Re: [ccp4bb] Tricky MR problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rhys, with good 2.0A data you could try S-SAD, or MR-SAD. For the latter I recommend autorickshaw (http://www.embl-hamburg.de/Auto-Rickshaw/). Best, Tim On 10/01/2012 09:26 PM, RHYS GRINTER wrote: Hi All, I'm currently working on solving the structure of a protein by molecular replacement. The protein is around 30kDa and likely has a two beta-prism domains, linked by a long curved two stranded sheet based on the structure of an analogue. There are also a number of other structures which represent a single homologous beta-prism domain. I've tried to find MR solution using the analogue and various truncation/AA substitution models based on it with no success. I've also tried single domain ensembles of the other homologous structures, also with no success. I think the problem is the overall sequence homology is quite low between my protein and the available structures (35% for the analogue and around 20% for the other models. I was curious as to how someone with more experience would tackle this problem. Just for background, the datasets I have are 2 to 2.7 angstroms with pretty nice stats. The space group is most likely C2221 with two molecules per ASU (giving around 58% solvent). Thanks, Rhys Grinter PhD Candidate University of Glasgow - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQapxiUxlJ7aRr7hoRAnljAKCSi4mxkp0BJ/FvrLQNJszCtLtToACgya1H SN6qckg9//iN2KrNU/oxMXE= =ZOpN -END PGP SIGNATURE-
[ccp4bb] Call for proposals for MX beamline at ALBA Synchrotron
Dear all, The MX beamline at the Alba Synchrotron (Barcelona), BL13-XALOC, is now open for user proposal applications. Worldwide institutes are eligible for beamtime, which is established based on the peer-reviewed proposals. The beamline is included in the Biostruct-X http://www.biostruct-x.eu/ funding program for transnational beam time access within EU. In order to apply, please register at the Alba User Office Application (http://useroffice.cells.es http://useroffice.cells.es/ ). Application deadline is October 10, 2012, for the period May-December, 2013. You can find information about the beamline at http://www.cells.es/Beamlines/XALOC Experimental setup includes: * In-vacuum undulator IVU21, 2-m long * Tuneable energy range 5.5-21 keV, DE/E = 2×10-4 * User defined beam shaping from 10µm-200µm vertically and 50µm-200µm horizontally, less on demand * Vertical beam divergence 0.1µrad * Possibilty to work in focused beam (small beam) or unfocused beam (small vertical divergence 0.03µrad) * Pilatus 6M detector * Microdiffractometer (MD2) with Mini-kappa goniometer MK3 * Automatic sample changer (CATS), 90 sample storage capacity (SPINE pin compatibility) * Bruker AXS X-Flash fluorescence detector * Common MX software installed Near future upgrades include 96-well crystallization plates scanning. Best regards, Jordi Juanhuix Gibert Experiments Division, CELLS-ALBA Synchrotron Carretera BP 1413, de Cerdanyola a Sant Cugat, km 3,3 E-08290 Cerdanyola del Vallès, Barcelona Tel: (+34) 93 592 43 22 www.cells.es http://www.cells.es/
[ccp4bb] Professor Dame Louise Johnson
It is with great sadness that I would like to inform the crystallographic community of the death of one of the great pioneers of the field, Professor Dame Louise Johnson. Those of us who had the privilege to work alongside her benefitted greatly from her vision for extending technique and instrumentation such that increasingly complex problems could be successfully solved and found her quiet determination to succeed inspirational. Dr. Liz Duke Diamond Light Source Harwell Science and Innovation Campus Chilton, Didcot Oxon OX11 0DE UK Tel. +44 (0) 1235 778057 Mob. +44 (0)7920 138148 -- This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] Faculty Position Vacancy
