Re: [ccp4bb] Dry shipper in limbo
Hi all, In addition to the statements above, our experience has shown that using the Customs broker as described on the CLS webpage has been helpful. Our weekly shipments from Seattle to Saskatoon typically make it overnight, worst case the next day. Also, test your dewars. They should keep cold for a good week. With simple tests one can identify dewars that are on their way out. Glad that your dewar turned up and that the great staff at CLS could fit you in. Cheers, Jan On Fri, Jul 28, 2023 at 1:09 PM Dr. Kevin M Jude wrote: > Hi all, thanks for the responses on and off list. > > > > Yesterday I got my case assigned to someone in the international shipping > division, gave a physical description of my shipping case and expressed the > perishable nature of the contents. My dewar turned up in Calgary last night > and was just delivered to CLS, hopefully in cold condition. My contact at > CLS was able to give my time (yesterday) to another user and get me > rescheduled for the weekend. I had shipped Monday for Thursday beamtime, > hoping to avoid limbo over the weekend, but maybe in the future I’ll aim a > little earlier. > > > > Besides the on-list responses, I had a couple of helpful off-list replies: > > > > BW duct-tapes an airtag into his shipping cases to help keep an eye on them > > > > SG says be sure to include USCMA/CUSMA certificate of origin for shipments > within North America, along with statement that the samples are > non-hazardous, for research purposes, with no commercial value (and don’t > assign a high value to the shipment). When contacting FedEx ask for a > supervisor in the international shipping division. Customs inspectors may > be less tied up late at night. > > > > > > *From: *CCP4 bulletin board on behalf of Dr. > Kevin M Jude > *Date: *Thursday, July 27, 2023 at 8:16 PM > *To: *CCP4BB@JISCMAIL.AC.UK > *Subject: *[ccp4bb] Dry shipper in limbo > > My first adventure in international crystallography is off to an > inauspicious start. On Monday, I sent a dry shipper “overnight” from > California to Saskatchewan, but it has been stuck in the Memphis FedEx > facility for a few days. I’ve gotten several conflicting explanations of > the status from FedEx on the phone, but the most likely seems that it has > “pre-cleared” customs and yet has not yet made it to Calgary. It’s not > clear whether anyone actually knows where the shipping case is, since I was > asked to give a physical description of it. Is there anything else I can do > from a few thousand miles away, or do I just have to wait this out? > > > > -- > > Kevin Jude, PhD > > Structural Biology Research Specialist, Garcia Lab > > Howard Hughes Medical Institute > > Stanford University School of Medicine > > Beckman B177, 279 Campus Drive, Stanford CA 94305 > > Phone: (650) 723-6431 > > > -- > > 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 > -- Jan Abendroth UCB BioSciences Seattle / Bainbridge Island, WA, USA home: jan.abendr...@gmail.com work: jan.abendr...@ucb.com 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] coot 0.9.8.1 and phenix mtz files
Hi all, not sure if this appropriate for this BB, since right at the interface between CCP4, Coot and Phenix. I wonder if someone else also experiences these issues after upgrading to CCP4 8.0 (or 8.001) and with that to Coot 0.9.8.1. This happens both on OSX and windows. - coot *mydata*.pdb *mydata*.mtz will only open up the PDB but ont the mtz file. The latter can be opened via the Load menu. - The Coot window launched from the phenix gui does not displany the pdb or the map. Any pointers would be appreciated. Thanks! Jan -- Jan Abendroth UCB BioSciences Seattle / Bainbridge Island, WA, USA home: jan.abendr...@gmail.com work: jan.abendr...@ucb.com 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] PDB deposition of structure solved with a Robetta model
Hi Bernhard, That sounds fine. I have used the term 'RoseTTAfold/AlphaFold2 model' in that field for a few SSGCID depositions. Many times, this field does not really provide an accurate description of the model that was used: You might trim a model, use separate domains, use MoRDa that might select domains from various sources, etc. Cheers, Jan On Mon, Feb 7, 2022 at 5:24 AM Loll, Bernhard wrote: > Dear all, > > I have recently solved a structure by molecular replacement with a > search model calculated by the Robetta server. > > I am in the process to deposit the coordinates. Now, I am wondering > which information I should give on the starting model. Routinely, I > would provide the the PDB code, which is a mandatory item for the > deposition. > > How can I keep the information that I used the Robetta calculated model? > > In advance thanks for your valuable answers. > > Cheers, > > Bernhard > > -- > Dr. Bernhard Loll > Freie Universitaet Berlin > Fachbereich Biologie, Chemie, Pharmazie > Institut fuer Chemie und Biochemie > AG Strukturbiochemie > Takustr. 6 > D-14195 Berlin > Germany > > Phone: +49 (0) 30 838-57348 > Fax: +49 (0) 30 838-457348 > Email: l...@chemie.fu-berlin.de > Homepage: > http://www.bcp.fu-berlin.de/en/chemie/biochemie/research-groups/wahl-group/mitarbeiter/Dr__Bernhard_Loll.html/ > > > > 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/ > -- Jan Abendroth UCB BioSciences Seattle / Bainbridge Island, WA, USA home: jan.abendr...@gmail.com work: jan.abendr...@ucb.com 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] diffdump in CCP4 7.1
Hi all, It looks as if the utility ‘diffdump’ is no longer part of the standard linux CCP4 7.1 distribution. It has been a very handy tool for preparing XDS input files. Does anyone know if there is an equivalent script in CCP4 7.1? Thanks, Jan -- Jan Abendroth UCB BioSciences Seattle / Bainbridge Island, WA, USA home: jan.abendr...@gmail.com work: jan.abendr...@ucb.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories
bespoke shipping case. > > > > Thanks for any insights that might satisfy my curiosity and/or prevent > future mishaps of this sort. > > > > Cheers, > > > > Pat > > > > __ > > > > Patrick J. Loll, PhD > > Professor of Biochemistry & Molecular Biology > > Drexel University College of Medicine > > Room 10-102 New College Building > > 245 N. 15th St. > > Philadelphia, PA 19102-1192 USA > > > > (215) 762-7706 > > pj...@drexel.edu > > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1%26d%3DDwMFaQ%26c%3DDbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo%26r%3DHK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ%26m%3DtHIcVAtKk5YdRxIBzLho11ppNDkaH-avpnFs_37lwH0%26s%3DPYxKUwCdRR-6mIIlKRTPRWC1bueGjj3go5N923mkOnk%26e%3D=02%7C01%7Csyun-ru.yeh%40EINSTEINMED.ORG%7C0ebfe1e3b7bf41e63f2908d8190520c5%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637286857110104764=SGqRILIMeGpclr85hC5g0wi1jRX%2Bnq%2B40IGwzfmlBKE%3D=0> > > > > -- > > Jan Dohnalek, Ph.D > Institute of Biotechnology > > Academy of Sciences of the Czech Republic > > Biocev > > Prumyslova 595 > > 252 50 Vestec near Prague > > Czech Republic > > Tel. +420 325 873 758 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1%26d%3DDwMFaQ%26c%3DDbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo%26r%3DHK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ%26m%3DtHIcVAtKk5YdRxIBzLho11ppNDkaH-avpnFs_37lwH0%26s%3DPYxKUwCdRR-6mIIlKRTPRWC1bueGjj3go5N923mkOnk%26e%3D=02%7C01%7Csyun-ru.yeh%40EINSTEINMED.ORG%7C0ebfe1e3b7bf41e63f2908d8190520c5%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637286857110104764=SGqRILIMeGpclr85hC5g0wi1jRX%2Bnq%2B40IGwzfmlBKE%3D=0> > > > > -- > Jan Dohnalek, Ph.D > Institute of Biotechnology > Academy of Sciences of the Czech Republic > Biocev > Prumyslova 595 > 252 50 Vestec near Prague > Czech Republic > > Tel. +420 325 873 758 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=02%7C01%7Csyun-ru.yeh%40EINSTEINMED.ORG%7C0ebfe1e3b7bf41e63f2908d8190520c5%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637286857110114764=snT6Z1Jxlrc%2Fzk%2BiK2si6D%2B9We6QCjZzomLAbdYMzX0%3D=0> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Abendroth UCB BioSciences Seattle / Bainbridge Island, WA, USA home: jan.abendr...@gmail.com work: jan.abendr...@ucb.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] dewar horror stories
ED1=CCP4BB=1 > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1%26d%3DDwMFaQ%26c%3DDbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo%26r%3DHK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ%26m%3DtHIcVAtKk5YdRxIBzLho11ppNDkaH-avpnFs_37lwH0%26s%3DPYxKUwCdRR-6mIIlKRTPRWC1bueGjj3go5N923mkOnk%26e%3D=02%7C01%7Csyun-ru.yeh%40EINSTEINMED.ORG%7C0ebfe1e3b7bf41e63f2908d8190520c5%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637286857110104764=SGqRILIMeGpclr85hC5g0wi1jRX%2Bnq%2B40IGwzfmlBKE%3D=0> > > > > -- > > Jan Dohnalek, Ph.D > Institute of Biotechnology > > Academy of Sciences of the Czech Republic > > Biocev > > Prumyslova 595 > > 252 50 Vestec near Prague > > Czech Republic > > Tel. +420 325 873 758 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1%26d%3DDwMFaQ%26c%3DDbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo%26r%3DHK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ%26m%3DtHIcVAtKk5YdRxIBzLho11ppNDkaH-avpnFs_37lwH0%26s%3DPYxKUwCdRR-6mIIlKRTPRWC1bueGjj3go5N923mkOnk%26e%3D=02%7C01%7Csyun-ru.yeh%40EINSTEINMED.ORG%7C0ebfe1e3b7bf41e63f2908d8190520c5%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637286857110104764=SGqRILIMeGpclr85hC5g0wi1jRX%2Bnq%2B40IGwzfmlBKE%3D=0> > > > > -- > Jan Dohnalek, Ph.D > Institute of Biotechnology > Academy of Sciences of the Czech Republic > Biocev > Prumyslova 595 > 252 50 Vestec near Prague > Czech Republic > > Tel. +420 325 873 758 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=02%7C01%7Csyun-ru.yeh%40EINSTEINMED.ORG%7C0ebfe1e3b7bf41e63f2908d8190520c5%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637286857110114764=snT6Z1Jxlrc%2Fzk%2BiK2si6D%2B9We6QCjZzomLAbdYMzX0%3D=0> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > -- Jan Abendroth UCB BioSciences Seattle / Bainbridge Island, WA, USA home: jan.abendr...@gmail.com work: jan.abendr...@ucb.com 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] powdery residue on pucks?
