Re: [ccp4bb] Molrep error -
Dear Jon -- it looks to me that it is trying to open a file that does not exist because of the path name... I'm not an expert in MolRep, but you defined PATH_SCR and PATH_OUT with the same names; the problem might then be that it tried to open a file located in the PATH_SCR/ PATH_OUT... (or the opposite). Perhaps if you try the following it could work: /usr/local/ccp4-6.1.0/ccp4-6.1.0/bin/molrep PATH_SCR /home/caruthej/ bo3/ccp4/ PATH_OUT bo3P1_11_molrep_ HKLIN /home/caruthej/bo3/P1/ ccp4/merged.mtz MODEL /home/caruthej/bo3/P1/cns/model.pdb Sorry if it doesn't help. Kind regards. -- Leo -- On 27 Feb 2010, at 04:31, Jonathan Marvin Caruthers wrote: The program run with command: /usr/local/ccp4-6.1.0/ccp4-6.1.0/bin/ molrep PATH_SCR /home/caruthej/bo3/ccp4/bo3P1_11_molrep_ PATH_OUT /home/caruthej/bo3/ccp4/bo3P1_11_molrep_ HKLIN /home/caruthej/ bo3/P1/ccp4/merged.mtz MODEL /home/caruthej/bo3/P1/cns/model.pdb Chavas Leonard, Ph.D. Assistant Professor Structural Biology Research Center Photon Factory High Energy Research Organization (KEK) 305-0801 Tsukuba Oho 1-1 Japan Tel: +81(0)29-864-5642 (4901) Fax: +81(0)29-864-2801 e-mail: leonard.cha...@kek.jp Science Advisory Board (BIT Life Sciences) Editorial Board (JAA) http://pfweis.kek.jp/~leo
[ccp4bb] Post-doctoral position
Dear all -- please find here an announce for a post-doctoral position in this wonderful country that is Japan. Hope to see many of you applying. Kind regards -- Leo -- ### STARTS HERE ### Post-doctoral position. Structural Biology Research Center, Tsukuba, Japan [Closing date] All documents should arrive at the latest on the 29th of January 2010. [Job description] The Structural Biology Research Center offers a state of the art international and stimulating environment for research in a multi- disciplinary framework. Notably, molecular structural biology research in the field of intracellular transport and posttranslational modification including ubiquitylation is vigorously pursued and tightly linked with development and operation of synchrotron protein crystallography beamlines at the Photon Factory. We are looking for an enthusiastic post-doctoral fellow to work on proteins involved in intracellular transport and posttranslational modification processes. Some of the recent publications on the relevant research areas include: • Rahighi S, Ikeda F, Kawasaki M et al. (2009) Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell 136:1098-1109 • Dikic I, Wakatsuki S, Walters KJ (2009) Ubiquitin-binding domains - from structures to functions. Nat Rev Mol Cell Biol 10:659-671 • Chavas LM, Ihara K, Kawasaki M et al (2008) Elucidation of Rab27 recruitment by its effectors: structure of Rab27a bound to Exophilin4/ Slp2-a. Structure. 16:1468-77 • Kudo N, Kimagai K, Tomishige N et al. (2008) Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide. Proc Natl Acad Sci U S A. 105:488-93 • Hirano S, Suzuki N, Slagsvold T et al. (2006) Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain. Nat Struc Mol Biol. 13:1031-2 More information can be obtained on the following website: http:// pfweis.kek.jp/eng/index.html. [Qualifications and Experience] Motivated applicants should have a Ph.D. in a relevant field. Working experience in molecular biology and biochemistry is required. Previous experience with large-scale protein expression, purification, crystallization, structure determination, and structure analysis will be considered advantageous. Experience in the field of intracellular transport or posttranslational modifications would be a plus. [Contract] The contract will be issued on a yearly basis with possible extensions. The future employee will benefit from the social insurance, travel allowance and assistance with housing in accordance with the institute restrictions. [Start of the contract] Ideally, the contract will start from April 2010. Nevertheless, the exact starting date stays open to discussion with the candidate. [Applications] To apply, please send a cover letter, CV (in English) with a summary of your previous work and research skills (A4, 1-2 sheets), reprints of your key papers, your research aspirations (A4, 1-2 sheets), and the contact information of two professional references. When possible, the required documents should be submitted by e-mail. [Inquiries and contact information] When possible, the candidates should apply by e-mail. Please address all communications to Mrs. Ishikawa Gin (gin.ishik...@kek.jp). Prof. Soichi Wakatsuki Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK). 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan. Tel: +81-(0)29-879-6178 - Fax: +81-(0)29-879-6179 e-mail: soichi.wakats...@kek.jp ## ENDS HERE @@ Chavas Leonard, Ph.D. Assistant Professor Structural Biology Research Center Photon Factory High Energy Research Organization (KEK) 305-0801 Tsukuba Oho 1-1 Japan Tel: +81(0)29-864-5642 (4901) Fax: +81(0)29-864-2801 e-mail: leonard.cha...@kek.jp Science Advisory Board (BIT Life Sciences) Editorial Board (JAA) http://pfweis.kek.jp/~leo
Re: [ccp4bb] To get the crystal faster...
