTS, http://www.russelllab.org/cgi-bin/tools/pints.pl Hope that helps. Best, Julia -- Dr. Julia Griese Assistant Professor, Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ From: CCP4 bulletin board on behalf of Andrew Lovering Reply-To: Andrew Lovering Date: Wednesday, 23 November 2022 at 11:17 To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] PDBeMotif and like methods Dear CCP4 list, I have just tried accessing the “old” EBI PDBeMotif link and it is non-functional. Assuming that it may or may not be moved/unavailable, I am asking what your favourite methods are for mapping similar residue interactions in dissimilar folds i.e. if you have a nice network of 3 residues on “your” fold, what are the ways in which you can then find a similar arrangement on others? Thanks! Andy To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy 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] Postdoctoral fellowship in experimental structural biology at Uppsala University
Dear all, I have an opening for a postdoctoral fellow in my group at the Department of Cell and Molecular Biology, Uppsala University, Sweden. The project aims to study the DNA recognition mechanism of a metal-responsive transcription factor. The successful candidate should have experience in macromolecular X-ray crystallography, single-particle cryo-EM or NMR spectroscopy, as well as protein production and purification. Experience of complementary techniques in biochemistry and biophysics would be a benefit. For more information about the position please see the attached document. Please note that suitable candidates must have obtained their PhD no earlier than 6 years ago and be able to start at the latest in March 2023. Please also note that this position is funded by a stipend. Informal inquiries and applications should be sent to Julia Griese, julia.gri...@icm.uu.se<mailto:julia.gri...@icm.uu.se>, with subject header “Postdoc in Structural Biology”, no later than November 30, 2022. Best regards, Julia -- Dr. Julia Griese Assistant Professor, Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy 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/ Postdoc in Structural Biology.pdf Description: Postdoc in Structural Biology.pdf
Re: [ccp4bb] Quantifying electron density inside of a given volume
Dear Neno, Mapman can do exactly that too. Shameless plug: How to do it is described in this paper: http://scripts.iucr.org/cgi-bin/paper?S2059798319009926 Mapman appears to available on github now: https://github.com/martynwinn/Uppsala-Software-Factory Best, Julia -- Dr. Julia Griese Assistant Professor, Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ From: CCP4 bulletin board on behalf of Neno Vuksanovic Reply-To: Neno Vuksanovic Date: Wednesday, 10 August 2022 at 16:00 To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] Quantifying electron density inside of a given volume Dear All, I would like to quantify electron density inside of positive Fo-Fc blobs in active sites of multiple protomers in the map and compare them. I am aware that I can interpolate maps and obtain density values at coordinate points using either MapMan, Chimera or Coot, but I would like to know if there is a tool that would let me designate a sphere of a certain volume and calculate total electron density inside it? Best Regards, Neno To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy 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] Open postdoc position in structural biology/biochemistry/biophysics at Uppsala University
Posting on behalf of Cecilia Blikstad: We have a fully funded postdoc position for a structural biologist or biochemist at Uppsala University, Sweden. The position focuses on cyanobacterial CO2 fixation, in particular molecular details of assembly and regulation of the carboxysome, a 250+ megadalton protein based microcompartment, encapsulating Rubisco and carbonic anhydrase for efficient CO2 fixation. For more information see https://www.uu.se/en/about-uu/join-us/details/?positionId=524833 or send an email to Cissi (cecilia.bliks...@kemi.uu.se<mailto:cecilia.bliks...@kemi.uu.se>). Best, Julia (Any inquiries or applications directed to me will not be answered, I am only posting this on behalf of Cissi.) -- Dr. Julia Griese Assistant Professor, Docent Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy 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] the complex structure of protein and DNA