We call this 'synchrotron dust', but our suspicion is the same that is is a breakdown product of the foam. It happens more often with old dewars than with newer ones. Once this happens, it is a good time to test the dewars. Cheers, Jan On Fri, Feb 21, 2020 at 4:40 PM Diana Tomchick < diana.tomch...@utsouthwestern.edu> wrote: > I believe my technician decided that it was due to the breakdown of the > adsorbent foam in our oldish shipping dewar, as it stopped happening once > we replaced that particular dewar. > > But I would be open to other explanations. > > Diana > > ** > Diana R. Tomchick > Professor > Departments of Biophysics and Biochemistry > UT Southwestern Medical Center > 5323 Harry Hines Blvd. > Rm. ND10.214A > Dallas, TX 75390-8816 > diana.tomch...@utsouthwestern.edu > (214) 645-6383 (phone) > (214) 645-6353 (fax) > > On Feb 21, 2020, at 6:33 PM, Emilia C. Arturo (Emily) > wrote: > > > EXTERNAL MAIL > > Hi All, > > We have been noticing lately that our crystal pucks return from different > beamlines coated with the same powdery material. For the record, we > typically undo our pucks, clean the assemblies and dry out the > pucks within a day of receiving the shipping dewar, but notice the same > thing regardless of how long between receiving the dewar and disassembling > the pucks. Have any of you experienced this sort of thing, or have > suggestions of what might be the cause and/or the powdery material? > > Regards, > Emily. > > -- > "Study as if you were going to live forever; live as if you were going to > die tomorrow." - Maria Mitchell > > "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May > Alcott > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > CAUTION: This email originated from outside UTSW. Please be cautious of > links or attachments, and validate the sender's email address before > replying. > > > > -- > > UT Southwestern > > Medical Center > > The future of medicine, today. > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- Jan Abendroth UCB BioSciences Seattle / Bainbridge Island, WA, USA home: jan.abendr...@gmail.com work: jan.abendr...@ucb.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] map rotation
Thanks, Eleanor! what i really want to do with this script is to compare ligand binding sites from many structures in several space groups. So, I want to move coordinates and density onto one reference molecule. Since we ran into issues, I used this dimer structure as a simple test case. The script you outlined, only recreates the same density w/o any rotation. mapmask \ mapin AB_full-cell.ccp4 \ xyzin B.pdb \ mskout B.msk \ << eof border 5 eof maprot \ mapin AB_full-cell.ccp4 \ mskin B.msk \ mapout B_rot.map \ << eof MODE to AVER rota euler 152.440 110.24328.112 TRANS -42.212 5.510 -57.243 end eof Btw, I had to remove the rota euler 0 0 0 / trans 0 0 0 lines. Maprot complained about too many operators. The odd thing -to me- is that when I shift a map around molecule B or the dimer (mapmask with border 5) with a small amount ( euler 1 0 0 or trans 0.5 0.5 0.5) the map does not look jagged at the edges of the molecule, while it does when I rotate the full amount to match B on A: maprot \ wrkin AB-5.map \ mapout AB_rot.map \ << eof CELL xtal 61.0100 142.360068.280090.97.198090. GRID xtal 100 228 112 MODE to AVER rota euler 1 0 0 TRANS 0 0 0 end eof Cheers, Jan On Mon, Mar 25, 2019 at 3:49 AM Eleanor Dodson wrote: > Hmm - I find maprot extremely confusing, but remember a wrkmap does not > use any symmetry so maybe that is why some is lost. > > I would have done this, but I havent tested it. And the documentation is > SERIOUSLY confusing!! > > Do I understand you want to ADD the density for mol B to that of Mol A > > > mapmask mapin whole-cell.map > xyzin A.pdb > mskout A-mol.msk > > Then > maprot > mapin whole-cell.map > mskin A-mol.msk ! only density withing this mask > is interesting > mapout A-mol.map > > MODE to > > AVER > > rota euler 0 0 0! to pick up mol A density > > trans 0 0 0 > > > rota euler 152.440 110.24328.112 ! to rotate map by B to A > rotation > > TRANS -42.212 5.510 -57.243 > > end > > > > > > On Mon, 25 Mar 2019 at 04:58, Jan Abendroth > wrote: > >> Hi all, >> thanks for the feedback. Suggestions like coot or pymol won't work for us >> well, since we will have to do this with dozens of structures/maps.So, I'd >> rather have this scripted. >> >> Still running into some issues that I think relate to maprot. >> My understanding is that I first have to create a map covering molecule B >> that I want to map on A. Checking the extend of the map in chimera confirms >> that this worked: >> >> >> mapmask \ >> >> mapin 2mol_2mFo-DFc.map \ >> >> xyzin 2mol_B.pdb \ >> >> mapout 2mol_2mFo-DFc_B.map \ >> >> << eof >> >> border 5 >> >> eof >> >> >> Next, I need to rotate/translate the map in maprot. Since in maprot, >> mapin requires a map that covers the unit cell, I use wrkin and 'mode to' >> as below. In this script, the cell and grid values are the same mapdump >> provides me for the map. The rotation and translation are from superpose, >> RMSD of that superposition is 0.5Å. >> >> >> maprot \ >> >> wrkin 2mol_2mFo-DFc_B.map \ >> >> mapout 2mol_2FoFc_rot.map \ >> >> << eof >> >> CELL xtal 61.0100 142.360068.280090.97.198090. >> >> GRID xtal 100 228 112 >> >> MODE to >> >> AVER >> >> rota euler 152.440 110.24328.112 >> >> TRANS -42.212 5.510 -57.243 >> >> eof >> >> >> The issue now is that the superposed map for the center of molecule A >> looks great. Towards the edges of the molecule it gets weaker, does not >> match up with the molecule or stops entirely. Again, molecule and maps >> between A and B, as visualized in Coot by NCS hopping, are very similar. >> >> >> I am still quite puzzled by what is happening. I guess I am missing >> something in maprot. Any input would be appreciated. This is public >> data, so I would be happy to share the data. >> >> >> Cheers, >> >> Jan >> >> >> >> On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth >> wrote: >> >>> Hi all, >>> this should be easy, scripting the rotation of a map. >>> Purpose for this is: Superimpose several structures of the same protein >>> that crystallized in different space groups, and then drag the maps along. >>> As a simple test, I took a dimeric protein and try to superimpose >
Re: [ccp4bb] map rotation
Hi all, thanks for the feedback. Suggestions like coot or pymol won't work for us well, since we will have to do this with dozens of structures/maps.So, I'd rather have this scripted. Still running into some issues that I think relate to maprot. My understanding is that I first have to create a map covering molecule B that I want to map on A. Checking the extend of the map in chimera confirms that this worked: mapmask \ mapin 2mol_2mFo-DFc.map \ xyzin 2mol_B.pdb \ mapout 2mol_2mFo-DFc_B.map \ << eof border 5 eof Next, I need to rotate/translate the map in maprot. Since in maprot, mapin requires a map that covers the unit cell, I use wrkin and 'mode to' as below. In this script, the cell and grid values are the same mapdump provides me for the map. The rotation and translation are from superpose, RMSD of that superposition is 0.5Å. maprot \ wrkin 2mol_2mFo-DFc_B.map \ mapout 2mol_2FoFc_rot.map \ << eof CELL xtal 61.0100 142.360068.280090.97.198090. GRID xtal 100 228 112 MODE to AVER rota euler 152.440 110.24328.112 TRANS -42.212 5.510 -57.243 eof The issue now is that the superposed map for the center of molecule A looks great. Towards the edges of the molecule it gets weaker, does not match up with the molecule or stops entirely. Again, molecule and maps between A and B, as visualized in Coot by NCS hopping, are very similar. I am still quite puzzled by what is happening. I guess I am missing something in maprot. Any input would be appreciated. This is public data, so I would be happy to share the data. Cheers, Jan On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth wrote: > Hi all, > this should be easy, scripting the rotation of a map. > Purpose for this is: Superimpose several structures of the same protein > that crystallized in different space groups, and then drag the maps along. > As a simple test, I took a dimeric protein and try to superimpose molecule > B along with the map on molecule A. > > The execution should be straightforward: > a) take a map that covers the unit cell (fft), > b) generate a mask around molecule B (mapmask), > c) apply rotation/translation that I obtain from superimposing molecule B > on molecule A. > > The issue is that the obtained map covers both molecule A and B (not a big > deal), more importantly, it cuts of certain areas on both molecules. > Molecule A and B have low RMSDs (0.5Å). > > I must be missing something fairly obvious, have not been able to see > what. Feedback would be much appreciated. Scripts are below. > > Thanks! > Jan > > mapmask \ > > mapin 2mol_2mFo-DFc.map \ > > xyzin 2mol_B.pdb \ > > mskout 2mol_2mFo-DFc_2mol_B.msk \ > > << eof > > border 2 > > eof > > > maprot \ > > mapin 2mol_2mFo-DFc.map \ > > mskin 2mol_2mFo-DFc_2mol_B.msk \ > > wrkout 2mol_2mFo-DFc_rot.map \ > > << eof > > MODE from > > AVER > > ROTA euler 152.440 110.24328.112 > > TRANS -42.212 5.510 -57.243 > > eof > -- > Jan Abendroth > Seattle / Bainbridge Island, WA, USA > home: Jan.Abendroth_at_gmail.com > > -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] map rotation
Hi all, this should be easy, scripting the rotation of a map. Purpose for this is: Superimpose several structures of the same protein that crystallized in different space groups, and then drag the maps along. As a simple test, I took a dimeric protein and try to superimpose molecule B along with the map on molecule A. The execution should be straightforward: a) take a map that covers the unit cell (fft), b) generate a mask around molecule B (mapmask), c) apply rotation/translation that I obtain from superimposing molecule B on molecule A. The issue is that the obtained map covers both molecule A and B (not a big deal), more importantly, it cuts of certain areas on both molecules. Molecule A and B have low RMSDs (0.5Å). I must be missing something fairly obvious, have not been able to see what. Feedback would be much appreciated. Scripts are below. Thanks! Jan mapmask \ mapin 2mol_2mFo-DFc.map \ xyzin 2mol_B.pdb \ mskout 2mol_2mFo-DFc_2mol_B.msk \ << eof border 2 eof maprot \ mapin 2mol_2mFo-DFc.map \ mskin 2mol_2mFo-DFc_2mol_B.msk \ wrkout 2mol_2mFo-DFc_rot.map \ << eof MODE from AVER ROTA euler 152.440 110.24328.112 TRANS -42.212 5.510 -57.243 eof -- Jan Abendroth Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Acrimboldo BORGES standard libraries
Hi all, I have been trying to install the BORGES standard libraries to run ACRIMBOLDO with them. This is an installation of the libraries on top of a CCP4 installation using 'ccp4sm'. The libraries download, the installation finishes and the libraries end up in the following folder: $CCP4/bin/destination/BORGES_LIBS I selected 'edit set up file' while running 'ccp4sm'. Still, the standard libraries show in ccp4i remain greyed out, only CUSTOM is an option. The ccp4.setup-sh file does not seem to have a reference to BORGES. I wonder what I am missing to get this installed. Thanks, Jan -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
[ccp4bb] Speaker opportunity at ACA 2018, session: Current state of instrumentation, automation, status and future