Dear James -- One possible issue you might have as well is oxidation. Your sample might need to be in a different step... and would therefore require some time before getting to this step. I personally noticed (in few cases) that when my crystals took time to grow, it was either because they were degraded, they needed a disulfide bond to be formed (oxidation level), or they needed to be unfolded / refolded (in a different conformation), the latest one being a rare case. HTH. Kind regards. -- Leo -- On 12 Oct 2009, at 00:27, james09 pruza wrote: Dear crystallographers, Sorry for the non-ccp4 query. I am new to this field and need some suggestions. My question is, why some protein takes longer time to crystallize, say 6-8 months, and it is the only condition to get the crystals.? What are the ways to get the crystals faster. The crystal appears with 60% of 2-Methyl, 2-4 Pentane Diol and only at 4 degree with very low concentration of NaCl. I have got some of the sugggestions earlier from the CCP4-discussion board for microseeding, but it did not work. All suggestions from the experts are welcome. Thanks. James Chavas Leonard, Ph.D. Assistant Professor Structural Biology Research Center Photon Factory High Energy Research Organization (KEK) 305-0801 Tsukuba Oho 1-1 Japan Tel: +81(0)29-864-5642 (4901) Fax: +81(0)29-864-2801 e-mail: leonard.cha...@kek.jp Science Advisory Board (BIT Life Sciences) Editorial Board (JAA) http://pfweis.kek.jp/~leo
Re: [ccp4bb] I compressed my images by ~ a factor of two, and they load and process in mosflm faster
Dear all -- I cannot remember exactly, but I thought we had a long discussion on the rightness of using compressed images, especially when considering the loss of information while doing so. What was the conclusion of the debate again? (sorry, too lazy to dig in the archives). -- Leo -- On 18 Sep 2009, at 23:50, Graeme Winter wrote: Hi David, If the data compression is carefully chosen you are right: lossless jpeg2000 compression on diffraction images works very well, but is a spot slow. The CBF compression using the byte offset method is a little less good at compression put massively faster... as you point out, this is the one used in the pilatus images. I recall that the .pck format used for the MAR image plates had the same property - it was quicker to read in a compressed image that the raw equivalent. So... once everyone is using the CBF standard for their images, with native lossless compression, it'll save a fair amount in disk space (=£/$), make life easier for people and - perhaps most importantly - save a lot of data transfer time. Now the funny thing with this is that if we compress the images before we store them, the compression implemented in the file system will be less effective... oh well, can't win em all... Cheers, Graeme 2009/9/18 Waterman, David (DLSLtd,RAL,DIA) david.water...@diamond.ac.uk: Just to comment on this, my friend in the computer game industry insists that compression begets speed in almost all data handling situations. This will be worth bearing in mind as we start to have more fine- sliced Pilatus 6M (or similar) datasets to deal with. Cheers, David. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of William G. Scott Sent: 17 September 2009 22:48 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] I compressed my images by ~ a factor of two, and they load and process in mosflm faster If you have OS X 10.6, this will impress your friends and save you some disk space: % du -h -d 1 mydata 3.5Gmydata mv mydata mydata.1 sudo ditto --hfsCompression mydata.1 mydata rm -rf mydata.1 % du -h -d 1 mydata 1.8Gmydata This does hfs filesystem compression, so the images are still recognized by mosflm, et al. I think they process a bit faster too, because half the information is packed into the resource fork. 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 Chavas Leonard, Ph.D. Assistant Professor Structural Biology Research Center Photon Factory High Energy Research Organization (KEK) 305-0801 Tsukuba Oho 1-1 Japan Tel: +81(0)29-864-5642 (4901) Fax: +81(0)29-864-2801 e-mail: leonard.cha...@kek.jp Science Advisory Board (BIT Life Sciences) Editorial Board (JAA) http://pfweis.kek.jp/~leo
Re: [ccp4bb] [OFF TOPIC] his-tag doesn't bind
Dear Fred -- just to check... are you sure you have the His-tag? Might have been cleaved somehow? You might want to increase the number of His in the tag as well. HTH. -- Leo -- On 27 Jan 2009, at 21:00, Fred wrote: Hi ccp4 list, I am trying to purify a his-tag protein by metal affinity chromatography. The protein was expressed in inclusion bodies and its his-tag doesn't bind the Qiagen Ni resin in denatured conditions (urea 8M or GndHCl 6M). Playing with NaCl and detergents didn't help much. Any help is appreciated. Fred Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: leonard.cha...@manchester.ac.uk http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] suggestions for UV spectrometer