Physical Biochemist/Biophysicist The Biochemistry and Cellular and Molecular Biology Department (BCMB) at the University of Tennessee at Knoxville (UTK) is soliciting applications for a full-time, tenure-track position at the rank of ASSISTANT PROFESSOR, to begin August 1, 2013. The BCMB Department (http://web.bio.utk.edu/bcmb) has 32 faculty members with core strengths in structural biology, plant biology, and developmental genetics. We seek applicants who use contemporary experimental biophysical methods to explore fundamental molecular, cellular, or physiological processes. The ideal candidate will develop an innovative and extramurally funded research program that complements existing areas of strength including membrane structure/function, protein trafficking, signal transduction, chromatin structure, and enzyme structure/function. Applicants must have a Ph.D. and postdoctoral experience in an appropriate discipline with evidence of high quality research, a strong commitment to teaching, and the ability to teach introductory biochemistry and/or physical biochemistry as well as more advanced graduate courses in their area. Applicants should send a single PDF containing a cover letter, curriculum vitae, concise outline of current and future research interests, and statement of teaching effectiveness to biophysi...@utk.edumailto:biophysi...@utk.edu. Applicants should arrange for three letters of recommendation to be sent electronically to referencelett...@utk.edumailto:referencelett...@utk.edu. Further inquiries can be directed to Dr. Barry D. Bruce, (865-974-4082; bbr...@utk.edumailto:bbr...@utk.edu). Review of applications will begin on October 15, 2012 continue until the position is filled. The Knoxville campus of the University of Tennessee is seeking candidates who have the ability to contribute in meaningful ways to the diversity and intercultural goals of the University. The University of Tennessee is an EEO/AA/Title VI/Title IX/Section 504/ADA/ADEA institution in the provision of its education and employment programs and services. All qualified applicants will receive equal consideration for employment without regard to race, color, national origin, religion, sex, pregnancy, marital status, sexual orientation, gender identity, age, physical or mental disability, or covered veteran status.
[ccp4bb] Tricky MR problem
Thanks for your help everyone! It seems that the Balbes pipeline, followed by density modification in Phenix has done the trick Rhys
Re: [ccp4bb] Tricky MR problem
That's good to know, Rhys. But would you mind sharing why did it work with Balbes? Is there a big change in the position of the domains as related to your first searching model, or huge loops that had been removed? Carlos Em 02/10/2012, às 14:42, RHYS GRINTER escreveu: Thanks for your help everyone! It seems that the Balbes pipeline, followed by density modification in Phenix has done the trick Rhys
[ccp4bb] How to output water molecules with Phaser?
Hi all, I am using Phaser 2.5.1 for molecular replacement. I like to keep tightly bound water molecules (HOH) in the input pdb file. Phaser 2.1.4 outputs all HOH lines in the input pdb file to the output pdb file, but Phaser 2.5.1 doesnot. I am wondering if there is any way to carry input HOH lines to the output file with Phaser 2.5.1. Best, Koji
Re: [ccp4bb] How to output water molecules with Phaser?
As a deliberate choice, we changed Phaser so that it would omit all HETATM records from the model used for molecular replacement. This was largely because when extensive water structure was carried along, it could mess up the molecular replacement calculation. However, if you want something carried along as part of the model, you should be able to do that simply by changing HETATM to ATOM in the lines of the atoms in the PDB file that you want to keep. I'd suggest being selective in doing this and making sure you're only including the ones you're deliberately choosing. The very latest version of Phaser is a bit more clever. One side effect is that Se-Met residues were left out of the models, but now Phaser recognises the codes of some modified amino acids and carries them along. Best wishes, Randy Read On 2 Oct 2012, at 15:32, Koji Yonekura wrote: Hi all, I am using Phaser 2.5.1 for molecular replacement. I like to keep tightly bound water molecules (HOH) in the input pdb file. Phaser 2.1.4 outputs all HOH lines in the input pdb file to the output pdb file, but Phaser 2.5.1 doesnot. I am wondering if there is any way to carry input HOH lines to the output file with Phaser 2.5.1. Best, Koji -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] How to output water molecules with Phaser?
