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Yaoqi Professor Yaoqi Zhou | Research Leader Institute for Glycomics Griffith University | Gold Coast campus | QLD 4222 | Institute for Glycomics (G24) Room 2.10 T +61 7 5552 8228 | F +61 7 5552 9040 | email yaoqi.z...@griffith.edu.au <mailto:yaoqi.z...@griffith.edu.au> http://sparks-lab.org <http://sparks-lab.org/> (Group webpage) http://griffith.edu.au/institute-glycomics <http://griffith.edu.au/institute-glycomics> (Institute Webpage) > On 25 Jul 2017, at 9:01 AM, CCP4BB automatic digest system > <lists...@jiscmail.ac.uk> wrote: > > There are 14 messages totaling 9878 lines in this issue. > > Topics of the day: > > 1. Buccaneer places residues in different asymmetric units (3) > 2. Primer design (7) > 3. PhD position at University of Oslo > 4. Postdoctoral position at Boston Children’s Hospital > 5. About weighting factor settings in new ccp4i2 (2) > > ---------------------------------------------------------------------- > > Date: Mon, 24 Jul 2017 16:56:51 +0800 > From: Lingxiao Zeng <lxz...@connect.hku.hk> > Subject: Buccaneer places residues in different asymmetric units > > Dear All, > > I tried to use buccaneer to build a model. The starting model is a partial > model, after model building the Rwork and Rfree are reasonable but buccaneer > places residues in different asymmetric units and the model looks really > weird. > > Is there any way to build the model into the same ASU or put different parts > together after model building? Thanks! > > > > Best, > > Alice > > -- > Lingxiao Zeng > PhD candidate > School of Biomedical Sciences > The University of Hong Kong > > ------------------------------ > > Date: Mon, 24 Jul 2017 10:35:17 +0100 > From: Jon Agirre <jon.agi...@york.ac.uk> > Subject: Re: Buccaneer places residues in different asymmetric units > > Dear Alice, > > there's an option in both ccp4i and ccp4i2 interfaces that lets you tell > Buccaneer that you want to build the new model in the same place as the > partial model supplied - see my screenshots for reference. It might not be > on by default and perhaps it should be. > > Please be aware that most newer developments and improvements will be put > on the ccp4i2 interface to Buccaneer - it would be helpful if you could > have a go and let us know what you think! > > Hope this helps, > > Jon > > On 24 July 2017 at 09:56, Lingxiao Zeng <lxz...@connect.hku.hk> wrote: > >> Dear All, >> >> >> I tried to use buccaneer to build a model. The starting model is a partial >> model, after model building the Rwork and Rfree are reasonable but >> buccaneer places residues in different asymmetric units and the model looks >> really weird. >> >> >> Is there any way to build the model into the same ASU or put different >> parts together after model building? Thanks! >> >> >> >> >> Best, >> >> Alice >> >> -- >> Lingxiao Zeng >> PhD candidate >> School of Biomedical Sciences >> The University of Hong Kong >> >> > > > -- > Dr Jon Agirre > York Structural Biology Laboratory / Department of Chemistry > University of York, Heslington, YO10 5DD, York, England > http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ > Twitter: @alwaysonthejazz > +44 (0) 1904 32 8270 > > ------------------------------ > > Date: Mon, 24 Jul 2017 11:26:00 +0000 > From: syed ibrahim <b_syed_ibra...@yahoo.com> > Subject: Primer design > > Hello All > > I am interested in cloning a gene from a plant. I searched the database only > partial sequence is available, ie: for 160 residues only. The full length of > the protein is around 570 residues. I designed forward primer and I have no > clue to design reverse primer. > > Any help > > Thank you > > Syed > > ------------------------------ > > Date: Mon, 24 Jul 2017 07:41:15 -0400 > From: Artem Evdokimov <artem.evdoki...@gmail.com> > Subject: Re: Primer design > > Have to do primer walking in a cdna library first. > > Artem > > On Jul 24, 2017 7:26 AM, "syed ibrahim" < > 0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hello All > > I am interested in cloning a gene from a plant. I searched the database > only partial sequence is available, ie: for 160 residues only. The full > length of the protein is around 570 residues. I designed forward primer and > I have no clue to design reverse primer. > > Any help > > Thank you > > Syed > > ------------------------------ > > Date: Mon, 24 Jul 2017 17:12:39 +0530 > From: Debasish Kumar Ghosh <dkgh...