Hi, I agree with Mark, the R factors suggest that your model is more or less complete. It does not seem like that DNA is bound to your protein. Without knowing more about your project, it’s hard to make specific suggestions, but here goes: * Have you actually checked that there is DNA in the complex crystals? (There can be other reasons why you have different cell parameters and space groups with and without DNA. It may just be different crystal forms. Were they crystallized in the same condition?) If not, wash the crystals, run them on a gel and stain for DNA. * If you do have phosphate or sulphate in the crystallization condition, try to find a different condition without. It may well compete with DNA binding, since your affinity is low. * Does the protein recognize a specific DNA sequence? If not, it may bind to different parts of the DNA molecule that you give it, and you will have lots of problems getting a complex crystal structure because you don’t have a uniform complex. The affinity you state being rather on the low side, I would suspect that this may be an issue. * If you haven’t already, try different lengths of dsDNA. How much do you know about the footprint of the protein on DNA? How much do you know about the affinity of the protein for different DNA lengths? You need to find the sweet spot between affinity and length, i.e. the DNA should not be so short that it doesn’t bind well to the protein, but not so long that the complex won’t crystallize well because the DNA ends are floppy. You don’t say anything about the size of the protein, but 18 bp seems quite short to me, like that might be exactly the footprint of the protein on the DNA, but nothing more. Adding a few bp might help. * This wouldn’t be my immediate next step since your problem seems to be that there isn’t any DNA in the crystals (at least not bound to the protein) in the first place, and you obviously need to solve that problem first, but using DNA with sticky ends can help to form crystal contacts and generate better crystals. * Finally, are you sure about the space groups? Your R factors certainly suggest that you’re right, but P222 and P2 without any screw axes are very unusual. Also worth mentioning, although that doesn’t seem to be the issue here, is that DNA can cause pseudosymmetry that leads to space group misidentification, i.e. it looks like higher symmetry than it really is because the DNA is almost, but not really perfectly symmetrical. This can happen especially if you have a more or less palindromic DNA sequence, which is often the case with sequence-specific DNA-binding proteins. Best, Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4982 http://www.icm.uu.se/structural-biology/griese-lab/ From: CCP4 bulletin board on behalf of Mark Roe Reply-To: Mark Roe Date: Friday, 17 December 2021 at 12:16 To: "CCP4BB@JISCMAIL.AC.UK" Subject: Re: [ccp4bb] the complex structure of protein and DNA Hi, With this resolution and R-factors, I would guess you are not missing that much – certainly not large bits of DNA. Do you have Phosphate or Sulphate in the crystallisation buffer? If so, you may just be seeing Phosphate/Sulphate where the DNA would bind. Cheers, Mark Dr S.M. Roe, X-Ray Facility Manager, Tel. (+44) 01273 678863 (Office) School of Life Sciences, Tel. (+44) 01273 872896 (X-Ray Lab) University of Sussex, Tel. (+44) 0782 5501579 (Mobile) Falmer, East Sussex. E-mail m@sussex.ac.uk<mailto:m@sussex.ac.uk> BN1 9RQ Web http://www.sussex.ac.uk/lifesci/roelab/ From: CCP4 bulletin board on behalf of Meiting Yang Reply to: Meiting Yang Date: Friday, 17 December 2021 at 08:04 To: "CCP4BB@JISCMAIL.AC.UK" Subject: Re: [ccp4bb] the complex structure of protein and DNA Dear Petr, Thank you very much for your reply! The complex structure was refined finally to 2.44 Å resolution with an Rwork of 23.7% and an Rfree of 27.4%. We didn't try automatic DNA building tools, I don't know much about this. Thank you very much for your advice, I'm going to study it. Could you please give some specific suggestions about automatic DNA building tools? Thank you very much. At 2021-12-17 15:01:44, "Petr Kolenko" wrote: >Dear Yang Meiting, >There are few things to know bet
Re: [ccp4bb] Mean B factors and number of atoms (Refmac/baverage)
Answer to self: the number of non-H atoms per chain can be found in the PDB validation report! Duh! I guess I’ll trust the average B values reported by Refmac. /Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4043 http://www.icm.uu.se/structural-biology/griese-lab/ From: CCP4 bulletin board on behalf of Julia Griese Reply-To: Julia Griese Date: Thursday, 26 November 2020 at 15:11 To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] Mean B factors and number of atoms (Refmac/baverage) Hi all, I’m writing a Table 1 and getting a bit confused when it comes to number of atoms and average B factors. Refmac has these in the table in the GUI, but the atom numbers in that table seem to include H, and I’m only interested in non-H atoms. As an example, the PDB file says: REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS: 8351 Which agrees with the total count minus TER cards, so that seems to be correct. However, the table in the GUI for this refinement run looks like this: Chain mean B(No. atoms) AAA 41.4( 2193 ) BBB 57.7( 3499 ) CCC 57.7( 3499 ) DDD 41.7( 2212 ) EEE 60.3(923 ) FFF 60.6(920 ) aaa 55.4( 1323 ) ddd 56.0( 1346 ) GGG 34.3( 1 ) GaG 42.7( 1 ) GbG 34.3( 1 ) GcG 40.1( 1 ) GdG 40.6( 1 ) GeG 35.8( 1 ) GfG 34.2( 1 ) GgG 43.2( 1 ) HHH 40.6(136 ) You can easily see