Hi Randy When you say carried along are you saying that they are used as part of the molecular replacement search? Or are they temporarily put aside and them simply added to the PDB in frame with the molecular replacement solution (but are not part of the weighted structure factors output in the final mtz)? F On Oct 2, 2012, at 7:55 AM, Randy Read rj...@cam.ac.uk wrote: As a deliberate choice, we changed Phaser so that it would omit all HETATM records from the model used for molecular replacement. This was largely because when extensive water structure was carried along, it could mess up the molecular replacement calculation. However, if you want something carried along as part of the model, you should be able to do that simply by changing HETATM to ATOM in the lines of the atoms in the PDB file that you want to keep. I'd suggest being selective in doing this and making sure you're only including the ones you're deliberately choosing. The very latest version of Phaser is a bit more clever. One side effect is that Se-Met residues were left out of the models, but now Phaser recognises the codes of some modified amino acids and carries them along. Best wishes, Randy Read On 2 Oct 2012, at 15:32, Koji Yonekura wrote: Hi all, I am using Phaser 2.5.1 for molecular replacement. I like to keep tightly bound water molecules (HOH) in the input pdb file. Phaser 2.1.4 outputs all HOH lines in the input pdb file to the output pdb file, but Phaser 2.5.1 doesnot. I am wondering if there is any way to carry input HOH lines to the output file with Phaser 2.5.1. Best, Koji -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] How to output water molecules with Phaser?
Hi, I meant to say that they're included as part of the model for structure factor calculation and in the output PDB file. Best wishes, Randy On 2 Oct 2012, at 16:05, Francis E Reyes wrote: Hi Randy When you say carried along are you saying that they are used as part of the molecular replacement search? Or are they temporarily put aside and them simply added to the PDB in frame with the molecular replacement solution (but are not part of the weighted structure factors output in the final mtz)? F On Oct 2, 2012, at 7:55 AM, Randy Read rj...@cam.ac.uk wrote: As a deliberate choice, we changed Phaser so that it would omit all HETATM records from the model used for molecular replacement. This was largely because when extensive water structure was carried along, it could mess up the molecular replacement calculation. However, if you want something carried along as part of the model, you should be able to do that simply by changing HETATM to ATOM in the lines of the atoms in the PDB file that you want to keep. I'd suggest being selective in doing this and making sure you're only including the ones you're deliberately choosing. The very latest version of Phaser is a bit more clever. One side effect is that Se-Met residues were left out of the models, but now Phaser recognises the codes of some modified amino acids and carries them along. Best wishes, Randy Read On 2 Oct 2012, at 15:32, Koji Yonekura wrote: Hi all, I am using Phaser 2.5.1 for molecular replacement. I like to keep tightly bound water molecules (HOH) in the input pdb file. Phaser 2.1.4 outputs all HOH lines in the input pdb file to the output pdb file, but Phaser 2.5.1 doesnot. I am wondering if there is any way to carry input HOH lines to the output file with Phaser 2.5.1. Best, Koji -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] How to output water molecules with Phaser?