@cdfd.org.in> > Subject: Re: Primer design > > Dear Syed, > > The process is very trivial to clone your gene of interest. Assuming your > gene is transcribed as mono-cistronic mRNA, take the oligodT primer as > reverse primer. First isolate the total RNA from the tissue or cells and do > the cDNA synthesis using oligodT primer followed by gene specific PCR with > forward primer and oligodT primer from the cDNA pool. Sequence the PCR > product to get to know the first stop codon in the ORF. Making the specific > reverse primer from the sequence is then just matter of time. > Hope this helps. > > Best wishes, > > Debasish > > CSIR- Senior Research Fellow (PhD Scholar) > C/o: Dr. Akash Ranjan > Computational and Functional Genomics Group > Centre for DNA Fingerprinting and Diagnostics > Hyderabad, INDIA > > Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com > Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) > Lab URL: > http://www.cdfd.org.in/labpages/computational_functional_genomics.html > > > > ----- Original Message ----- > From: "syed ibrahim" <0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> > To: CCP4BB@JISCMAIL.AC.UK > Sent: Monday, July 24, 2017 4:56:00 PM > Subject: [ccp4bb] Primer design > > Hello All > > I am interested in cloning a gene from a plant. I searched the database only > partial sequence is available, ie: for 160 residues only. The full length of > the protein is around 570 residues. I designed forward primer and I have no > clue to design reverse primer. > > Any help > > Thank you > > Syed > > ------------------------------ > > Date: Mon, 24 Jul 2017 13:22:03 +0100 > From: Eleanor Dodson <eleanor.dod...@york.ac.uk> > Subject: Re: Buccaneer places residues in different asymmetric units > > Or use PISA to position bits sensibly.. > Eleanor > > On 24 July 2017 at 10:35, Jon Agirre <jon.agi...@york.ac.uk> wrote: > >> Dear Alice, >> >> there's an option in both ccp4i and ccp4i2 interfaces that lets you tell >> Buccaneer that you want to build the new model in the same place as the >> partial model supplied - see my screenshots for reference. It might not be >> on by default and perhaps it should be. >> >> Please be aware that most newer developments and improvements will be put >> on the ccp4i2 interface to Buccaneer - it would be helpful if you could >> have a go and let us know what you think! >> >> Hope this helps, >> >> Jon >> >> On 24 July 2017 at 09:56, Lingxiao Zeng <lxz...@connect.hku.hk> wrote: >> >>> Dear All, >>> >>> >>> I tried to use buccaneer to build a model. The starting model is a >>> partial model, after model building the Rwork and Rfree are reasonable but >>> buccaneer places residues in different asymmetric units and the model looks >>> really weird. >>> >>> >>> Is there any way to build the model into the same ASU or put different >>> parts together after model building? Thanks! >>> >>> >>> >>> >>> Best, >>> >>> Alice >>> >>> -- >>> Lingxiao Zeng >>> PhD candidate >>> School of Biomedical Sciences >>> The University of Hong Kong >>> >>> >> >> >> -- >> Dr Jon Agirre >> York Structural Biology Laboratory / Department of Chemistry >> University of York, Heslington, YO10 5DD, York, England >> http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ >> Twitter: @alwaysonthejazz >> +44 (0) 1904 32 8270 >> > > ------------------------------ > > Date: Mon, 24 Jul 2017 13:18:25 +0000 > From: "Keller, Jacob" <kell...@janelia.hhmi.org> > Subject: Re: Primer design > > ....Or sequence the whole exome for what, $500-1000? > > JPK > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Debasish Kumar Ghosh > Sent: Monday, July 24, 2017 7:43 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Primer design > > Dear Syed, > > The process is very trivial to clone your gene of interest. Assuming your > gene is transcribed as mono-cistronic mRNA, take the oligodT primer as > reverse primer. First isolate the total RNA from the tissue or cells and do > the cDNA synthesis using oligodT primer followed by gene specific PCR with > forward primer and oligodT primer from the cDNA pool. Sequence the PCR > product to get to know the first stop codon in the ORF. Making the specific > reverse primer from the sequence is then just matter of time. > Hope this helps. > > Best wishes, > > Debasish > > CSIR- Senior Research Fellow (PhD Scholar) > C/o: Dr. Akash Ranjan > Computational and Functional Genomics Group Centre for DNA Fingerprinting and > Diagnostics Hyderabad, INDIA > > Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com > Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: > http://www.cdfd.org.in/labpages/computational_functional_genomics.html > > > > ----- Original Message ----- > From: "syed ibrahim" <0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> > To: CCP4BB@JISCMAIL.AC.UK > Sent: Monday, July 24, 2017 4:56:00 PM > Subject: [ccp4bb] Primer design > > Hello All > > I am interested in cloning a gene from a plant. I searched the database only > partial sequence is available, ie: for 160 residues only. The full length of > the protein is around 570 residues. I designed forward primer and I have no > clue to design reverse primer. > > Any help > > Thank you > > Syed > > ------------------------------ > > Date: Mon, 24 Jul 2017 19:02:19 +0530 > From: Debasish Kumar Ghosh <dkgh...