Hi all, The Industrial Crystallography SIG of the American Crystallographic Association will host a session for the 2018 ACA meeting titled “Current state of instrumentation, automation, status and future”. We are looking for speakers for this session. The session should cover both robotic automation or computational automation, or the integration of both. This could be for the in-house lab, as well as for beamlines. Basically, anything that supports high throughput crystallography in one way or another. We would like to encourage developers of new instrumentation to speak, as well as users. We do not want to turn this into a product show though. The talks are expected to be around 15-20min long. If you are interested in presenting, please send a title and a draft abstract to the session hosts. Matt Clifton, Nurix Inc., mclif...@nurix-inc.com<mailto:mclif...@nurix-inc.com> Jan Abendroth, Beryllium Discovery, jabendr...@be4.com<mailto:jabendr...@be4.com> Thanks and best wishes, Matt Clifton Jan Abendroth JAN ABENDROTH, Dr. Core Leader, CrystalCore P 206-780-8925 F 206-780-8547 Seattle | Boston | USA | be4.com [cid:image001.png@01D350FE.EE91E390]
Re: [ccp4bb] Tricky MR problem
Hi Rhys, there is nothing wrong with experimental phases. If a few MR attempts fail, there aren't any real red flags with your crystal form, and you have a few decently diffracting crystals at hand, soak them for a little bit in your favourite heavy atom. We found that soaks in 500-1000mM Na or K iodide in your precipitant solution are very successful. Many crystals tolerate such high iodide concentrations well. Iodide has a very strong anomalous signal in house and binds to a variety of sites. For SSGCID, this has become our main technique to obtain experimental phases. With the great software packages available nowadays, you can have an initial structure within minutes after finishing the data set. For a recent review of this old technique see here: http://www.ncbi.nlm.nih.gov/pubmed/21359836 Best wishes, Jan -- Jan Abendroth Emerald BioStructures / SSGCID Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com On Oct 1, 2012, at 12:26 PM, RHYS GRINTER r.grinte...@research.gla.ac.uk 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
[ccp4bb] Phaser and space groups
Hi all, we have been running into a space group issue when we start phaser (2.5.1) through ccp4i since the installation of ccp4-6.3.0: We typically scale data in the point group and then let Phaser go through various space groups. Even though the corresponding line appears in the input file SGALTERNATIVE SELECT LIST SGALTERNATIVE TEST P41 rotation and translation function would only run in the space group provided by the mtz file. Obviously it does not matter for the rotation function. As a work around one can edit the input file (run view com file), by replacing the two lines mentioned above with SPACEGROUP P41 This is a bit inconvenient though. Any ideas what is going wrong with the standard way? Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
[ccp4bb] refmac5, SIGF/SIGIMEAN labels
Hi all, we noticed a strange behaviour of refmac5.7.0029 that comes with CCP4-6.3. We run a most basic script: 5 rounds of restrained refinement with all default parameters. The input mtz file contains besides H/K/L and FreeR_flag, IMEAN/SIGIMEAN, and F/SIGF. Refmac 5.6.0117 outputs F/SIGF, while Refmac 5.7.0029 outputs F/SIGIMEAN, see mtzdmp output below. Any ideas? Cheers, Jan CCP4 6.2: Refmac_5.6.0117 version 5.6.0117 : 13/06/11 Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC 0 22 0 100.00 8.4 8.4 47.42 2.40 H H 2 NONE 0 34 0 100.00 12.7 12.7 47.42 2.40 H K 3 NONE 0 38 0 100.00 14.4 14.4 47.42 2.40 H L 4 NONE0.019.0 0 100.00 9.44 9.44 47.42 2.40 I FreeR_flag 5 NONE 11.4 2203.4 123 99.28 291.26 291.26 47.42 2.40 F F 6 NONE3.287.0 123 99.2820.5220.52 47.42 2.40 Q SIGF 7 NONE0.3 12246.7 0 100.00 299.12 299.12 47.42 2.40 F FC 8 NONE0.0 360.0 0 100.00 177.62 177.62 47.42 2.40 P PHIC 9 NONE0.1 2176.5 0 100.00 261.72 261.72 47.42 2.40 F FC_ALL 10 NONE0.0 360.0 0 100.00 178.73 178.73 47.42 2.40 P PHIC_ALL 11 NONE0.0 2230.3 0 100.00 272.42 272.42 47.42 2.40 F FWT 12 NONE0.0 360.0 0 100.00 179.06 179.06 47.42 2.40 P PHWT 13 NONE0.0 1672.5 0 100.0057.7457.74 47.42 2.40 F DELFWT 14 NONE0.0 360.0 0 100.00 169.39 169.39 47.42 2.40 P PHDELWT 15 NONE 0.000 1.000 0 100.000.7470.747 47.42 2.40 W FOM CCP4 6.3: Refmac_5.7.0029 version 5.7.0029 : 25/06/12 Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC 0 22 0 100.00 8.4 8.4 47.42 2.40 H H 2 NONE 0 34 0 100.00 12.7 12.7 47.42 2.40 H K 3 NONE 0 38 0 100.00 14.4 14.4 47.42 2.40 H L 4 NONE0.019.0 0 100.00 9.44 9.44 47.42 2.40 I FreeR_flag 5 NONE 10.9 2108.7 123 99.28 278.90 278.90 47.42 2.40 F F 6 NONE2.2 1407.1 123 99.2854.1054.10 47.42 2.40 Q SIGIMEAN 7 NONE0.1 12718.0 0 100.00 288.12 288.12 47.42 2.40 F FC 8 NONE0.0 360.0 0 100.00 176.98 176.98 47.42 2.40 P PHIC 9 NONE0.0 2029.2 0 100.00 248.94 248.94 47.42 2.40 F FC_ALL 10 NONE0.0 360.0 0 100.00 180.23 180.23 47.42 2.40 P PHIC_ALL 11 NONE0.0 2188.2 0 100.00 261.08 261.08 47.42 2.40 F FWT 12 NONE0.0 360.0 0 100.00 179.22 179.22 47.42 2.40 P PHWT 13 NONE0.0 1556.5 0 100.0055.5355.53 47.42 2.40 F DELFWT 14 NONE0.0 360.0 0 100.00 167.97 167.97 47.42 2.40 P PHDELWT 15 NONE 0.000 1.000 0 100.000.7440.744 47.42 2.40 W FOM 16 NONE0.1 2270.0 0 100.00 267.05 267.05 47.42 2.40 F FC_ALL_LS 17 NONE0.0 360.0 0 100.00 180.30 180.30 47.42 2.40 P PHIC_ALL_LS -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
Re: [ccp4bb] Large unit cell, overlaps
Hi Jason, don't really think that the overall scaling stats look very good. Even for such a long unit cell, we have plenty of in-house data (even with a smaller detector) with much lower Rmerge, typically below 0.15. Possibly monoclinic with beta close to 90deg? This might also explain the shifting distance you mention. Check the detailed output of the pointless log file, not only the last few lines. Check the section where Rmeas is reported for each symmetry element. If you have one or two axes sticking out a bit there, reduce symmetry. This table of pointless has shown to be most valuable in several cases. Good luck. Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com On Jul 16, 2012, at 8:28 PM, Jason Busby wrote: Hi, The autoindexing picks this unit cell pretty much unambiguously, and the profiles look reasonable. These are crystals of a very large heterodimer (2177 residues), and this unit cell would have 2 heterodimers and 56% solvent, which seems reasonable. Scaling and merging produce reasonable statistics (I used aimless, not XSCALE): Overall InnerShell OuterShell Low resolution limit 19.91 19.91 3.04 High resolution limit 2.99 16.38 2.99 Rmerge (within I+/I-) 0.339 0.040 0.907 Rmerge (all I+ and I-)0.348 0.045 0.949 Rmeas (within I+/I-) 0.360 0.042 0.994 Rmeas (all I+ I-)0.359 0.046 0.997 Rpim (within I+/I-)0.119 0.014 0.393 Rpim (all I+ I-) 0.085 0.012 0.291 Rmerge in top intensity bin0.053- - Total number of observations 1981569 5075 44784 Total number unique 112524 338 4559 Mean((I)/sd(I)) 10.6 53.4 2.6 Mn(I) half-set correlation CC(1/2) 0.993 0.999 0.527 Completeness98.8 43.7 82.1 Multiplicity17.6 15.0 9.8 Rmerge is high in the outer shell, but looks ok to me across the rest of the data. The oscillation angle is correct. The native data set also indexes with the same spacegroup and a slightly smaller unit cell (a=134 b=148 c=274), I attributed the difference to the Pt soak. The only ambiguity is one of the screw axes, so it may be P22121 or P212121. My XDS.INP has SPOT_RANGE commented out so I believe the default is to use all the data for indexing. Cheers, Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 17/07/2012, at 3:02 PM, Bosch, Juergen wrote: Hi Jason, if you look at the generated profiles in INTEGRATE.LP do they seem reasonable ? Does XSCALE.LP produce reasonable I/SigI statistics and expected Rvalues ? If not this might be another hint at wrong cell/spacegroup perhaps. You can try collecting spots from your whole data set with SPOT_RANGE= [start frame] [end frame] and then index the data. If you get too many strong spots you can select the top 5000 from SPOT.XDS. Is the oscillation correct in your script ? Jürgen P.S. we just collected some data on a 460Å cell On Jul 16, 2012, at 5:52 PM, Jason Busby wrote: Hi, I have a crystal with a large unit cell in P21221 (a=134 b=151 c=276) and I'm wondering if I have a problem with overlaps. I have a native dataset, and am trying to get phases. I've collected a Pt soak data set on our home source with a 0.5˚ oscillation angle, but the anomalous signal drops off after about 8Å. I am wondering if this is a problem due to overlaps at higher resolution. The Pt dataset has been integrated with XDS, and there don't seem to be too many rejects, but looking at FRAME.CBF it looks like the predicted spots are overlapping at higher resolution. You can see a zoomed-in part of FRAME.CBF here: http://imgur.com/1WShV Should I be concerned with this? The crystal mosaicity from XDS is 0.25, so fairly low. What can I do about this, should I try smaller oscillation angles? Thanks, Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department
Re: [ccp4bb] effective iodide conc. for SAD data
Hi Rajesh, it can be a bit all over the place: For quick soaks, we typically use 500mM-1000mM. A good starting point might be to simply replace the NaCl concentration in your protein buffer. By some serendipity we also managed to solve a structure by I/S SAD after a 1mM NaI soak. One iodide had found its way into a nice binding pocket. For co-crystallization, mostly 200mM should be fine. Another approach could be to supplement your cryo buffer with iodide, replacing NaCl. NaI is highly soluble in ethylene glycol. Also see here: http://www.ncbi.nlm.nih.gov/pubmed/21359836 Good luck! Cheers, Jan -- Jan Abendroth Emerald Bio Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com On May 3, 2012, at 6:51 AM, Rajesh Kumar wrote: Dear All, I have very thin crystals but diffracting. I was not able to handle them easily for iodide soak. I always lost the crystals during manipulation and other big crystals obtained after seeding doesn't even give any diffraction. I tried for co-crystallizing with NaI. The crystals appear only up to 20 mM in 1:2 (3ul drop of 1 ul protein and 2ul reservoir). Is this concentration of iodide is enough for SAD data ( if it had good incorporation) ? I appreciate your help. Thanks Rajesh
[ccp4bb] pdb_extact and refmac5.6
Hi all, we typically use pdb_extract to generate pdb files with a good header. There seems to be an issue with logfiles from refmac5.6.0117, distributed with the current ccp4 version, and pdb_extract. pdb_extract version-3.006 is distributed with ccp4-6.2.0. While reading the refmac log file, pdb_extract chokes with a segmentation fault. When run without reading in the refmac log file, the program complains about the following missing link, both in the linux and osx distribution of ccp4. Can not open file (/usr/local/ccp4/ccp4-6.2.0/ccp4-6.2.0//src/harvest_app_/pdb_extract/pdb-extract-data/mmcif_pdbx_2.items) in get_lines_from_file pdb_extract version-3.010, as downloaded form the rcsb webpage also chokes on the refmac5 logfile with a segmentation fault. Any ideas how to treat the new refmac log files in pdb_extract? Thanks a lot. Jan -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?