Dear Randy, I just noticed that Phaser 2.5.1 sets the occupancies of attached sugers e.g. NAG, NAM etc. to zero, which caused Buster to crash. Resetting the occupancies to one solved the problem, but other refinement programs may not crash and may cause people unknowingly carrying on zero occupancy sugars. It might be better not to reset the occupancies. Herman PS: Buster crashing with zero occupancy sugars does not look correct to me either. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read Sent: Tuesday, October 02, 2012 4:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to output water molecules with Phaser? As a deliberate choice, we changed Phaser so that it would omit all HETATM records from the model used for molecular replacement. This was largely because when extensive water structure was carried along, it could mess up the molecular replacement calculation. However, if you want something carried along as part of the model, you should be able to do that simply by changing HETATM to ATOM in the lines of the atoms in the PDB file that you want to keep. I'd suggest being selective in doing this and making sure you're only including the ones you're deliberately choosing. The very latest version of Phaser is a bit more clever. One side effect is that Se-Met residues were left out of the models, but now Phaser recognises the codes of some modified amino acids and carries them along. Best wishes, Randy Read On 2 Oct 2012, at 15:32, Koji Yonekura wrote: Hi all, I am using Phaser 2.5.1 for molecular replacement. I like to keep tightly bound water molecules (HOH) in the input pdb file. Phaser 2.1.4 outputs all HOH lines in the input pdb file to the output pdb file, but Phaser 2.5.1 doesnot. I am wondering if there is any way to carry input HOH lines to the output file with Phaser 2.5.1. Best, Koji -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Overlapping transparent surface representations in Pymol
I am assuming you are after something like a difference map of the two surfaces. http://www.pymolwiki.org/index.php/Map_set Map_set command can average, copy, difference, maximum, minimum, sum and unique Hope this is what you are after. Dan
Re: [ccp4bb] How to output water molecules with Phaser?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Koji, in case that suits your needs you could do a superposition of the input model (including HETATM) onto the output model. This would move the HETATM's in place. By then deleting the model and merging HETATM's with the output model (e.g. in coot) you've got your result (unless you really want phaser to take the HETATM's scattering into account). Best, Tim On 10/02/2012 05:37 PM, Koji Yonekura wrote: Dear Randy, Thank you so much for your reply. I know your concept on water and other small molecules. I had changed HETATM to ATOM, but Phaser 2.5.1 still didnot output those HOH lines, but Phaser 2.1.4 kept all HOH lines starting with ATOM. Phaser 2.5.1 keeps all other ligands and small molecules if starting with ATOM. Version 2.5.1 seems to not output only HOH lines. Best, Koji As a deliberate choice, we changed Phaser so that it would omit all HETATM records from the model used for molecular replacement. This was largely because when extensive water structure was carried along, it could mess up the molecular replacement calculation. However, if you want something carried along as part of the model, you should be able to do that simply by changing HETATM to ATOM in the lines of the atoms in the PDB file that you want to keep. I'd suggest being selective in doing this and making sure you're only including the ones you're deliberately choosing. The very latest version of Phaser is a bit more clever. One side effect is that Se-Met residues were left out of the models, but now Phaser recognises the codes of some modified amino acids and carries them along. Best wishes, Randy Read - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQaxZzUxlJ7aRr7hoRAsbZAJ9qizfHCalh2SBPK8KrlD2y7Z3rTwCg9ZRd u9XXIJjo83vNkIVNq+aWgS0= =xPiv -END PGP SIGNATURE-
Re: [ccp4bb] Professor Dame Louise Johnson
This indeed is sad news for today. I just wanted to note that Professor Johnson's early papers on time-resolved crystallography truly inspired me to continue in crystallography, influenced my decision for my first postdoctoral position and to push the limits. I still have the carefully highlighted photocopies (yes used a photocopier and a real bound journal in gradual school) in my filing cabinet next to my office. My condolences to those close to her and her family. Gloria On Tue, Oct 2, 2012 at 6:40 AM, elizabeth.d...@diamond.ac.uk wrote: It is with great sadness that I would like to inform the crystallographic community of the death of one of the great pioneers of the field, Professor Dame Louise Johnson. ** ** Those of us who had the privilege to work alongside her benefitted greatly from her vision for extending technique and instrumentation such that increasingly complex problems could be successfully solved and found her quiet determination to succeed inspirational. ** ** Dr. Liz Duke Diamond Light Source Harwell Science and Innovation Campus Chilton, Didcot Oxon OX11 0DE UK ** ** Tel. +44 (0) 1235 778057 Mob. +44 (0)7920 138148 ** ** -- This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Professor Dame Louise Johnson
