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Re: [ccp4bb] Chain ID number limit!

Thanks this must be a fix. I tried once but the loading file within the window did not give an option of .ciff (only for restraints). I will try again. On 07/24/2017 05:24 PM, Pavel Afonine wrote: Hi Lijun, it's not a problem if you use mmCIF or PDB with two-letter chain ID (both

Re: [ccp4bb] Chain ID number limit!

Hi Lijun, it's not a problem if you use mmCIF or PDB with two-letter chain ID (both supported in Phenix). Pavel On Mon, Jul 24, 2017 at 5:09 PM, Lijun Liu wrote: > Hi: this must be an old problem but I would like to know if there are > other ideas to make things easier.

[ccp4bb] Chain ID number limit!

Hi: this must be an old problem but I would like to know if there are other ideas to make things easier. I solved a structure that contains 240 helices of identical sequences in the asymmetric unit. Handling so many chains is really a headache as pdb contains only a single column for chain

Re: [ccp4bb] Buccaneer places residues in different asymmetric units

Here's a new(er) trick with Coot: Centre on an atom in a symmetry-related molecule where you want your model chain to be Extensions -> Modelling -> Symm Shift Reference Chain Here. Paul. On 25/07/2017 00:05, Diana Tomchick wrote: Or use Coot to generate the symmetry mates, then write out

Re: [ccp4bb] Buccaneer places residues in different asymmetric units

Or use Coot to generate the symmetry mates, then write out the symmetry-related coordinates. Many ways to achieve the same outcome, Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern

Re: [ccp4bb] 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

[ccp4bb] 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

Re: [ccp4bb] 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

[ccp4bb] 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

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

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 Best, DKG - Original Message - From: "Jacob Keller"

Re: [ccp4bb] 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

Re: [ccp4bb] Buccaneer places residues in different asymmetric units

Or use PISA to position bits sensibly.. Eleanor On 24 July 2017 at 10:35, Jon Agirre 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

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

Re: [ccp4bb] Primer design

Have to do primer walking in a cdna library first. Artem On Jul 24, 2017 7:26 AM, "syed ibrahim" < 048c02cac012-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

[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

[ccp4bb] 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