[ccp4bb] modified amino acids

I am looking for a list of all modified amino acids found in protein structures (in PDB). Three letter codes and geometry files will be wonderful. Thanks Debasish

Re: [ccp4bb] New PDB validation reports

Glad you brought it up Katherine. Debasish From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Katherine Sippel Sent: Thursday, July 10, 2014 2:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] New PDB validation reports Hi all, I've been playing with the new PDB validation

Re: [ccp4bb] PDB passes 100,000 structure milestone

I think for questionable structures and those representing retracted paper, PDB should be able to ask the depositors for raw data and leave it for the community to decide if they still want to use the structure for science. If the depositors can't or would not submit the data, it should be

[ccp4bb] Recovering crystals from dry drops

Would you please share your experience and comments on recovering protein crystals from dry (or almost dry hanging drops) for data collection. I found some beautiful crystals in hanging drops that were set up three years ago; from the color of the crystals ( the protein binds a colored

[ccp4bb] skin on crystal

We crystallized a protein at 4 and 22 deg C in different conditions: from ammonium sulfate in acetate buffer pH 5 and PEG4000 in Hepes buffer at pH 7.5 In both cases the drops have a slimy skin (almost feels like DNA). We therefore think that the skin is generated from the protein. I am sure

[ccp4bb] PDB structure validation

I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file before deposition. It will save a lot time and perhaps would improve the quality of deposited structures. Debasish

Re: [ccp4bb] PDB structure validation

Molprobity doesn't analyze density fit. New PDB validation now reports density fit analysis etc. From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Thursday, October 31, 2013 10:28 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation yes

Re: [ccp4bb] PDB structure validation

: longingforadmiss...@gmail.com [mailto:longingforadmiss...@gmail.com] On Behalf Of Mahesh Lingaraju Sent: Thursday, October 31, 2013 10:32 AM To: Debasish Chattopadhyay Subject: Re: [ccp4bb] PDB structure validation Hi One can do an unofficial validation in Adit server ( one of the pdb deposition services

[ccp4bb] PDB validation

No complaints about PDB stuff, they are always helpful. Debasish University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934-0480

Re: [ccp4bb] PDB structure validation

for all the suggestions. Debasish From: Bosch, Juergen [mailto:jubo...@jhsph.edu] Sent: Thursday, October 31, 2013 10:48 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation You do use Coot and look at the density plots right ? Phenix

Re: [ccp4bb] PDB structure validation

Thanks Randy. That would be fantastic. From: Randy Read [mailto:rj...@cam.ac.uk] Sent: Thursday, October 31, 2013 11:02 AM To: Debasish Chattopadhyay Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB structure validation Yes, the intention at the PDB sites is to make available a standalone

Re: [ccp4bb] PDB structure validation

Thank you everybody for your inputs. Already four suggested the QC server. I think at this point we have enough ideas. Once again, thanks for your attention. Debasish From: Kumar, Abhinav [mailto:abhin...@slac.stanford.edu] Sent: Thursday, October 31, 2013 6:49 PM To: Debasish Chattopadhyay Cc

Re: [ccp4bb] OT: Who's Afraid of Peer Review?

My editorial suggestion: My suspicion is that many structural papers are not read beyond the author list and title, if at all should be corrected as follows: My suspicion is that many papers are not read beyond the author list and title, if at all. Debasish -Original Message- From:

[ccp4bb] Protein concentration for crystallization

What would be a convenient way to estimate what percentages of proteins have been crystallized in a concentration range, for example 5-30 mg? Debasish Chattopadhyay University of Alabama at Birmingham CBSE-250 1025 18th Street South, Birmingham, Al-35294 USA Ph: (205)934-0124; Fax: (205)934

Re: [ccp4bb] Protein concentration for crystallization

. Debasish From: Orru, Roberto [mailto:roberto.o...@emory.edu] Sent: Monday, June 10, 2013 5:04 PM To: Debasish Chattopadhyay Subject: RE: Protein concentration for crystallization Dear Debasish, On my memory there are 2 way (but I cannot say that are the only 2!) First: if you have the structure and you

Re: [ccp4bb] Negative FoFc around ligand

Kavya, Does your ligand contain any heavier atom (S, P or other)? Is it possible that your ligand binds in different orientations? So your atom X could actually be atom Y? Debasish -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kavyashree

[ccp4bb] pymol help?

I am trying to manually move a molecule (pdb) onto another molecule (pdb) in pymol. I opened molecules separately. When I use the middle button on my mouse both move together, as if one object. I will appreciate any help. Thanks Debasish

Re: [ccp4bb] Off-topic Thrombin cleavage

Thrombin works pretty good without any added calcium. We routinely added thrombin to whatever buffer the protein is in provided it doesn't have a lot of DTT. Some beta-mercaptoethanol is alright. What is the source of your thrombin? -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] zinc fingre

Yes, Rajesh, I completely agree with Pius. There is absolutely nothing wrong in asking a question on ccp4bb. The suggestion 'read a book and search on-line information sources' is a good one on any subject. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]

Re: [ccp4bb] zinc fingre

Read a book. If you can't find a book then ask the all knowing Google. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Tuesday, April 03, 2012 10:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] zinc fingre Dear All, I am trying to crystallize a

Re: [ccp4bb] Substitution to glycerol during crystallogenesis

We use ethylene glycol and glycerol mainly to reduce nucleation (or showering of crystals). However, we also found that these two additives may not be interchangeable, that is effects of these reagents were markedly different on crystallization behavior of a particular protein. Debasish

Re: [ccp4bb] Sad News, Defend our CCP4BB community

I wonder if it is time to restrict users who places these discussions on the board. If each of us spend even a minute on such a subject, it is such a huge waste of time. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenhua Zhang Sent:

Re: [ccp4bb] very strange lattice: high anisotropy, 78% solvent content and maybe merohedral twinning

How about plotting the solvent content along with resolution limits of the structures? From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel Afonine Sent: Wednesday, December 14, 2011 12:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very strange lattice: high

[ccp4bb] Posting

I would like to see the electron density map (2Fo-FC, Fo-Fc, omit map) for ligands on 2-fold symmetry in protein structure. If any of you can send some images I will appreciate it. Thanks Debasish Debasish Chattopadhyay, Ph.D. University of Alabama at Birmingham