What a great lady to have inspired so many, and to remind us how welcoming the field of X-ray crystallography has been in general for women because of people like Dr. Johnson, Dorothy Hodgkin, and Rosalind Franklin, and many others. On Tue, Oct 2, 2012 at 12:03 PM, Gloria Borgstahl gborgst...@gmail.comwrote: This indeed is sad news for today. I just wanted to note that Professor Johnson's early papers on time-resolved crystallography truly inspired me to continue in crystallography, influenced my decision for my first postdoctoral position and to push the limits. I still have the carefully highlighted photocopies (yes used a photocopier and a real bound journal in gradual school) in my filing cabinet next to my office. My condolences to those close to her and her family. Gloria On Tue, Oct 2, 2012 at 6:40 AM, elizabeth.d...@diamond.ac.uk wrote: It is with great sadness that I would like to inform the crystallographic community of the death of one of the great pioneers of the field, Professor Dame Louise Johnson. ** ** Those of us who had the privilege to work alongside her benefitted greatly from her vision for extending technique and instrumentation such that increasingly complex problems could be successfully solved and found her quiet determination to succeed inspirational. ** ** Dr. Liz Duke Diamond Light Source Harwell Science and Innovation Campus Chilton, Didcot Oxon OX11 0DE UK ** ** Tel. +44 (0) 1235 778057 Mob. +44 (0)7920 138148 ** ** -- This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Professor Dame Louise Johnson
As a devoted reader of the Protein Crystallography - the first and only comprehensive manual of the protein crystallography, I express my deep sorrow on the departure from us of DBE Commander, Professor Louise Johnson. May her soul rest in peace. In full honor, Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 2, 2012, at 20:45 , Laurie Betts wrote: What a great lady to have inspired so many, and to remind us how welcoming the field of X-ray crystallography has been in general for women because of people like Dr. Johnson, Dorothy Hodgkin, and Rosalind Franklin, and many others. On Tue, Oct 2, 2012 at 12:03 PM, Gloria Borgstahl gborgst...@gmail.com wrote: This indeed is sad news for today. I just wanted to note that Professor Johnson's early papers on time-resolved crystallography truly inspired me to continue in crystallography, influenced my decision for my first postdoctoral position and to push the limits. I still have the carefully highlighted photocopies (yes used a photocopier and a real bound journal in gradual school) in my filing cabinet next to my office. My condolences to those close to her and her family. Gloria On Tue, Oct 2, 2012 at 6:40 AM, elizabeth.d...@diamond.ac.uk wrote: It is with great sadness that I would like to inform the crystallographic community of the death of one of the great pioneers of the field, Professor Dame Louise Johnson. Those of us who had the privilege to work alongside her benefitted greatly from her vision for extending technique and instrumentation such that increasingly complex problems could be successfully solved and found her quiet determination to succeed inspirational. Dr. Liz Duke Diamond Light Source Harwell Science and Innovation Campus Chilton, Didcot Oxon OX11 0DE UK Tel. +44 (0) 1235 778057 Mob. +44 (0)7920 138148 -- This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] Off topic: Synchrotron
Dear all I have off topic questions. Why can't electrons continuously circulate the ring at synchrotrons instead being refilled every few hours? Does new electrons injected into the ring affect MX data collection? Secondly, is it impossible to have all MX beamlines with insertion device as the source and all of them tunable? Thank you.
Re: [ccp4bb] Off topic: Synchrotron
Good questions! I have off topic questions. Not exactly off topic. Why can't electrons continuously circulate the ring at synchrotrons instead being refilled every few hours? The electrons are traveling in pretty small packets. Eventually they get too close to one another, and they repel one another and get pushed out of the packet. Does new electrons injected into the ring affect MX data collection? If it's top-up filling, the little bumps could cause a problem. Ask the beam-line manager. If it's periodic refilling, every several hours, you don't take data during the filling time, so when you restart you'll find a new, stronger beam. That increase in intensity ought to be corrected in the scale factors when you reduce data. (There is more to it than this, and maybe you'll get more answers.) Secondly, is it impossible to have all MX beamlines with insertion device as the source and all of them tunable? Not impossible. Just takes money. Bob
Re: [ccp4bb] Overlapping transparent surface representations in Pymol
On 10/03/2012 12:09 AM, Christopher Browning wrote: Dear All, I was wondering if anybody knows how one can have two transparent surfaces overlapping but then being able to see how the 2 intersect using PYMOL. At the moment, if I have two transparent surfaces overlapping I don't see how they overlap internally, only externally. I can see how they overlap internally if one surface is transparent and the other is solid, but that is not quite what I'm after. If Pymol Map_set proposed by Dan is not what you want, maybe you should try the show as mesh mode of Pymol. Regards, F.
