Re: [ccp4bb] does 12 A diffraction worth optimization

Hi Natalia, One rule of thumb in crystallography: anything is possible! We have seen many cases of individual proteins (or their complexes with small molecules, proteins or nucleic acids) where we ended up with structures starting from low resolution initial crystals. So before taking a

[ccp4bb] does 12 A diffraction worth optimization

Hello, I got crystals of protein-nucleic acid complex, rod-shape, reproducible, don’t visibly get damaged upon freezing; however they gave diffraction only to about 12 A. I tried several crystals. My question is whether such crystals worth optimization. Clearly a 4A diffracting crystal could

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

I misstated something earlier, and I would like to correct the record: Magic Eye books instruct you on using wall-eyed stereo (with excellent instructions, highly recommended!). Currently (with computer monitors) I find cross-eyed much easier (and I think more people should try it). Thanks, Nat

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

Hi Nat, could you be referring to side-by-side stereo in this (computer monitor) use case? http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node97.html W. On Fri, Mar 2, 2018 at 2:41 PM, nathanielclar5 . wrote: > To learn how to cross eyes, just hold you index fingers

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

To learn how to cross eyes, just hold you index fingers strait up, ~12-18 inches from your eyes, and cross your eyes until the two fingers overlap to form a third finger in the middle. Then practice holding your eyes there. You can also practice with ceiling tiles, floor tiles, anything that

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

You already have stereo built in, just turn on 'cross eyed stereo' and learn to cross your eyes! It's brighter than any 3d monitor, requires no hardware, and no, it won't hurt your eyes (even for hours at a time) Nat On Fri, Mar 2, 2018 at 11:01 AM, Jim Fairman

Re: [ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

Daniel, To best of my knowledge, options for 3d stereo on Mac are limited to Zalman: https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Zalman_Stereo If you're willing to go to Linux or Windows, you can do an Nvidia Quadro Card with a 120 or 144Hz monitor with a 3D Vision glasses kit.

[ccp4bb] 3-D Coot Capable Computer Monitor/Glasses for Mac Laptop?

I'm looking for some computer hardware advice. I have a MacBook Pro with a "Retina" screen and an Intel HD Graphics 4000 1536 MB graphics card, running OS X 10.11.16 ("El Capitan"), and I would like to view structures in 3-D in Coot. Which computer monitors and which 3-D glasses brands would

[ccp4bb] Positions in membrane protein structural biology

Hi all, We have two positions available at the Structural Genomics Consortium (SGC) in Oxford, a post-doc and a technician position, to work with Liz Carpenter's group on human integral membrane protein structural biology. The post-doc position will involve running and optimizing our pipeline

Re: [ccp4bb] phenix refinement about cis-proline

Dear Niegel, May be Shijun had to cancel his registration to the PhenixBB as I had to do since 2015 due to "too many bounces" whatever the email address I used, professional, yahoo or gmail ?... Has this been fixed at some point ? All the best,Philippe  Philippe BENAS, Ph.D. Laboratoire de

Re: [ccp4bb] Protein-Protein Interaction prediction

Hi Sayli -  PrePPI may be helpful if you're interested in interactions among human proteins. http://honig.c2b2.columbia.edu/preppi/ Cheers, Jared

Re: [ccp4bb] validating a homlology model

Dear Careina, Your message is a bit confusing... Which kind of validation are you referring to? Do you want to check the geometrical quality of the backbone and side-chain rotamers, or do you want to evaluate how likely it is that the fold proposed by homology actually represents the fold of

Re: [ccp4bb] validating a homlology model

Hi Careina, This is a little confusing. A homology model *is* a set of coordinates (usually provided as a PDB file by most servers/packages I know of). The MolProbity site at http://molprobity.biochem.duke.edu/ allows you to upload your own PDB file, and in my experience is quite forgiving

Re: [ccp4bb] Protein-Protein Interaction prediction

Dear Sayli, I have used cluspro in past: https://cluspro.bu.edu/publications.php Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S. The ClusPro web server for protein-protein docking. *Nature Protocols.*2017 Feb;12(2):255-278 Best, Dipak On Fri, Mar 2, 2018 at

[ccp4bb] AW: [ccp4bb] validating a homlology model

Dear Careina, If you do not have coordinates, what do you have then? A sequence alignment? In that case you can look at the %identity and %homology to see how well the known structure fits the unknown structure. If you do have coordinates in some other format generated by some modeling

Re: [ccp4bb] validating a homlology model

On 02/03/2018 11:44, Careina Edgooms wrote: What programs are best used for validate homology models? I know of molprobity but if there are no coordinates I cannot use it. Is there a way to use such programs with homology models? Also I wish to use pdbepisa for to charaterise dimer

[ccp4bb] validating a homlology model

Dear all What programs are best used for validate homology models? I know of molprobity but if there are no coordinates I cannot use it. Is there a way to use such programs with homology models? Also I wish to use pdbepisa for to charaterise dimer interface but again for homology model this

Re: [ccp4bb] Protein-Protein Interaction prediction

Dear Sayli Here are some options from Table 10.1 of this book chapter https://link.springer.com/chapter/10.1007/978-94-024-1069-3_10 cons-PPISP Uses sequence profiles and solvent accessibility for residues and their neighbours http://pipe.scs.fsu.edu/ppisp.html