... strange, I have not seen any problems installing ARPwARP 7.1 on a new CCP6-6.2.0 install on - linux centos - os-x snow leopard, here I initially ran into write permissions issues and wound up changing the ownership of the /Applications/ccp4-6.2.0 directory Cheers Jan On Jul 27, 2011, at 9:00 PM, ccp4 wrote: A plea from West Australia too. I was sitting with someone yesterday who was trying to install it on a Mac , and finding it a nightmare. He finally got it set up as a local installation, whereupon it promtly failed. The message said See refmac-last.log but that told us nothing, and indeed refmac seemed to have worked.. Can someone - either CCP4 or arp-warp people check this out? Eleanor On Wed, 27 Jul 2011 20:35:50 -0700, Ethan Merritt merr...@u.washington.edu wrote: On Wednesday, 27 July 2011, you wrote: Hi Jonathan, seems to be a UW centered day today on the BB (Eric, Jan, you, me). Have the permissions changed ? I assume you are installing as root ? Wouldn't be surprised if Ethan replies soon :-) Sure. I hit the same problem trying to install Arp/wARP on Mandriva. The specific error message you quote comes because the install script fails to create the temp directory before trying to unpack into it. You can fix that by creating the directory by hand first. Unfortunately, that doesn't help very much. The next thing that happens is that the ccp4i installer complains that the tarball is not recognized as a ccp4i install tarball. I gave up at that point. Ethan Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 27, 2011, at 20:31, Jonathan Kay jp...@u.washington.edu wrote: Hi all, I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install went through fine, but when I went to install the ARP/wARP GUI (via System Administration - Install/uninstall task), I received the following error in the shell window I started ccp4i from: UnpackTaskArchive: uncompress failed to create /tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz /tmp is not at all full and has plenty of inodes left. (running the install.sh from the arp_warp_7.1 directory doesn't install it either) I have searched around for some solutions, but haven't found anything really relevant. The odd thing I have another x86_64 machine running RHEL 5 that I can do the exact same install method and it works (and using the install.sh from arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that might be causing problems? Anyone have any suggestions? Thanks! Jonathan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
Re: [ccp4bb] xds question: inverse beam, lots of wedges
Pat, at least give it a try with the one sweep approach. We have collected plenty of 360deg data sets on a Rigaku system which requires two omega sweeps at phi 0 and 180 deg. These data sets are for in-house phasing. We haven't seen big issues with running XDS over these images as one continuous sweep. Monitoring scalefactors might be a good indicator. Good luck Jan On Mar 31, 2011, at 3:08 PM, Patrick Loll wrote: We've just collected a number of inverse beam data sets. It turns out the crystals showed little radiation damage, so we have a lot of data: 2 x 360 deg for each crystal, broken up into 30 deg wedges. The collection order went like this: 0-30 deg, 180-210, 30-60, 210-240, etc. Now, assuming no slippage, I could simply integrate the first set of data (non-inverse?) in one run: 0-360 deg. However, since the 12 individual wedges making up this 360 deg sweep were not collected immediately one after the other, I don't expect the scale factors for individual images to vary smoothly (there should be discontinuities at the boundaries between wedges). If I do integrate the data in one fell swoop, am I in danger of introducing errors? For example, I seem to recall that denzo had built-in restraints to ensure that scale factors for adjacent images didn't vary by too much. Is there a similar restraint that in XDS that I might run afoul of? The alternative is to integrate each each wedge separately, but with 24 wedges per xtal, this is starting to look a little tedious. Cheers, Pat -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
[ccp4bb] mosflm in script mode
Hi all, I have been trying to use mosflm in script mode, in a quick-n-dirty effort to pipe some information from labelit.index into a simple data collection strategy. While doing that, I run into the following issue. I have not been able to find a way to read in image information without starting the old gui. Is there a command in the current mosflm versions to run it in shell mode only? Below the script that I have been using. Any ideas? Thanks Jan --- ipmosflm summary integrate02.sum eof DIRECTORY ../images TEMPLATE image_###.img IMAGE 1 HKLOUT integration02.mtz GENFILE integration02.gen #detector-take defaults #UIS_PIXEL 0.102400 #UIS_SIZE 3072 NUSPOT OFF BEAM 155.400500 158.807700 DISTANCE 299.775600 TWOTHETA 0.0 WAVE 0.977400 #beam SYNCHROTRON POLARIZATION 0.9 DIVERGENCE 0.100 0.020 DISPERSION 0.0001 MOSAICITY 0.60 SYMMETRY p2 RESOLUTION 3.5 MATRIX integration02.mat PROFILE OVERLOAD PARTIALS RASTER 19 19 9 4 4 SEPARATION 1.80 1.80 CLOSE REFINEMENT RESID 7.5 REFINEMENT INCLUDE PARTIALS RESID 10.0 #High s/n scanner adsc strategy auto stats on go end exit eof -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
[ccp4bb] refmac5 and spericity restraints
Hi there, I am refining a 1.3AA structure for SSGCID using -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
[ccp4bb] refmac5 and sphericity restraints, 2nd attempt
Hi there, apologies for the previous email, hit the send button too early. Hope everyone could stand the suspense for the continuation of the story ;-) Here we go: I am refining a 1.3AA structure for SSGCID using refmac5.5.102 or 109, OSX. A typical grey zone case for anisotropic refinement, yet it improves Rfactors by some 2%. A few B factors go a bit wild though: MAKE_U_POSITIVE. Therefore, I try to restrain the sphericity using the SPHER keyword. Even though the logfile acknowledges the keyword, the refinements with spher=2 and spher=5 are identical. Is this keyword still active? Cheers Jan On Mon, Feb 8, 2010 at 6:29 AM, Jan Abendroth jan.abendr...@gmail.comwrote: Hi there, I am refining a 1.3AA structure for SSGCID using -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
Re: [ccp4bb] Arp/wArp error
Hi all, I ran into that several times in the monoclinic space groups. ARP/wARP does not seem to like the C121 notation, yet likes the C2 notation. Same for P121 vs. P2. Re-assigning the SG eg. in CAD using the correct notation or the SG number is an easy remedy. Cheers Jan On Tue, Dec 1, 2009 at 8:57 AM, Eleanor Dodson c...@ysbl.york.ac.uk wrote: One easy suggestion - try buccaneer and refinement! Eleanor The Arp/warp people will have to fix this.. Anita Lewit-Bentley wrote: Dear all, I have a nice MAD map produced by Sharp and would like to trace a chain into it using Arp/wArp. When I input the mtz file via the CCP4i interface, I get the following message: Cannot extract ARP/wARP asymmetric unit limits The job will fail if run Well it DOES fail when run! My space group is C2 (given as C121 in the mtz file header), the mtz file is a standard structure factor file generated by CAD (adding Sharp phases to native data which are at a higher resolutino than the MAD data) and I just don't see what is going wrong. I am using CCP4 6.1.2 and Arp 7.0.1, with the CCP4Interface version 2.0.5 running on Mac OSX version 10.5.8. Any advice will be extremely welcome! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr -- -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA http://www.emeraldbiostructures.com work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] sulfur sad phasing
Hi Matthias, S-SAD seems to require really strong diffraction, high symmetry, and high data redundancy. In the end, the S ano signal is pretty weak even at longer wavelength. While S-SAD might work, Iodide soaks might be a much more practical approach. Iodide has some 6 electrons at CuKa. ... has given us 2 structures for SSGCID during the past month... Cheers Jan On Nov 11, 2009, at 4:16 AM, Matthias Zebisch wrote: Dear bb! What is the optimal wavelength for Sulfur SAD phasing? Is it 1.9A or should one go below that to reduce absorption/damage. Also, would the same wavelength be appropriate to maximize anomalous scattering to position chlorides, calcium, sulfate in already phased structures? Thanks in advance, Matthias -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] xds and cell refinement in cI