@cdfd.org.in> > Subject: Re: Primer design > > No need of the whole exome. Sequencing The second PCR product will do the job > I guess. Second PCR (from the cDNA pool) with specific forward primer and and > oligodA reverse primer. Surely a matter of less than $3 > > Best, > > DKG > > > ----- Original Message ----- > From: "Jacob Keller" <kell...@janelia.hhmi.org> > To: "Debasish Kumar Ghosh" <dkgh...@cdfd.org.in>, CCP4BB@JISCMAIL.AC.UK > Sent: Monday, July 24, 2017 6:48:25 PM > Subject: RE: Primer design > > ....Or sequence the whole exome for what, $500-1000? > > JPK > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Debasish Kumar Ghosh > Sent: Monday, July 24, 2017 7:43 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Primer design > > Dear Syed, > > The process is very trivial to clone your gene of interest. Assuming your > gene is transcribed as mono-cistronic mRNA, take the oligodT primer as > reverse primer. First isolate the total RNA from the tissue or cells and do > the cDNA synthesis using oligodT primer followed by gene specific PCR with > forward primer and oligodA primer from the cDNA pool. Sequence the PCR > product to get to know the first stop codon in the ORF. Making the specific > reverse primer from the sequence is then just matter of time. > Hope this helps. > > Best wishes, > > Debasish > > CSIR- Senior Research Fellow (PhD Scholar) > C/o: Dr. Akash Ranjan > Computational and Functional Genomics Group Centre for DNA Fingerprinting and > Diagnostics Hyderabad, INDIA > > Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com > Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: > http://www.cdfd.org.in/labpages/computational_functional_genomics.html > > > > ----- Original Message ----- > From: "syed ibrahim" <0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> > To: CCP4BB@JISCMAIL.AC.UK > Sent: Monday, July 24, 2017 4:56:00 PM > Subject: [ccp4bb] Primer design > > Hello All > > I am interested in cloning a gene from a plant. I searched the database only > partial sequence is available, ie: for 160 residues only. The full length of > the protein is around 570 residues. I designed forward primer and I have no > clue to design reverse primer. > > Any help > > Thank you > > Syed > > ------------------------------ > > Date: Mon, 24 Jul 2017 15:33:29 +0000 > From: Kaare Bjerregaard-Andersen <kaare.bjerregaard-ander...@kjemi.uio.no> > Subject: PhD position at University of Oslo > > Dear all, a PhD student position is now available at the Department of > Chemistry, University of Oslo, Norway. Please find the announcement attached. > The project focuses on the implementation of neutron based methods in the > study of a surface-active bacterial colonization factor and is supervised by > Prof. Ute Krengel and Assoc. Prof. Reidar Lund. Application deadline is 1st > of september. > > > Link to the position: > > https://www.jobbnorge.no/ledige-stillinger/stilling/140728/phd-research-fellow-in-structural-biology-and-soft-matter-technologies? > > > best > > Kaare Bjerregaard-Andersen > > > > > -- > Kaare Bjerregaard-Andersen, M.Sc., Ph.D. > Post-doctoral researcher > Ute Krengel group > Department of Chemistry > University of Oslo > P.O.Box 1137 Blindern > 0318 Oslo, Norway > > phone +47 92553589 > email kaar...@kjemi.uio.no > > ------------------------------ > > Date: Mon, 24 Jul 2017 15:43:15 +0000 > From: "Keller, Jacob" <kell...@janelia.hhmi.org> > Subject: Re: Primer design > >> No need of the whole exome. Sequencing The second PCR product will do the >> job I guess. Second PCR (from the cDNA pool) with specific forward primer >> and and oligodA reverse primer. Surely a matter of less than $3 > > $3 is a major understimation, but I see your point. On the other hand, it is > important to consider new technologies, and it would be a service to the > scientific community to publish the exome somewhere, so other researchers > would not have to spend their $3. > > JPK > > > > > > Best, > > DKG > > > ----- Original Message ----- > From: "Jacob Keller" <kell...@janelia.hhmi.org> > To: "Debasish Kumar Ghosh" <dkgh...