Dear Tim -- On 4 Dec 2008, at 15:16, Tim Gruene wrote: we would like to purchase a UV spectrometer for measuring protein concentrations (280nm), and I would like to here your comments and especially recommendations. I love the Nanodrop system... I know you said you don't want anything fancy, but I like to spend as little protein as possible when measuring its concentration, and I like it fast and reproducible. Plus, in my hands, the Nanodrop system give very reproducible results. Small problem... expensive... You can find infos there: http://www.nanodrop.com/nd-1000-overview.html HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] Definition of salt bridge
Dear Francisco -- On 15 Oct 2008, at 17:05, Francisco J. Enguita wrote: how can you define a salt-bridge within a protein structure ? According to Wikipedia: a salt bridge in proteins is a relatively weak ionic bond between positively and negatively charged side-chains of proteins. Now, at far as I understand (based on Structure and Mechanism in Protein Science - Alan Fersht), you have a salt bridge when two groups are making an hydrogen bond that is favored by electrostatic interaction, electrostatic energies being weak in water. To quote the author of the book, let say you have the following equilibrium: E-NH3+ --- OH2 + OH2 --- -O2C-S == E-NH3+ --- -O2C-S + H2O --- H2O The right-hand side equation would be more favorable, as the electrostatic interaction will be more stable than in the left-hand side where both ions would be in contact with water molecules. HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] precipitates
Dear Amit -- On 30 Sep 2008, at 14:16, amit sharma wrote: I am trying to crystallize a protein with a peptide attached to it via a 9aa linker. I am mostly getting precipitates in conditions carrying salts. I have tried optimization screens by varying the pH and salt concentrations, but in vain. Can anyone please suggest ways by which I could optimize the conditions further? Among all the possibilities, you can: - try to crystallize without salt ; - change the temperature ; - dilute your protein ; - add some isopropanol (or other) to make the solution smoother ; - change your linker size ; - ... HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] creating alternate conformations using PyMol
Dear Neeraj -- On 26 Sep 2008, at 22:48, Neeraj wrote: Is there an easy way to do this in pymol which will help me rotate only a small fragment of the protein while keeping everything else static. What you can do is to generate two coordinate files, one without your loop, one with, and more around only the one with your loop... HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] protein complex crystallisation
Dear Ron -- On 20 Sep 2008, at 15:59, Ron hudson wrote: it is happily soluble and donot prcipitate at this pH in the same buffer. Just a quick question. How does your complex look like under DLS? You might still have soluble aggregates, which will precipitate... you can screen for soluble non-aggregates by varying the pH, and check all of this under DLS. HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] Unexplained electron density
Dear Maria -- On 19 Sep 2008, at 01:38, Maria Håkansson wrote: Any suggestions? In addition, could that be a water molecule present at (or near) a special position? Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] Phoenix robot
Dear Hao -- On 10 Sep 2008, at 02:00, jxqi wrote: Does anyone have the experience of using Phoenix robot automatically setup the crystal? Which plate the Phoenix could use such as 96-well sitting drop or hanging drop? If available could you also tell me the CAT NO. of hampton!!! Just to clarify my previous post a bit. The Phoenix installed in our lab is working properly, has been set up for sitting drops, and dispenses drops in Intelliplate which are 96 wells plates. I've been made to realize that the URL I sent is not the official link for the dispensing system, although it has a very nice video. To have more complete details, please follow this link: http://www.artrobbinsinstruments.com/phoenix.html Good luck. Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] Phoenix robot
Dear Hao -- On 10 Sep 2008, at 02:00, jxqi wrote: Does anyone have the experience of using Phoenix robot automatically setup the crystal? yes Which plate the Phoenix could use such as 96-well sitting drop or hanging drop? 96 sitting-drop If available could you also tell me the CAT NO. of hampton!!! ?? You might want to have a look there: http://www.rigaku.com/automation/phoenix.html HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] Building peptide in density using coot.