Hi all, thanks a lot for numerous replies. Graeme's suggestion to integrate in triclinic and let CORRECT sort out the space group worked and yielded nice data with reasonable Rsyms, I/ sig etc. When I then, though, re-enter the cell parameters etc (cp GXPARM.XDS XPARM.XDS) and just run INTEGRATE and CORRECT, the cell parameters won't refine any further, they stay right at the value given by XPARM.XDS. As Kay suggested, no cell parameter refinement in cubic (cI)? Cheers Jan On Oct 8, 2009, at 12:28 AM, Graeme Winter wrote: Hi Jan, Always worth a try is to process the data in P1 then assigning the symmetry in CORRECT - that way the cell constants can refine to what they want to. It also means you can check that the symmetry actually is cubic. For the majority of data sets in my experience it makes little difference whether you assign the lattice constraints during integration, unless they're wrong. Cheers, Graeme 2009/10/8 Jan Abendroth jan.abendr...@gmail.com: Hi all, I am running into a strange behaviour fo xds for a primitive cubic data set. Neither in the INTEGRATE nor in the CORRECT step the cell parameters are refined and stay exactly at the value specified in XDS.INP. R- factors and I/sigmas of the XSCALE run look suspiciously high/low. When I reduce the symmetry to tetragonal and run an otherwise identical XDS.INP script, the cell parameters are refined again. Any ideas? Thanks a bunch Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com
[ccp4bb] LINKR in refmac
Hi all, I am hitting the wall on this one: A disordered loop has been replaced with a short linker, which now is visible in the density. To be consistent, I maintain the original residue numbering and get a gap of residue numbers between the last original residue and the first residue of the loop. Refmac thinks that these residues are not supposed to be linked, and pulls them apart. How can I tell refmac to maintain the peptide link? Here is what I tried - the numbers above just for orientation 1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 LINKRC ASN B 729 N GLY B 741 ASN-GLY refmac comments in the log file ... however, still pulls the residues apart. WARNING : description of link:ASN-GLY is not in the dictionary link will be created with bond_lenth = 1.260 So, in my understanding it comes down to the question: how is a peptide bond referenced to in the dictionary? Any ideas are welcome! Thanks! Jan -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
[ccp4bb] LINKR in refmac
Hi all, I am hitting the wall on this one: A disordered loop has been replaced with a short linker, which now is visible in the density. To be consistent, I maintain the original residue numbering and get a gap of residue numbers between the last original residue and the first residue of the loop. Refmac thinks that these residues are not supposed to be linked, and pulls them apart. How can I tell refmac to maintain the peptide link? Here is what I tried - the numbers above just for orientation 1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 LINKRC ASN B 729 N GLY B 741 ASN-GLY refmac comments in the log file ... however, still pulls the residues apart. WARNING : description of link:ASN-GLY is not in the dictionary link will be created with bond_lenth = 1.260 So, in my understanding it comes down to the question: how is a peptide bond referenced to in the dictionary? Any ideas are welcome! Thanks! Jan -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] ccp4i problem - bad marshal data
Hi Charles and all, thanks a lot. That did the trick for ccp4i. There still are some marshal-related issues around. a) ccp4i after each job I get a message like this: CreateAnnotatedLogfile: failed for /../7_refmac5.log: Traceback (most recent call last): File /usr/local/ccp4-6.1.1/ccp4-6.1.1/share/smartie/baubles.py, line 18, in ? import smartie ValueError: bad marshal data b) xia2: [u...@sbl-emerald xia]# xia2 ../images/203289a7_a0001.img Traceback (most recent call last): File /usr/local/xia2/xia2-0.3.0.0/xia2-0.3.0.0//Applications/xia2.py, line 27, in ? from Handlers.Streams import Chatter ValueError: bad marshal data *ccp4* provides /usr/local/ccp4-6.1.1/Python-2.4.5/bin/python *centos5.3* runs python-2.4.3-24 Any ideas what happens there? Cheers Jan On Wed, Jun 3, 2009 at 3:31 AM, Ballard, CC (Charles) charles.ball...@stfc.ac.uk wrote: Hi Jan can you delete all .pyc files from $CCP4/share/dbccp4i and try to launch again. marshal is concerned with python object serialization, in particular pyc files, which may not be compatible across versions. What version of python is the machine using, and has it been updated recently. Charles Ballard CCP4 -- *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Jan Abendroth *Sent:* 02 June 2009 22:56 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] ccp4i problem - bad marshal data Hi all, we a one weird problem with one of our machines. Upon launching ccp4i, we get an error message in the shell window: [us...@pahto ~]$ ccp4i bad marshal data Then, once the interface finally starts after quite a while a new window opens with the following message. None of the previous projects are visible any more. CCP4i is currently configured to use the database server dbccp4i to access the job database, but has failed to either start or connect to the server this time. You can continue to use CCP4i and the interface should still operate normally, although some advanced functions may not be available. Next time you start CCP4i it will try again to use the database server. If you wish to disable this behaviour then select the option to automatically disable use of the server in future sessions. Any ideas how to get out of this? Thanks Jan -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com -- Scanned by iCritical. -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
[ccp4bb] ccp4i problem - bad marshal data
Hi all, we a one weird problem with one of our machines. Upon launching ccp4i, we get an error message in the shell window: [us...@pahto ~]$ ccp4i bad marshal data Then, once the interface finally starts after quite a while a new window opens with the following message. None of the previous projects are visible any more. CCP4i is currently configured to use the database server dbccp4i to access the job database, but has failed to either start or connect to the server this time. You can continue to use CCP4i and the interface should still operate normally, although some advanced functions may not be available. Next time you start CCP4i it will try again to use the database server. If you wish to disable this behaviour then select the option to automatically disable use of the server in future sessions. Any ideas how to get out of this? Thanks Jan -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
[ccp4bb] ccp4i problem - bad marshal data
Hi all, we a one weird problem with one of our machines. Upon launching ccp4i, we get an error message in the shell window: [us...@pahto ~]$ ccp4i bad marshal data Then, once the interface finally starts after quite a while a new window opens with the following message. None of the previous projects are visible any more. CCP4i is currently configured to use the database server dbccp4i to access the job database, but has failed to either start or connect to the server this time. You can continue to use CCP4i and the interface should still operate normally, although some advanced functions may not be available. Next time you start CCP4i it will try again to use the database server. If you wish to disable this behaviour then select the option to automatically disable use of the server in future sessions. Any ideas how to get out of this? Thanks Jan -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
[ccp4bb] nad woes
Hi all, is there any wisdom on NAD out there? I experience some strange behaviour of this common cofactor. With moderately convincing density, probably low occupancy of a cofactor that came along for the ride from E coli, Refmac5.5.0088 pulls the AN6 atom out of the adenine plane. With my own library that puts planar restraints on the adenine ring this seems to be fixed. Coot during real space refinement or regularisation using either the standard or my own dictionary handles the purine ring just fine, however, totally garbles up the nicotineamide. Btw, I use the * nomenclature. Cheers Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] ccp4i / refmac issue
Hi all,
yes, re-running jobs was the issue. So, creating a new job did the
trick.
Thanks for all the various feedback!
Jan
On Mar 6, 2009, at 12:43 AM, Paul Fyfe wrote:
Hi Jan,
I had exactly the same problem. It happens (for me) when you try and
re-run a job created for a previous version of refmac. All you need
to do is create a new Refmac job and it should work.
Cheers,
Paul
Dr Paul K. Fyfe
Division of Biological Chemistry and Drug Discovery
College of Life Sciences
MSI/WTB Complex
University of Dundee
Dow Street
Dundee DD1 5EH
Jan Abendroth jan.abendr...@gmail.com 03/06/09 6:40 AM
Hi all,
I keep on getting the following error message when I try to start a
refmac job through ccp4i with ccp4 version 6.1.1. This initially only
happened in a linux installation, now all of a sudden appeared in a
osx installation as well. The interface hangs when starting the job.
It also occurs for files that refined w/o any problems before. Any
ideas what is going on here?
Thanks for any input.
Jan
~~~
Top level CCP4 directory is /usr/local/ccp4-6.1.1
Using CCP4 programs from /usr/local/ccp4-6.1.1/bin
can't set ATOM(0): variable isn't array
while executing
set [subst $root]([subst $indx0])
(procedure ExecuteScript line 50)
invoked from within
ExecuteScript $system(SCRIPT)
(script arm line 8)
invoked from within
switch $system(RUN_MODE) \
script {
source [file join $env(CCP4I_TOP) src execute.tcl]
source [file join $env(CCP4I_TOP) src job_utils...
