Re: [ccp4bb] Density around PEG

2017-12-13 Thread Prem Prakash
What is your occupancy of PEG here ?,you should also look at it. Best Prem On Thu, Dec 14, 2017 at 6:37 AM, sanjeev kumar wrote: > Thanks, I'll check it out. > > On Wed, Dec 13, 2017 at 8:06 PM Anthony Addlagatta < > anthonyaddlaga...@gmail.com> wrote: > >> This could be

Re: [ccp4bb] coordinate transformation

2017-12-13 Thread Paul Emsley
On 13/12/2017 13:50, Kajander, Tommi A wrote: Hello, If someone could point this out would be very helpful... Wasnt there a simple script somewhere that would transfer coordinates close to origin - if they for some reason are not? Just cant find anything right away. At the risk of not

Re: [ccp4bb] Density around PEG

2017-12-13 Thread sanjeev kumar
Thanks, I'll check it out. On Wed, Dec 13, 2017 at 8:06 PM Anthony Addlagatta < anthonyaddlaga...@gmail.com> wrote: > This could be 2-mercaptoethanol. > > Anthony > > On Wed, Dec 13, 2017 at 11:24 PM, sanjeev kumar > wrote: > >> Hi all, >> Can someone suggest what could

Re: [ccp4bb] Overlapping ligand electron density

2017-12-13 Thread Diana Tomchick
Matt, Modeling two molecules that occupy overlapping binding sites in a structure simply involves designating them as alternate conformers, with the same chain and residue number, and an occupancy that sums to 1.0. For example, if you have an AMP and an ADP that occupy the same binding site,

Re: [ccp4bb] Overlapping ligand electron density

2017-12-13 Thread Bernhard Rupp
Only two comments: a. At that resolution, constrained group occupancy refinement should work reasonably well (provided you can model the 2 entities). Then you also do not have clashes between the molecules, because Occ(A)+Occ(B)=1, meaning when one (A) is there, the other one (B) is

Re: [ccp4bb] Overlapping ligand electron density

2017-12-13 Thread Pearce, N.M. (Nick)
It’s definitely possible to have a superposition of states: https://www.ncbi.nlm.nih.gov/m/pubmed/28291761/ You need to use alternate conformers to generate the different states of the crystal. Thanks, Nick On 13 Dec 2017, at 20:12, Matthew Bratkowski

[ccp4bb] Overlapping ligand electron density

2017-12-13 Thread Matthew Bratkowski
Hello all, I am working on a ligand binds near the active site of the protein, such that part of the ligand would clash with part of the natural substrate. I recently co-crystallized the enzyme with both molecules and solved the crystal structure to high resolution (around 1.4 angstrom).

Re: [ccp4bb] coordinate transformation

2017-12-13 Thread Bartosz Sekula
Hi Tommy, Try ACHESYM, it is very useful: http://achesym.ibch.poznan.pl/ Here is the link to the publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257622/ Good luck, Bartosz

Re: [ccp4bb] coordinate transformation

2017-12-13 Thread Keller, Jacob
Wouldn't the PISA server do something like this? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kajander, Tommi A Sent: Wednesday, December 13, 2017 8:50 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] coordinate transformation Hello, If someone could point this out

[ccp4bb] coordinate transformation

2017-12-13 Thread Kajander, Tommi A
Hello, If someone could point this out would be very helpful... Wasnt there a simple script somewhere that would transfer coordinates close to origin - if they for some reason are not? Just cant find anything right away. Sure i have done this before... Thanks, Tommi

Re: [ccp4bb] PyMol question

2017-12-13 Thread Johannes Cramer
you can try the 'hide cell' command. This should hide the unit cell box, however, I don't know why it is not displayed in your 'unrendered' gui... Cheers, Johannes 2017-12-11 23:47 GMT+01:00 Cygler, Miroslaw : > Hi, > When I loaded the ed map into PyMol v1.8.4.1 and