that this adds up to a lot more than 8351 atoms. The numbers for the G chain (metal ions) and the H chain (water) are correct, whereas the numbers for the macromolecule chains appear to include H. (If I run a refinement with H output to the final file, I get approximately the same number of atoms in total, though not quite.) But what I’m really interested in is of course the number of non-H atoms per chain. I don’t want to count all the atoms by hand… I used to use baverage to calculate average B factors (and that would also give me the number of non-H atoms per chain), but can’t get that to work on the command line and can’t find it in the i2 GUI. I don’t have the old ccp4i anymore. So if anyone could either tell me how to get baverage to work, or if there is another way to extract these numbers, I would much appreciate it! Best, Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4043 http://www.icm.uu.se/structural-biology/griese-lab/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy 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/
[ccp4bb] Mean B factors and number of atoms (Refmac/baverage)
Hi all, I’m writing a Table 1 and getting a bit confused when it comes to number of atoms and average B factors. Refmac has these in the table in the GUI, but the atom numbers in that table seem to include H, and I’m only interested in non-H atoms. As an example, the PDB file says: REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS: 8351 Which agrees with the total count minus TER cards, so that seems to be correct. However, the table in the GUI for this refinement run looks like this: Chain mean B(No. atoms) AAA 41.4( 2193 ) BBB 57.7( 3499 ) CCC 57.7( 3499 ) DDD 41.7( 2212 ) EEE 60.3(923 ) FFF 60.6(920 ) aaa 55.4( 1323 ) ddd 56.0( 1346 ) GGG 34.3( 1 ) GaG 42.7( 1 ) GbG 34.3( 1 ) GcG 40.1( 1 ) GdG 40.6( 1 ) GeG 35.8( 1 ) GfG 34.2( 1 ) GgG 43.2( 1 ) HHH 40.6(136 ) You can easily see that this adds up to a lot more than 8351 atoms. The numbers for the G chain (metal ions) and the H chain (water) are correct, whereas the numbers for the macromolecule chains appear to include H. (If I run a refinement with H output to the final file, I get approximately the same number of atoms in total, though not quite.) But what I’m really interested in is of course the number of non-H atoms per chain. I don’t want to count all the atoms by hand… I used to use baverage to calculate average B factors (and that would also give me the number of non-H atoms per chain), but can’t get that to work on the command line and can’t find it in the i2 GUI. I don’t have the old ccp4i anymore. So if anyone could either tell me how to get baverage to work, or if there is another way to extract these numbers, I would much appreciate it! Best, Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4043 http://www.icm.uu.se/structural-biology/griese-lab/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy 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] Postdoctoral Fellowship in Structural Biology at Uppsala University
Dear all, I have an opening for a postdoctoral fellow in my group at the Department of Cell and Molecular Biology, Uppsala University. The project aims to study the structure and function of metal-responsive transcription factors. The successful candidate should have an excellent track record and experience in X-ray crystallography as well as protein expression and purification. Experience of complementary techniques in biochemistry and biophysics would be a benefit. For more information about the position and how to apply please see the job post on ResearchGate: https://www.researchgate.net/job/944899_Postdoctoral_Fellowship_in_Structural_Biology You are welcome to contact me for more information, but please apply through ResearchGate. Best regards, Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4043 http://www.icm.uu.se/structural-biology/griese-lab/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy 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] Postdoctoral researcher position in Structural Biology at Uppsala University
Dear all, I have an opening for a postdoctoral researcher in my group at the Department of Cell and Molecular Biology, Uppsala University. The project aims to study the structure and function of metal-responsive transcription factors. The successful candidate should have an excellent track record and experience in X-ray crystallography as well as protein expression and purification. Experience of complementary techniques in biochemistry and biophysics would be a benefit. For more information about the position and how to apply please see: http://uu.se/en/about-uu/join-us/details/?positionId=199363 You are welcome to contact me for more information, but please note that you have to apply through the university system. Applications sent directly to me cannot be processed. Best regards, Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se phone: +46-(0)18-471 4043