@cdfd.org.in>, CCP4BB@JISCMAIL.AC.UK > Sent: Monday, July 24, 2017 6:48:25 PM > Subject: RE: Primer design > > ....Or sequence the whole exome for what, $500-1000? > > JPK > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Debasish Kumar Ghosh > Sent: Monday, July 24, 2017 7:43 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Primer design > > Dear Syed, > > The process is very trivial to clone your gene of interest. Assuming your > gene is transcribed as mono-cistronic mRNA, take the oligodT primer as > reverse primer. First isolate the total RNA from the tissue or cells and do > the cDNA synthesis using oligodT primer followed by gene specific PCR with > forward primer and oligodA primer from the cDNA pool. Sequence the PCR > product to get to know the first stop codon in the ORF. Making the specific > reverse primer from the sequence is then just matter of time. > Hope this helps. > > Best wishes, > > Debasish > > CSIR- Senior Research Fellow (PhD Scholar) > C/o: Dr. Akash Ranjan > Computational and Functional Genomics Group Centre for DNA Fingerprinting and > Diagnostics Hyderabad, INDIA > > Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com > Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: > http://www.cdfd.org.in/labpages/computational_functional_genomics.html > > > > ----- Original Message ----- > From: "syed ibrahim" <0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> > To: CCP4BB@JISCMAIL.AC.UK > Sent: Monday, July 24, 2017 4:56:00 PM > Subject: [ccp4bb] Primer design > > Hello All > > I am interested in cloning a gene from a plant. I searched the database only > partial sequence is available, ie: for 160 residues only. The full length of > the protein is around 570 residues. I designed forward primer and I have no > clue to design reverse primer. > > Any help > > Thank you > > Syed > > ------------------------------ > > Date: Mon, 24 Jul 2017 13:27:12 -0400 > From: Bing Chen <bc...@crystal.harvard.edu> > Subject: Postdoctoral position at Boston Children’s Hospital > > A postdoctoral position is available immediately in Dr. Bing Chen’s > laboratory at Boston Children’s Hospital/Harvard Medical School. > > The ongoing projects include 1) biochemical and structural studies to > elucidate molecular mechanisms of how HIV-1 enters host cells, 2) design > and production of HIV-1 envelope-based immunogens, and 3) development of > antiviral therapeutics. > > For our recent publications, please see: > > Cai et al., Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):4477-4482. > (https://www.ncbi.nlm.nih.gov/pubmed/28396421 > <https://www.ncbi.nlm.nih.gov/pubmed/26113642>) > > Dev et al., Science. 2016 Jul 8;353(6295):172-5. > (https://www.ncbi.nlm.nih.gov/pubmed/27338706 > <https://www.ncbi.nlm.nih.gov/pubmed/27338706>) > > Chen et al., Science. 2015 Jul 10;349(6244):191-5. > (https://www.ncbi.nlm.nih.gov/pubmed/26113642 > <https://www.ncbi.nlm.nih.gov/pubmed/26113642>) > > A strong background in protein biochemistry and/or structural biology is > required. We are particularly interested in those who are highly > motivated and willing to tackle difficult problems. Applicants should > send a cover letter, CV, and contact information of three references to > Bing Chen (bc...@crystal.harvard.edu <mailto:bc...@crystal.harvard.edu>). > > ------------------------------ > > Date: Mon, 24 Jul 2017 20:44:45 +0000 > From: Tom Peat <tom.p...@csiro.au> > Subject: Re: Primer design > > A lot of plant genomes are big- wheat for example is 12 Gb, so it may not be > quite as trivial as one might expect. > cheers, tom > > Tom Peat > Proteins Group > Biomedical Program, CSIRO > 343 Royal Parade > Parkville, VIC, 3052 > +613 9662 7304 > +614 57 539 419 > tom.p...@csiro.au > > ________________________________________ > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Keller, Jacob > <kell...@janelia.hhmi.org> > Sent: Tuesday, July 25, 2017 1:43 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Primer design > >> No need of the whole exome. Sequencing The second PCR product will do the >> job I guess. Second PCR (from the cDNA pool) with specific forward primer >> and and oligodA reverse primer. Surely a matter of less than $3 > > $3 is a major understimation, but I see your point. On the other hand, it is > important to consider new technologies, and it would be a service to the > scientific community to publish the exome somewhere, so other researchers > would not have to spend their $3. > > JPK > > > > > > Best, > > DKG > > > ----- Original Message ----- > From: "Jacob Keller" <kell...@janelia.hhmi.org> > To: "Debasish Kumar Ghosh" <dkgh...