Dear Tarique -- On 2 Sep 2008, at 12:58, Tarique wrote: Can any body tell me how to build peptide fragment of 5-6 residues using coot,if the sequence is known.I am working at 2.1 angstroms resolution map. If the peptide you're trying to build is a loop, and the density is visible, you can use the Fit Loop option, straight forward to understand. Now, if you're trying to build a peptide not related to your protein, e.g. a ligand, I would start by importing a single alanine.pdb file that would contain the coordinates for an alanine, place the alanine in the density you can see, and start to build from it. You can still mutate with the proper amino acids later on. Please note that I'm still working on an hold version of Coot, without any fancy additional options :) HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] Refmac out-put file header information
Dear Yusuf -- On 8 Aug 2008, at 06:01, Yusuf Akhter wrote: My data is 95.4% of completeness at Signal/noise =-3. I noticed that in the header of out-put PDB file from Refmac shows 100% completeness. Could you precise where do you see 100% completeness in the PDB header (overall reflections or highest resolution shell)? Also, is you 95.4% completeness for the all range of your data, or is it for the highest resolution shell? I'm not quite sure, but I think to remember I had the same problem with one of my data, which was complete 98% overall, but Refmac gave me an output of 100% for the highest resolution shell (which was true actually!). Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Marie Curie Actions Fellow Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] 27.5% R/29% Rfree for 1.75A structure (details updated)
Dear Jinjin Zhang -- On 29 Jul 2008, at 22:34, JINJIN ZHANG wrote: 1. Protein 100 aa, peptide 6 aa, co-crystalized 2. Space group: P43212. Overall R-fac: 0.03. Redundancy: 5 for 98% of reflections. B-factor:55 3. CNS refinement 4. Phenix xtriage checked, no twinning is suspected. 5. Water molecules added What about the hight resolution shell completeness, I/sig, Rfac, redund? How many molecule per asymm? What is the B-fac for your ligand? Did you assign all the side chain correctly? If you have for instance 2 prot / asymm, would that be possible to have a swapping? How is your electron density? DId you try the TLS refinement as well? At this resolution, I'm guessing you can ask an automatic program to build the all chain (not so long). Did you try Arp/wArp? What would be the final stats after such building? HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] SUMMARY: synchrotron remote data collection
Dear all -- On 22 Jul 2008, at 00:45, Tom Caradoc-Davies wrote: Beamline 3BM1 at the Australian Synchrotron I believe in Japan as well there is a remote control available, at SPring8. It is called Mail-in system. You can probably find more informations there: http://www.spring8.or.jp/en/about_us/organization/ research_utilization/biology HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
Re: [ccp4bb] refmac5
Dear Sajid -- Thanks for your suggestions to run revise. Suggestions from Mike Latchem helped me to overcome the problem. I have another question. I am trying to run REFMAC5. It is giving some warning message. # There is no file name for parameter MAPOUT1 The CCP4 program is lable to fail. Please enter a file name and Run again # After dismissing the warning message the program is not running. I do not know about this parameter file. Any suugestions please I believe this has been a problem previously reported, as it is in the problem page of the ccp4: http://www.ccp4.ac.uk/problems.php HTH Kind regards. Leo Chavas Leonard, Ph.D. Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot
Dear Joe -- Does anyone have information about how long it takes to set up a 96- well tray for the crystallization robots available? Besides cost per tray and maintenance cost, another important feature we consider is the time for setting up a 96-well tray. It is an important factor since we are talking about sub-microliter drops. The japanese protein-crystallization system (PXS) can handle 7680 drops / hour, from sample and solution disposal to sealing and incubator storage. You can have a look at the movie: http://pfweis.kek.jp/system/PXS.html or at the paper (PubMed 16929107). HTH. Kind regards. Leo Chavas Leonard, Ph.D. Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Feature of CCP4i for 6.0.99 (SIGF/Weight label menu)