(file /usr/local/ccp4-6.1.1/share/ccp4i/bin/ccp4ish.tcl line
145)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4ish.tcl]
(file /usr/local/bin/ccp4ish line 12)
--
Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island WA, USA
work: JAbendroth_at_decode.is
home: Jan.Abendroth_at_gmail.com
The University of Dundee is a registered Scottish charity, No:
SC015096
--
Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island WA, USA
work: JAbendroth_at_decode.is
home: Jan.Abendroth_at_gmail.com
[ccp4bb] unit cell flags in mtz files and refmac
Hi all, I am trying to follow good practices and keep my set of free reflections between data sets, eg. in this case between an in-house low resolution and a synchrotron high resolution data set. High resolution data from hkl2000 were imported through the ccp4i task, keeping the low resolution FreeRs. This mtz file contains both unit cells, see below. The refined data set contains only one unit cell description, unfortunately the one from the FreeR (refmac5.5.72 and refmac5.5.70). As the two unit cells are sufficiently different, coot displays the model towards the edge of the density, real space refinement pulls the model back in the middle, refmac then starts with really high Rs and pulls the model back out. When using rather ancient refmac5.2.0019, the mtz file has the correct unit cell description. Btw. both refinements look about the same. The only difference is a rather annoying shift of the electron density that is displayed in coot based on different unit cell in the mtz file. Is there a way to tell refmac which of the two unit cells to put in the output mtz file? Intuitively, it should be the one from which the amplitudes originate? Cheers Jan *mtz file after import* 1 myprotein high_reso synchrotron 79.0610 79.0610 311.7950 90. 90. 90. 1.0 2 myprotein low_resol rotating_anode 78.5860 78.5860 311.1900 90. 90. 90. 1.54180 *refmac5.5.0072* 2 myprotein low_reso rotating_anode 78.5860 78.5860 311.1900 90. 90. 90. 1.54180 *refmac5.2.0019:* 1 myprotein high_reso synchrotron 79.0610 79.0610 311.7950 90. 90. 90. 1.0 -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] unit cell flags in mtz files and refmac
Thanks a lot, Garib, as always, there is a new version of refmac just out that fixes all the problems. Cheers Jan 2009/2/26 Garib Murshudov ga...@ysbl.york.ac.uk I think we have fixed this problem just recently. The problem was related with refmac not being able to pick correct dataset from mtz. IF there was one dataset in mtz then there was no problem Please have a look: www.ysbl.york.ac.uk/refmac/latest_refmac.html Garib On 26 Feb 2009, at 21:52, Jan Abendroth wrote: Hi all, I am trying to follow good practices and keep my set of free reflections between data sets, eg. in this case between an in-house low resolution and a synchrotron high resolution data set. High resolution data from hkl2000 were imported through the ccp4i task, keeping the low resolution FreeRs. This mtz file contains both unit cells, see below. The refined data set contains only one unit cell description, unfortunately the one from the FreeR (refmac5.5.72 and refmac5.5.70). As the two unit cells are sufficiently different, coot displays the model towards the edge of the density, real space refinement pulls the model back in the middle, refmac then starts with really high Rs and pulls the model back out. When using rather ancient refmac5.2.0019, the mtz file has the correct unit cell description. Btw. both refinements look about the same. The only difference is a rather annoying shift of the electron density that is displayed in coot based on different unit cell in the mtz file. Is there a way to tell refmac which of the two unit cells to put in the output mtz file? Intuitively, it should be the one from which the amplitudes originate? Cheers Jan *mtz file after import* 1 myprotein high_reso synchrotron 79.0610 79.0610 311.7950 90. 90. 90. 1.0 2 myprotein low_resol rotating_anode 78.5860 78.5860 311.1900 90. 90. 90. 1.54180 *refmac5.5.0072* 2 myprotein low_reso rotating_anode 78.5860 78.5860 311.1900 90. 90. 90. 1.54180 *refmac5.2.0019:* 1 myprotein high_reso synchrotron 79.0610 79.0610 311.7950 90. 90. 90. 1.0 -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] refmac 5.5.063 vs. 5.5.066
Thanks a lot, Pavol, that indeed did the trick. refmacRwork Rfree RMSDb RMSDan 5.5.0063 0.1682 0.2118 0.0204 1.717 5.5.0066 0.1781 0.2247 0.0205 1.764 5.5.0070 0.1663 0.2102 0.0204 1.719 Cheers Jan On Dec 19, 2008, at 2:21 AM, Pavol Skubak wrote: Hi Jan, the difference between 5.5.0063 and 5.5.0066 is just a few bugfixes. However, unfortunately one of them introduced a new bug to 5.5.0066 which has been fixed in the later versions. Could you please upgrade to the latest version (currently 5.5.0070) from http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_stable/ That should fix the problem (please let us know if it does not) Pavol. -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] iMosflm 1.0.0
Hi Luke, the new imosflm is really wonderful with its easy access to mosflm, its plenty graphic diagnostics and the quick pointless/scala access. A couple of questions that came up using it during data collection: - Is there any imosflm-specific documentation? - Is there a possibility to read in a parameter file? During data collection it is very convenient with good ol' mosflm to have a parameter file in which one only has to change eg. dcb16-5 to dcb16-6 and everything else is set up, rather than clicking through the file tree to find the images. Also, some beamlines notoriously have a slightly off beam centre in the file header which can be addressed with such a parameter file, or the default gain might be off a bit... - Is there a simple way to add images? Eg. when one has fired up imosflm 10 images have been collected, if I then want to refine cell parameters with two wedges 90 deg apart and want to integrate the full data set. At this point it seems that I can only add one image at a time. Thanks a lot for any pointers Cheers Jan On Nov 13, 2008, at 9:18 AM, Luke Kontogiannis wrote: Dear all, When we released iMosflm 1.0.0 on 17th October 2008, I accidentally uploaded a zip archive with an old version of the imosflm source code for Windows. If you downloaded the iMosflm for Windows zip archive between 17 October and 13 November 2008, you are running iMosflm 1.0.0 gc (gold candidate). You can see which version you are running by clicking on the Help menu and selecting About iMosflm In iMosflm 1.0.0 gc the QuickSymm and QuickScale buttons do not work properly and the mtz files are placed in the mosdir directory in the imosflm root directory If you download imosflm.zip from 13 November 2008 onwards, you will be running iMosflm 1.0.0, 13th November 2008. The output mtz files will be saved in the mosdir directory under your home folder e.g C:/Documents and Settings/Luke Kontogiannis/mosdir and the instructions on the Windows section of the imosflm website on how to get Baubles to work should get you up and running. Unix/Linux/Mac OS X users are unaffected. Thanks to the CCP4 team for pointing this out and apologies to all Windows users. Luke http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] xds and Saturn troubles
Hi all, thanks a lot for all the replies! Using the very current version of XDS fixed all the problems, really nice data, structure solved, yet another one for SSGCID. re input file: attached the XDS.INP file that worked for the Saturn 944+ detector. Thanks again! Jan 2008/9/4 Jan Abendroth [EMAIL PROTECTED] Hi all, a bit off-topic, but maybe someone knows an answer. I am trying to run xds on data collected on our new sparkling Saturn detector. Using the basic xds script that worked beautifully for older Saturn94 detectors, xds now dies with the following error message during the INIT phase: !!! ERROR !!! ILLEGAL RAXIS_COMPRESSION_RATIO Any ideas what this might be? Thanks a lot Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com Saturn2_XDS.INP Description: Binary data
[ccp4bb] xds and Saturn troubles
Hi all, a bit off-topic, but maybe someone knows an answer. I am trying to run xds on data collected on our new sparkling Saturn detector. Using the basic xds script that worked beautifully for older Saturn94 detectors, xds now dies with the following error message during the INIT phase: !!! ERROR !!! ILLEGAL RAXIS_COMPRESSION_RATIO Any ideas what this might be? Thanks a lot Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com
[ccp4bb] refmac, twin - really low Rfactors
Hi all, kind of a weird problem - the R-factors of a refinement using the new twin refinement in refmac are low, almost suspiciously low: A good 1.9AA data set, space group H3/R3, many statistics starting with truncate's cumulative intensity distribution clearly suggest twinning. The structure (SSGCID target) was solved by MR, very rigid beta-helix (see 3bxy, very cool fold!), maps nice. I use refmac 5.5.0046 for refinement, with and without the new TWIN flag. Here my concerns: Despite 0.3/0.7 twin domains as suggested by various programs and refined by refmac, the difference of between the Rs of the twinned refinement and the non-twinned refinement are constantly rather little: 0.143/0.174 for the twinned case, 0.218/0.275 for the non- twinned case. This seems rather low to me for a quite high twin fraction. Plus the R-factors for the twinned case are really low for a 1.9AA structure. As expected, the maps from the twin treatment are a bit nicer that for the non-twinned treatment. Any reasons for concerns or just a very rigid structure that refines really well or refmac handling twinning really nicely? Thanks for any input Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com
Re: [ccp4bb] Change reflection file names
try the unix tool mmv. jan On Aug 7, 2008, at 1:40 AM, yanming Zhang wrote: All UNIX gurus, I need to change 300 image file names sequentially, such as: XXX_10001.img to XXX_101.img XXX_10002.img to XXX_102.img Obviously, using UNIX 'mv' to work on 300 files is stupid. Anyone can give me a very simple UNIX shell file to finish the job quickly? Thank you! Yanming -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com
[ccp4bb] sketcher and nitrogen in rings
Hi experts, whenever create a ligand description with the sketcher that contains a saturated ring with nitrogens (piperidine, piperazine, etc) it flattens the nitrogens a la sp2 and consequently does weird things to the ring puckering. One can artificially protonate the nitrogen to get a sp3 geometry or fiddle around with the cif file. Is there a proper way to make it right in the first place? Thanks Jan
[ccp4bb] monomer library sketcher troubles
Hi all, our library sketcher all of a sudden started acting up after working just fine. - read in or draw a structure works fine, - Create library description - a message pops up: Error running Libcheck program see /tmp/jabendroth/7547_tmp Sorry - this means we can not list the monomers in the currently selected library - this file is shown below - if the warning message is dismissed, all the fields in the create library window are populated, hit run Error: can't read monomer_lib(typelist): no such variable - the same happens on various computers and for different users Any ideas? Thanks a lot! Jan tmp file # --- LIBCHECK --- /Vers 4.1.3 ; 19.12.2002/ Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /N/Y/A : N - means without DOC-file Y - with new contents A - means to keep old contents and add new information with DOC-file program creates batch file: libcheck.bat _DOC: # # Keywords: # #FILE_L: - additional library, means without this file #MON: - give info about this monomer # if = * , give list all monomers in the library #FILE_PDB:- input PDB_file , means without this file #FILE_SMILE:- input SMILE_file , means without this fil e # use keyword MON as compound_id #FILE_CIF:- input CIFile, means without this file #FILE_CSD:- input CSD CIFile, means without this file #HFLAG: Y/A/N - Y - hydrogen atoms where they are # A - with all hydrogen atoms # N - without hydrogen atoms #IND:N/Y - Y - create index of mon_lib.cif # output file: new_mon_lib_ind.cif #FILE_O: libcheck - output files /library,coords,ps/, name without # extention #FILE_L2: - additional library (FILE_L) will be added to this library # in this case program performs only adding #ANGLE: 0.0 - rotation angle for picture ( around X ) #LIST: M/S/L - S short output, L - long, M - medium #REF: Y/S,N,0 - 0 no refinement of new monomer # N only crd-ang and ang-crd # S plus torsion ref, Y plus restr.ref # #TEST: 0- for program testing only #COOR: N/Y- use Vobs from coords instead Videal #LCOOR: Y/N - Y use coords from lib description #NODIST: N/Y - Y not read the distributed library # (only with FILE_L) #SRCH: N/Y/0 - Y - global search, 0 - for MON from PDB_file # (only with NODIST = N) #--- type keyword parameters and/or --- #--- press key CR to run program --- -- -- MON : * - - Keywords: HFLAG : Y COOR : N LCOOR : Y SRCH : N REF : Y NODIST: N -- --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 4.12 _lib_update 20/09/07 -- NUMBER OF MONOMERS IN THE LIBRARY : 2436 with complete description: 454 NUMBER OF MODIFICATIONS:47 NUMBER OF LINKS:64 ERROR: in LIB_CREATE_INDEX2: not memory enough: BFONT COLOR=#FF!--SUMMARY_BEGIN-- CCP4: Fatal error, see above. /pre /html !--SUMMARY_END--/FONT/B
Re: [ccp4bb] Finding NCS operator from one heavy atom site?