Re: [ccp4bb] Overlapping transparent surface representations in Pymol
Try changing the transparency setting to Multi-Layer -- this will prevent the 2nd overlapping surface from appearing solid (assuming I understand you correctly) In the PyMOL menu bar, go to: Setting Surface Multi-Layer Hope that helps! Kip On Oct 2, 2012, at 11:09 AM, Christopher Browning wrote: Dear All, I was wondering if anybody knows how one can have two transparent surfaces overlapping but then being able to see how the 2 intersect using PYMOL. At the moment, if I have two transparent surfaces overlapping I don't see how they overlap internally, only externally. I can see how they overlap internally if one surface is transparent and the other is solid, but that is not quite what I'm after. Hope you can help. Chris -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40
Re: [ccp4bb] ideal rms bond length
Hi Faisal, There is no such thing as the ideal deviation from ideal geometry. As long as your rmsZ values are below 1 (which they are), it's okay. Note that, in contrast to popular belief, rmsd has no useful meaning for bonds and angles. Genarally, rmsZ goes down with resolution but the correlation is not that high. It does not mean that rmsZ should be a particular value at a certain resolution. That said, you should optimise your restraints to get the most likely model. In Refmac that means minimizing -LLfree. You can do this by hand, but there are also automated procedures to do that. Shameless plug: PDB_REDO has such an automated procedure. HTH, Robbie Joosten Date: Wed, 3 Oct 2012 03:19:48 +0530 From: faisaltari...@gmail.com Subject: [ccp4bb] ideal rms bond length To: CCP4BB@JISCMAIL.AC.UK Dear all i request you to please answer my basic query about the ideal acceptable rmsbond length obtained during refmac refinement..is the data acceptable in mine case which is as follows.. NcycRfactRfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.2090 0.2079 0.875226315. 11985.5 0.0278 1.389 2.718 1.261 0.198 1 0.2064 0.2284 0.850226313. 12201.1 0.0285 1.427 2.733 1.271 0.204 2 0.2076 0.2373 0.837226944. 12289.9 0.0248 1.242 2.598 1.200 0.187 3 0.2092 0.2429 0.828227495. 12341.7 0.0222 1.107 2.458 1.128 0.173 4 0.2100 0.2468 0.822227753. 12372.4 0.0211 1.053 2.377 1.086 0.166 5 0.2104 0.2500 0.818227942. 12395.7 0.0204 1.021 2.326 1.061 0.161 6 0.2108 0.2522 0.814228075. 12411.5 0.0200 0.999 2.289 1.042 0.158 7 0.2111 0.2537 0.812228162. 12421.8 0.0197 0.984 2.265 1.030 0.156 8 0.2113 0.2550 0.810228228. 12430.5 0.0194 0.971 2.243 1.020 0.154 9 0.2114 0.2559 0.809228300. 12436.1 0.0192 0.962 2.228 1.012 0.153 10 0.2116 0.2568 0.808228348. 12441.7 0.0191 0.957 2.218 1.008 0.152 11 0.2118 0.2574 0.807228394. 12446.2 0.0190 0.951 2.210 1.004 0.151 12 0.2119 0.2581 0.806228421. 12449.6 0.0189 0.948 2.203 1.001 0.151 13 0.2119 0.2585 0.805228440. 12452.7 0.0189 0.944 2.198 0.998 0.150 14 0.2120 0.2590 0.805228461. 12455.0 0.0188 0.941 2.194 0.996 0.150 15 0.2121 0.2593 0.804228480. 12456.9 0.0188 0.939 2.190 0.995 0.150 -- Regards Faisal School of Life Sciences JNU