Dear Serge -- While using the CCP4 version 6.0.99 during the Bangalore workshop, I realised that it is not any more possible to freely choose the weight/sigma labels from a mtz input file. In particular when trying to use phases coming from refmac (after MR + rigid body) with there FoM as input to DM (for NCS averaging) it is not possible to select the FOM from refmac as the weight for PHIC... While I fill that the 6.0.99 implemetation is safer in the way that it prevents easy wrong input of the weight/sigma, it is sometime necessary to be able to select 'non-standard' weight/sigma (using ie. the list labels possibilities present in 6.0). I've discussed the matter with Martyn during the workshop, but don't hesitate to ask me for more details if this messag is not clear enough. you can't do it at all, or is it only restricted to the interface (ie scripting still ok)? I'm currently still using 6.0, but some students here are using 6.0.99 and might have this problem, although not reported yet. Leo Chavas Leonard, Ph.D. Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Tough Low-Res MR
Dear James -- I have a tough ~3.5 Å (pushing it) MR problem where I have a solution of sorts, but because I'm working with a heterodimer of two closely related subunits (with two such heterodimers in the ASU) I have a 2**2 possibilities for the arrangement of these subunits in the ASU. Each subunit is composed of two more-or-less independent domains. Basically I'm looking for the best possible software to disambiguate this problem. I usually use CNS for these problems, but I think I may have exhausted its capabilities. I've heard that there have been some advances in MR in recent years, but I haven't kept up with all of the software. Does anyone have suggestions for packages to try? I usually run in parallel Phaser and Balbes (ie Molrep), and check which one gives me the best solution (stats map). The wonder with Balbes is that it tries automatically a large batch of possibilities, models. Now, as a personal feeling, although I could solve a couple of structures with Phaser for which I had problems using Molrep, I often get solutions that overlap / crash with the neighboring molecule using Phaser. Obviously, this might be due to my low resolution data (it was around 4 A if I recall correctly), but the fact that Balbes did worked properly for the same data... HTH Kind regards. Leo Chavas Leonard, Ph.D. Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] PISA parameters for surface area calculation
Dear Rafael -- I am using PISA to calculate the surface interface of a homdimeric protein. Does anyone know where I can find the parameters (probe radius, atomic radii, etc) PISA uses to calculate surface area? not sure, but would that help?: http://www.ebi.ac.uk/msd-srv/prot_int/picite.html HTH Kind regards. Leo Chavas Leonard, Ph.D. Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] shipping heavy-atom solutions using Fedex
Dear David, I'm not sure, but you might find something useful there: www.sddc.army.mil/sddc/ Content/Pub/11467/Attachment3.pdf HTH Kind regards. Leo Chavas Leonard, Ph.D. Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Different chains in the dimer
Dear Yang, Thanks for the reply. Both are P21. Point mutant. MR solved the mutant using native as a model. What about the crystal contacts of the region that changed then? Is it different in native and mutant forms? Both space groups are the same, but what about the cell dimensions? Again, the packing here might be of importance. Have a look at the neighboring molecules and how the act on the varying region. Also, how different is this region? 1 angstrom? 10 angstrom? BTW, what does HTH mean? I don't know myself... everybody is using it, so I'm using it as well :) H(ope)T(his)H(elps). Kind regards. Leo Chavas Leonard, Ph.D. Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] How to subscribe to the bulletin board
Dear Alok, I had become a member many years ago, and some of the students , postdocs in the lab also want to be included in the bulletin board membership, could you let me know what is the procedure, thanks very much follow the instructions specified in http://www.ccp4.ac.uk/ccp4bb.php HTH Kind regards. Leo Chavas Leonard, Ph.D. Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED]