[ccp4bb] Postdoctoral Fellowship in Molecular Biology at Uppsala University
Dear all, *A two-year postdoctoral fellowship, funded by the Carl Tryggers Foundation, is available in the group of Julia Griese in the Department of Cell and Molecular Biology at Uppsala University, Sweden. * Research in the Griese lab is at the intersection of structural biology, molecular biology and microbiology. We use X-ray crystallography in combination with a broad range of biochemical, biophysical and molecular biology techniques to understand the regulatory mechanisms governing prokaryotic metal homeostasis on a molecular and systemic level. The successful candidate will work within the project “Structural and functional characterization of metalloregulators in an actinomycete model organism”, with the aim to study the links between manganese and iron homeostasis and the oxidative stress response in this model organism. Please see *www.icm.uu.se/structural-biology/griese-lab/* <http://www.icm.uu.se/structural-biology/griese-lab/>for more information about our research. We are looking for a person with excellent track record and motivation to identify and solve scientific problems. The postdoctoral fellow will work on a project investigating the metalloregulatory network of the model organism /Saccharopolyspora erythraea, /with a focus on manganese and iron homeostasis and links to the oxidative stress response. This will involve genetic manipulation of the host organism to introduce reporter genes and create knock-outs, and physiological studies of the resulting strains, as well as functional characterization of the metal-sensing transcription factors /in vitro/ by different biochemical and/or biophysical techniques, depending on the successful candidate’s expertise and interests. The successful candidate will work in close collaboration with another postdoctoral researcher focusing on the structural characterization of the metal sensors. The group is hosted in an international, multidisciplinary and dynamic environment with extensive opportunities to learn new techniques. Required qualifications * A PhD in molecular biology, microbiology, biochemistry or a related area. * Documented experience of molecular biology. * Demonstrated scientific excellence; evidenced by publication track record as well as track record of presenting at national and international meetings. * Excellent oral and written communication skills in English. * Good interpersonal skills. Desired additional qualifications * Experience of biochemical or biophysical techniques such as DNA-binding assays, isothermal titration calorimetry or fluorescence spectroscopy. * Experience of promoter assays. * Experience of cultivation and genetic manipulation of actinomycetes. * Experience with metal- and/or DNA-binding proteins. The application should be written in English and include: 1. Letter of motivation with a short description of your research interests, and why you feel you are a good match for the project (one page). 2. CV, including a description of relevant skills and experiences, as well as a full publication list. 3. Copy of degree diploma and other official transcripts. 4. Names, e-mail addresses and telephone numbers to 2-3 reference persons. State their professional relation to you (e.g. PhD supervisor). In the event of special circumstances leading to a career break, these should be mentioned in the CV (with dates) so that the assessment of scientific output can take these factors into account. Examples of such special circumstances include a leave of absence due to sickness, parental leave, serving on commissions of trust, military service etc. ** *Starting date:*As soon as possible. Please indicate approximate starting date. ** *Informal inquiries and applications should be sent to Julia Griese, **julia.gri...@icm.uu.se* <mailto:julia.gri...@icm.uu.se>*, with subject header “Postdoc in Molecular Biology”, no later than March 31, 2018. * Are you considering moving to Sweden to work at Uppsala University? If so, you will find a lot of information about working and living in Sweden at *www.uu.se/joinus* <http://www.uu.se/joinus>. Best regards, Julia -- Dr. Julia Griese Assistant Professor Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se
[ccp4bb] Opening for a PhD student at Stockholm University
Posted on behalf of Prof. Martin Högbom Dear colleagues The Högbom lab at Stockholm University has an opening for a graduate student in an ERC-funded project regarding metalloprotein structural biochemistry. Methods include biochemistry, spectroscopy and standard as well as XFEL crystallography. Further information regarding the position and how to apply can be found here: http://www.su.se/english/about/vacancies/vacancies-new-list?rmpage=job=2634=UK Best regards, Julia -- Dr. Julia Griese Postdoctoral Researcher Department of Biochemistry and Biophysics Stockholm University 106 91 Stockholm Sweden phone: +46-(0)8-163 246 email: gri...@dbb.su.se
Re: [ccp4bb] Strange Ancient Diffraction Pattern...