Hi Partha, ncs6d did really great things to me a while ago. Similar case as yours, only one Met site in each of the 4 monomers, pretty horrible maps. I was amazed how ncs6d could sort its way through the maps and find the ncs operators. As a simple approach I just took a spherical map around the methionine site. In fact it seemed to be easier to find the ncs between two dimers first, improve the operators with imp and then search for the missing operators within the dimer. Sorry, don't have any clever scripts for that, did it all by hand. The maps improve a lot after averaging. However, almost needles to say that cloning, expressing, purifying, crystallizing and solving the same construct of an 85% seq. identical ortholog took less effort than messing around with the bad maps... Good luck Jan 2008/5/22 Partha Chakrabarti [EMAIL PROTECTED]: Hi, Apologies for a non CCP4 question in strict sense. I am trying to work out the NCS operators for a three wavelength Se-MAD data which has only one site. The map is hardly interpretable. I came across the USF Rave package and what I am aiming is creak a mask around the heavy atom site (found by SHELX or Solve) using mama or so, (ideally from resolve.mtz but not necessarily), translate it to the other heavy atom site(s), give a 6d search with NCS6d and perhaps refine the best CC a bit with imp. If it works, I could try use the NCS operator in DM or Resolve etc. I was wondering if someone has a C-shell scripts for dealing with such situation already. Of course if there are other programs for such a task within CCP4, could give it a try. Best Regards, Partha
[ccp4bb] ccp4mg and speed
Hi all, ... tried on the ccp4mg bb before ... ccp4mg is such a nice program, yet it is so slow in my hands. An average sized map calculated from a mtz file takes about 30s to display, while coot displays both 2FoFc and FoFc maps in about 5s. Is there anything I can do to speed things up? I use: - ccp4mg-1.1.1-Linux-Fedora-Core - coot-Linux-i386-fedora-6 - python2.4 - Fedora Core release 6 Thanks a lot for any hints. Jan
Re: [ccp4bb] Tough Low-Res MR
Hi all, just to second previous statements: Phaser has done wonders for me in a few tough cases, also at low resolution: Eg. various 6-10AA data sets with highly homologous search models. Or a rather bad search model: 1.8AA rmsd over ~50% of the residues. Often up to a point where the solution was correct, however model bias did not allow to get further. Sometimes it turned out to be helpful to increase the numbers of rotation solutions that are considered for the translation search. Cheers Jan ## deCODE biostructures Bainbridge Island 2008/2/21, Roger Rowlett [EMAIL PROTECTED]: James Stroud wrote: Hello All, 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? James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com Phaser and EPMR (now Open-EPMR) are among the best, and EPMR may actually work better in some cases without high resolution data. We've solved some really tough nuts to crack with both of these, and they are pretty fast to boot. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
[ccp4bb] ciftr troubles - now with logfile
... meant to include this logfile in my previous post: -Jan /sw/xtal/ciftr/ciftr-v2.053-prod-bin-darwin/bin/CIFTr -i output.cif Translating a mmCIF file [1] output.cif to PDB file output.cif.pdb Warning skipping item _computing.pdbx_density_modification is NOT in dictionary. Warning skipping item _data_extraction.software is NOT in dictionary. Warning skipping item _data_extraction.extraction_date is NOT in dictionary. Warning skipping item _data_extraction.version is NOT in dictionary. Warning skipping item _data_extraction.release_date is NOT in dictionary. Warning skipping item _data_extraction.location is NOT in dictionary. Warning skipping item _diffrn_detector.ndb_collection_date is NOT in dictionary. Warning skipping item _diffrn_radiation.rcsb_diffrn_protocol is NOT in dictionary. Warning skipping item _diffrn_source.rcsb_wavelength_list is NOT in dictionary. Warning skipping item _exptl_crystal.pdbx_mosaicity is NOT in dictionary. Warning skipping item _reflns.pdbx_number_measured_all is NOT in dictionary. Warning skipping item _reflns.pdbx_rmeas_mean is NOT in dictionary. Warning skipping item _reflns.pdbx_resolution_low_scale is NOT in dictionary. Warning skipping item _reflns.pdbx_resolution_high_scale is NOT in dictionary. Warning skipping item _reflns.pdbx_average_i_obs is NOT in dictionary. Warning skipping item _reflns.pdbx_average_sigmai_obs is NOT in dictionary. Warning skipping item _reflns_shell.pdbx_rejects is NOT in dictionary. Warning skipping item _reflns_shell.pdbx_rmeas_mean is NOT in dictionary. Warning skipping item _reflns_shell.pdbx_meani_over_sd is NOT in dictionary. Warning skipping item _reflns_shell.pdbx_number_centric is NOT in dictionary. Warning skipping item _reflns_shell.pdbx_number_anomalous is NOT in dictionary. Warning skipping item _reflns_shell.pdbx_rmerge_i_anomalous is NOT in dictionary. Warning skipping item _reflns_shell.pdbx_meani_over_sigi_anomalous is NOT in dictionary. Warning skipping item _reflns_shell.pdbx_pcv_mean is NOT in dictionary. Warning skipping item _struct.ndb_details is NOT in dictionary.
[ccp4bb] ciftr troubles
Hi all, has anyone sorted out how to get ciftr running? pdb_extract nicely bundles the information from the pdb header and additional information from the supplementary file (data_template.text, for instance) and writes it into the a cif file. CIFTr, however, does not re-translate lots of information into the header of a pdb file: such as completeness, RMSDs, sequence, ie. both information that has been in the header from the refmac pdb file and information from the supplementary file. Both linux and osx binaries, and the osx compilation behave this way. The compilation under linux dies during obj/regcomp.o. Could be a very handy tool! Any help how to get it running would be greatly appreciated. Thanks Jan
[ccp4bb] tricky molecular replacement III
Hi all, thanks to several tremendously helpful replies I got the molecular replacement, which I bugged the ccp4bb with during the last weeks, under control. Thanks for all the input, I'll send out a summary soon. One question remains, though: With an improved search model, the molecular replacement in Phaser got much stronger. This time, the correct rotation solution was on top of the list, and translation Z-scores were 10. ARP/wARP could not build into these maps, even after cross crystal averaging. In the end, no utter surprise given the low homology of the search model with my protein of interest. Molrep also succeeded with this model . After the standard sequence rotation/translation/rigid body, Molrep reported R-factors of 31% and 41% for data up to 4AA or 3AA, respectively. However, when I used the Molrep output for a rigid body refinement in Refmac, R-factors were at 55% for 4AA data. This huge gap of R-factors from Molrep and Refmac is really puzzling to me. Any ideas? Cheers Jan
Re: [ccp4bb] tricky molecular replacement
Hi all, thanks a lot for the various responses. When I tried to use a map as the serach model, I ran into various problems: again, the starting point is a weak, yet convincing molecular replacement solution in the hexagonal crystal form (1mol/asu) and no MR solution in P1 (2mol/asu, 2-fold in SRF). a) using phaser and defining the search model though DM map of the MR solution in the hexagonal form: Phaser stops as two space groups were used, p1 for the data set and P6... for the map b) - fft to create map after MR and DM of hexagonal form (map in P6..., asu) - mapmask to cover MR solution (in P6..., asu) - mapcutting using map and mask from prev steps (P6.., asu) - sfall to generate FC, phiC in large P1 cell: fatal disagreement between input info and map header c) same steps as in (b), however, using P6... and full unit cell - mapcutting: maprot dies with ccpmapin - Mask section lsec: recompile d) same steps as in (b), however, using P1 throughout - sfall dies with: Fatal disagreement between input info and map header e) same steps as in (c), however, using P1 and full unit cell - should not be different from case (d) - mapcutting: maprot dies with ccpmapin - Mask section lsec: recompile Any ideas? I btw. use the osx binaries from the ccp4 webpage. Thanks for any input! Cheers Jan On 11/2/07, Edward A. Berry [EMAIL PROTECTED] wrote: One other idea idea: 1. Solvent flattening on the hexagonal crystal 2. use the flattening mask to cut out the density of one molecule, put in a large P1 cell for calculating structure factors 3. Use the structure factors from the density of the hexagonal crystal to solve the triclinic crystal by molecular replacement. 4. If 3 works, multicrystal averaging to improve both crystals til the map is traceable. Jan Abendroth wrote: Hi all, I have a tricky molecular replacement case. One protein in two different crystal forms: hexagonal with 1 mol/asu, triclinic with 2 mol/asu (based on packing and self rotation). No experimental phases are available this far, however, there is a distant homology model. For the hexagonal crystals, phaser gives a solution with really good scores (Z 9, -LLG 50) and a good packing. While the correct solution is way down the list in the RF, the TF can separate it from the bulk of bad solutions. Slight changes in the model give the same solution. Maps are somehow ok, however, not good enough to enable arpwarp to build the model. It does not totally blow up either. For the triclinic crystal form with 2 molecules related by a two-fold which is not parallel to a crystal axis, phaser does not find a solution. Neither does molrep using the locked rotation function with the two-fold extracted by the SRF. As the homology between the data set should be higher than between the model in the data sets and the search model, I tried a cross rotation function between the two data sets. Strong peaks there should give the relation between the orientation of the molecule in the hexagonal crystal (that I believe I can find). With two rotations known and one translation undefined, I'd be left with only one translation that needs to be found. Then averaging within P1 or cross crystal might improve the density... Almn appears to be the only program in ccp4 that can do a cross rotation using Fs only, right?? I used the P1 data as hklin, the hexagonal data as hklin2. Almn comes back with two strong peaks (see below), however, now I am lost: - the first two peaks appear to be the same - are the Euler angles the ones I could use in a peak list for eg. Phaser? - does this procedure make sense at all? - any other ideas? Thanks a lot Jan almn.log: ## Peaks must be greater than 2.00 times RMS density 52.2161 Eulerian angles Polar angles Alpha Beta Gamma Peak OmegaPhi Kappa Direction cosines PkNo Symm: 1 2 Peak 1 1 1 1 323.7 143.4 18.5 540.892.9 62.6 143.80.4594 0.8867 -0.0511 1 1 2 323.7 143.4 78.5 540.883.2 32.6 145.90.8364 0.5351 0.1184 1 1 3 323.7 143.4 138.5 540.875.62.6 157.20.9674 0.0441 0.2495 1 1 4 323.7 143.4 198.5 540.871.9 332.6 174.40.8439 -0.4373 0.3108 1 1 5 323.7 143.4 258.5 540.8 107.2 122.6 167.0 -0.5149 0.8049 -0.2950 1 1 6 323.7 143.4 318.5 540.8 101.7 92.6 151.7 -0.0446 0.9781 -0.2034 1 1 7 143.7 36.6 41.5 540.8 161.7 321.1 175.00.2448 -0.1974 -0.9493 1 1 8 143.7 36.6 341.5 540.820.4 171.1 128.2 -0.3451 0.0540 0.9370 1 1 9 143.7 36.6