@cdfd.org.in>, CCP4BB@JISCMAIL.AC.UK > Sent: Monday, July 24, 2017 6:48:25 PM > Subject: RE: Primer design > > ....Or sequence the whole exome for what, $500-1000? > > JPK > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Debasish Kumar Ghosh > Sent: Monday, July 24, 2017 7:43 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Primer design > > Dear Syed, > > The process is very trivial to clone your gene of interest. Assuming your > gene is transcribed as mono-cistronic mRNA, take the oligodT primer as > reverse primer. First isolate the total RNA from the tissue or cells and do > the cDNA synthesis using oligodT primer followed by gene specific PCR with > forward primer and oligodA primer from the cDNA pool. Sequence the PCR > product to get to know the first stop codon in the ORF. Making the specific > reverse primer from the sequence is then just matter of time. > Hope this helps. > > Best wishes, > > Debasish > > CSIR- Senior Research Fellow (PhD Scholar) > C/o: Dr. Akash Ranjan > Computational and Functional Genomics Group Centre for DNA Fingerprinting and > Diagnostics Hyderabad, INDIA > > Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com > Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: > http://www.cdfd.org.in/labpages/computational_functional_genomics.html > > > > ----- Original Message ----- > From: "syed ibrahim" <0000048c02cac012-dmarc-requ...@jiscmail.ac.uk> > To: CCP4BB@JISCMAIL.AC.UK > Sent: Monday, July 24, 2017 4:56:00 PM > Subject: [ccp4bb] Primer design > > Hello All > > I am interested in cloning a gene from a plant. I searched the database only > partial sequence is available, ie: for 160 residues only. The full length of > the protein is around 570 residues. I designed forward primer and I have no > clue to design reverse primer. > > Any help > > Thank you > > Syed > > > ------------------------------ > > Date: Mon, 24 Jul 2017 22:01:15 +0000 > From: "Liu, Xu" <xu....@emory.edu> > Subject: About weighting factor settings in new ccp4i2 > > Hi, > > In the new cpp4-7.0.042 (ccp4i2), where can I put in the weighting factor for > B factor restrain weight (the ‘WBSKAL' setting) and/or x-ray terms relative > to geometric restrains (the ‘MATRIX’ setting ) in refmac5? Basically I want > to plug in those weighting factors from pdbredo into REFMAC5 for a few more > refinement but cannot find in new ccp4. > > Thanks! > > ________________________________ > > This e-mail message (including any attachments) is for the sole use of > the intended recipient(s) and may contain confidential and privileged > information. If the reader of this message is not the intended > recipient, you are hereby notified that any dissemination, distribution > or copying of this message (including any attachments) is strictly > prohibited. > > If you have received this message in error, please contact > the sender by reply e-mail message and destroy all copies of the > original message (including attachments). > > ------------------------------ > > Date: Mon, 24 Jul 2017 23:41:57 +0100 > From: Jon Agirre <jon.agi...@york.ac.uk> > Subject: Re: About weighting factor settings in new ccp4i2 > > Dear Xu, > > you can input those keywords in the text box under 'Advanced options' in > the 'refinement' task. Just make sure you click somewhere else after you're > done putting the keywords in in order to have the text validated by the > interface. > > Best regards, > Jon > > On 24 July 2017 at 23:01, Liu, Xu <xu....@emory.edu> wrote: > >> Hi, >> >> In the new cpp4-7.0.042 (ccp4i2), where can I put in the weighting factor >> for B factor restrain weight (the ‘WBSKAL' setting) and/or x-ray terms >> relative to geometric restrains (the ‘MATRIX’ setting ) in refmac5? >> Basically I want to plug in those weighting factors from pdbredo into >> REFMAC5 for a few more refinement but cannot find in new ccp4. >> >> Thanks! >> >> ________________________________ >> >> This e-mail message (including any attachments) is for the sole use of >> the intended recipient(s) and may contain confidential and privileged >> information. If the reader of this message is not the intended >> recipient, you are hereby notified that any dissemination, distribution >> or copying of this message (including any attachments) is strictly >> prohibited. >> >> If you have received this message in error, please contact >> the sender by reply e-mail message and destroy all copies of the >> original message (including attachments). >> > > > > -- > Dr Jon Agirre > York Structural Biology Laboratory / Department of Chemistry > University of York, Heslington, YO10 5DD, York, England > http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ > Twitter: @alwaysonthejazz > +44 (0) 1904 32 8270 > > ------------------------------ > > End of CCP4BB Digest - 23 Jul 2017 to 24 Jul 2017 (#2017-205) > *************************************************************