This one appears to be of a similar age. It has a most puzzling, but pretty pentagonal pattern (and a backstop). Unfortunately Mosflm doesn't appear to support the image format. /Julia On 01/04/15 13:08, Harry Powell wrote: Hi Jacob I noticed that there's no backstop shadow that might give a clue as to the direct beam position. Do you know what wavelength radiation was used to bake this? On 1 Apr 2015, at 12:03, Keller, Jacob wrote: Can anyone index this? It's got mostly split spots and a strange diffuse scattering background JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org mailto:kell...@janelia.hhmi.org *** roundmatzah.jpg Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) -- Dr. Julia Griese Postdoctoral Researcher Stockholm Center for Biomembrane Research Department of Biochemistry and Biophysics Stockholm University 106 91 Stockholm Sweden phone: +46-(0)8-162 778 email: gri...@dbb.su.se
Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box
Hi, As far as I can tell oil does not block diffusion of O2 whatsoever. You can keep larger volumes (≥1 ml) of solutions anoxic in air for several hours with dithionite (≥0.5%) to scavenge oxygen and a redox indicator dye such as phenosafranin to monitor the state of the solution. Small drops (large surface/volume ratio) however oxidize within seconds, whether or not they are covered with oil. Of course this may simply be because the oxygen gets in before the drop is covered with oil, but either way I don't see how you could set up anaerobic drops in an aerobic environment. Best, Julia On 18/03/15 14:47, Edward A. Berry wrote: Do you have evidence that the oil blocks diffusion of O2? O2 is a nonpolar molecule, generally much more soluble in oils than in water. I'm not sure about silicone oils, but I would think they also dissolve O2 readily. eab On 03/18/2015 08:02 AM, Patrick Shaw Stewart wrote: Hi Steve I have one more comment for this thread. The microbatch-under-oil method is very handy for anaerobic work: 1. You can keep the microbatch stock solutions in normal microtitre plates (polypropylene is best to reduce evaporation) for months, which hugely reduces the amount of degassing that you need to do. You will only use say 0.5 ul of stock per drop. 2. The oil offers a surprising amount of protection from oxidation, which may be helpful eg in harvesting. 3. Microbatch can be automated - in parallel to vapor diffusion if desired It's amazing how often (aerobic) microbatch produces far superior crystals to V.D. for no obvious reason - it's well worth trying for both screening and optimization. Best wishes Patrick On 11 March 2015 at 10:17, Stephen Carr stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwell.ac.uk wrote: Dear CCP4BBer's Apologies for the off-topic post, but the CCP4BB seems to be the best place to ask about crystallisation. I am looking to set up crystallisation in an anaerobic glove box and wondered how other people did this, specifically the crystallisation stage. My initial thoughts were to place a small crystallisation incubator inside the box, however the smallest I have come across so far (~27L) is still rather large. Has anyone come across smaller incubators? Alternatively are incubators even neccessary if the glove box is placed in a room with good air conditioning and stable temperature control? Any recommendations would be very helpful. Thanks in advance, Steve Carr Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwell.ac.uk tel 01235 567717 tel:01235%20567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. -- patr...@douglas.co.uk mailto:patr...@douglas.co.uk Douglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 -- Dr. Julia Griese Postdoctoral Researcher Stockholm Center for Biomembrane Research Department of Biochemistry and Biophysics Stockholm University 106 91 Stockholm Sweden phone: +46-(0)8-162 778 email: gri...@dbb.su.se