[ccp4bb] phaser and rotation function solutions
Hi all, in a rather weak molecular replacement the rotation solution that eventually produces a decent translation search (Z9 with a couple of clashes) is way down in the list of rotation function peaks. Sometimes this solution is included in the translation function, in similar runs it is not. Selecting the final selection criteria for peaks, number of peaks = 50 does not appear to change anything. When I do a separate rotation search with: final rot select number 50 save rot select number 50 I only get 6 peaks (down to Z = 3.33) when I run the fast rotation function, however, 50 peaks when I chose the brute rotation function. Any ideas? Thanks Jan
Re: [ccp4bb] mosflm and APS BM17
Hi all, thanks a lot for all the responses! As anticipated, the solution is rather simple - the origin of the beam: denzo refines to: x=82.6 y=80.3 mosflm reads from header: x=80.0 y=84.0 - bad indexing etc mosflm works with: x=82.6 y=80.3 No swapping of x and y between denzo and mosflm in this case. Cheers Jan On 8/22/07, Harry Powell [EMAIL PROTECTED] wrote: Hi I'd guess from the input file that the beam centre may be defined in a different reference frame to that which Mosflm expects in the image header; other possibilities are that the distance, wavelength, or something else (!) is wrong. Indexing is critically dependent on having the beam centre, distance and wavelength all being pretty close to the true values, though some indexing routines allow more latitude than others. My understanding (IMWBW) is that other programs (such as XDS or HKL2000) don't use the information in the image headers, and expect the parameters to be supplied by the user. With Mosflm, we try to make the user's life easier by trusting this information, especially from images collected at synchrotron beamlines; sometimes this trust is not warranted, and the user has to intervene! processing data collected on APS beamline BM17 on a MAR165 detector causes unexpected troubles. Even though the crystals are well-diffracting and the spots are sharp and well-resolved, indexing only works with a certain selection of frames, the refinement the goes totally hairwire. Probalby just a parameter or so set wrong. My input file in the attachment. The last three lines do not make much of a difference. Any ideas? Thanks! Cheers Jan mosflm.in: detector marccd directory ../Images template Image_0###.img image 001 nullpix 1 separation 0.95 0.95 close !LIMITS XMIN 0 XMAX 165 YMIN 0 YMAX 165 xscan 2048 yscan 2048 !SIZE 2048 2048 !PIXEL 0.07934 Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
[ccp4bb] xds, saturn94 and 2theta
Hi xds-experts, I am struggling to get xds running for Rigaku's Saturn94 detector with 2theta offset. Without 2theta offset, the Saturn92 input file from the xds webpage works just fine with the following modifications: NX=2084 NY=2084 QX=0.0451 QY=0.0451 ! modified by JA ORGX= 1024 ORGY= 1024!Detector origin (pixels). ORGX=NX/2; ORGY=NY/2 For a 2theta offset I additionally modified the following parameters: DIRECTION_OF_DETECTOR_X-AXIS=-0.9848 0.0 -0.1736 ! -cos2theta 0 sin2theta ORGX= 795 ORGY= 1070!measured in VIEW Here the question, as the indexing according to IDXREF.LP does not pick up a good solution. Sometimes it is close, eg. for solutions with a rather good score two axes ok, one off by several Å, sometimes all cell constants are just a little off (2-3Å for a 50/50/90 Å cell). - is the direction of the detector X-axis defined correctly (I also tried -cos2theta 0 -sin2theta) - how does one define the origin of the detector? a) approximate values for the center of the beam from VIEW (using 2084, 2084, 2, 0, l or b) b) the refined beam center values from eg. mosflm, translated into pixels? - any other parameters that need to be changed? - I also tried to use only a few or plenty of images for indexing. I know there are other programs for processing data, however, there are good reasons why I'd like to get this data set integrated with xds. Any ideas would be greatly appreciated! Cheers Jan -- Jan Abendroth University of Washington Institute of Biochemistry 1959 NE Pacific Street, K-426 Box 357742 Seattle, WA-98195 phone: +1-206-616-4510 fax: +1-206-685-7002
[ccp4bb] MSGPP cocktails for fragment crystallography
posted on behalf of Christophe Verlinde, MSGPP, University of Washington, Seattle Replies only to him, please. MSGPP: The recipes for our cocktails for fragment crystallography designed to aid in drug design are now available. More info is at this URL: faculty.washington.edu/verlinde/ Christophe L.M.J. Verlinde, Ph.D. Associate Professor Department of Biochemistry Biomolecular Structure Center University of Washington Health Sciences Building K-428A 1959 NE Pacific St. Seattle, WA 98195-7742 Phone:(206)543-8865 - Fax:(206)685-7002 email: [EMAIL PROTECTED] URL: www.bmsc.washington.edu/people/verlinde
[ccp4bb] scala and cell dimensions
Hi mosflm experts, last week's problem with mosflm solved, another one appearing. Scala fails with the error message below. These are ~10AA data. Scala finishes in p422, however dies in p222... Any ideas? Cheers Jan ~ scala.log Run(s):1 * Wavelength and cell extracted from Batch headers, with rms variation: * Wavelength: 1.541800 Cell:125.750 126.277 158.322 90.00090.00090.000 * rms0.00 rms 0.000 0.000 0.000 0.000 0.000 0.000 ERROR: cell deviates too much from constraint Relative length error0.000 Angle error 0.00 Cell constraints: Scala: *** Error in batch cell dimensions *** -- Jan Abendroth University of Washington Institute of Biochemistry 1959 NE Pacific Street, K-426 Box 357742 Seattle, WA-98195 phone: +1-206-616-4510 fax: +1-206-685-7002
Re: [ccp4bb] scala and cell dimensions
Thanks a lot, Graeme, using scala from ccp4 6.0.1 indeed did the trick (osx binaries). The data were processed with mosflm in fact. Cheers Jan Winter, G (Graeme) wrote: Hi Jan, This data is from XDS I'm guessing. Try Scala from CCP4 6.0.1 - this is a problem only with 602 I think. Cheers, Graeme -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jan Abendroth Sent: 29 May 2007 19:11 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] scala and cell dimensions Hi mosflm experts, last week's problem with mosflm solved, another one appearing. Scala fails with the error message below. These are ~10AA data. Scala finishes in p422, however dies in p222... Any ideas? Cheers Jan ~ scala.log Run(s):1 * Wavelength and cell extracted from Batch headers, with rms variation: * Wavelength: 1.541800 Cell:125.750 126.277 158.322 90.00090.00090.000 * rms0.00 rms 0.000 0.000 0.000 0.000 0.000 0.000 ERROR: cell deviates too much from constraint Relative length error0.000 Angle error 0.00 Cell constraints: Scala: *** Error in batch cell dimensions *** -- Jan Abendroth University of Washington Institute of Biochemistry 1959 NE Pacific Street, K-426 Box 357742 Seattle, WA-98195 phone: +1-206-616-4510 fax: +1-206-685-7002 -- Jan Abendroth University of Washington Institute of Biochemistry 1959 NE Pacific Street, K-426 Box 357742 Seattle, WA-98195 phone: +1-206-616-4510 fax: +1-206-685-7002
[ccp4bb] mosflm getbox error
Mosflm experts, mosflm dies on me with the error message below. Granted, it is really crappy data I am working with... Cannot find the getbox command in the documentation. Which would be appropriate values for xlines etc at low double digit resolution? Any ideas? Cheers Jan ... mosflm.lp ... Refinement cycle 2 Repeating refinement using the same list of 25 reflections 25 Spots to be measured IX,IY,NPBOX,NXX,NYY,NX,NY 6131555 5 0 0 3 3 ERROR, NON VALID BOX IN GETBOX If PROFILES XLINES, YLINES have been supplied then make sure the values are appropriate for the resolution limit being used. If they are, consult Andrew Leslie An unrecoverable error has occurred in GETBOX at mark 5; performing a clean shutdown of Mosflm -- Jan Abendroth University of Washington Institute of Biochemistry 1959 NE Pacific Street, K-426 Box 357742 Seattle, WA-98195 phone: +1-206-616-4510 fax: +1-206-685-7002
Re: [ccp4bb] Bio-rad DuoFlow
Hi all, joining this discussion late, however, it might worth mentioning that Amersham/GE has phased out the good old FPLC and is no longer providing neither service nor spare parts. Best to my knowledge the same will happen to the Äkta-FPLC system soon leaving the Explorer and Purifier their only systems, at least on the US market. -Jan Frank Lee wrote: Dear all, Thanks a lot for all the feedbacks on AKTA prime. They are so helpful that I have abandoned the idea of buying one. Now it is a choice between AKTA FPLC and Bio-rad DuoFlow. I heard that DuoFlow is not as robust as AKTA and that its parts break down often. The question is whether quality difference is worth price difference (~$10K). Any feebacks on DuoFlow would be highly appreciated! Best, Frank Food fight? http://answers.yahoo.com/dir/index;_ylc=X3oDMTFvbGNhMGE3BF9TAzM5NjU0NTEwOARfcwMzOTY1NDUxMDMEc2VjA21haWxfdGFnbGluZQRzbGsDbWFpbF90YWcx?link=asksid=396545367 Enjoy some healthy debate in the Yahoo! Answers Food Drink QA. http://answers.yahoo.com/dir/index;_ylc=X3oDMTFvbGNhMGE3BF9TAzM5NjU0NTEwOARfcwMzOTY1NDUxMDMEc2VjA21haWxfdGFnbGluZQRzbGsDbWFpbF90YWcx?link=asksid=396545367 -- Jan Abendroth University of Washington Institute of Biochemistry 1959 NE Pacific Street, K-426 Box 357742 Seattle, WA-98195 phone: +1-206-616-4510 fax: +1-206-685-7002
