Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-03-19 Thread Oliver Smart
On Mon, 9 Jan 2012, Soisson, Stephen M wrote: I will second Ian's recommendation for GRADE from the Global Phasing group. GRADE overcomes nearly all of the shortcomings we have encountered with other approaches for ligand dictionary generation. Steve, Thanks to you and to Ian Tickle for t

Re: [ccp4bb] unusual bond lengths in PRODRG cif file (Grade Web Server)

2012-03-19 Thread Oliver Smart
On Tue, 10 Jan 2012, Stephen Graham wrote: On 10 January 2012 09:50, John Liebeschuetz wrote: "...available to anyone who has access to the Cambridge Structural Database System" How many academic labs will bother / can afford to buy a CCSD license just to check the geometry of small molecule l

Re: [ccp4bb] unusual bond lengths in PRODRG cif file (Another possibility - direct use of QM)

2012-01-11 Thread Oliver Smart
On Mon, 9 Jan 2012, krish wrote: You can use Phenix.elbow or phenix.reel to load the coordinates of the small moleucle and optimize with AM1 (semi-empirical), then you should get reasonable geometirc parameters suc as bond length, bond angles and etc.   Hope this helps !   Cheers, Kri

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-11 Thread dusan turk
Hi Guys, I just want to make aware that apart form PRODRG etc there exist also PURY server http://pury.ijs.si/, which offers a possibility to create restraints for heteromolecules. It accepts PDB files, smiles format. Alternatively JME editor can be used to draw your compound. PURY: a databa

Re: [ccp4bb] : Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-10 Thread Gerard Bricogne
Dear Stephen, The thought that using the CSD via Mogul for generating good refinement dictionaries in the first place was THE way to go, rather than relying on the PDB to use the same information later to try and catch errors at the time of deposition, has been the driving force in the develo

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-10 Thread Martyn Winn
33 > Cambridge CB2 1EZ, UK Website: > http://www.ccdc.cam.ac.uk > > > > > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen > Graham > Sent: 10 January 2012 10:23 > To: CCP4BB@JISC

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-10 Thread Colin Groom
ehalf Of Stephen Graham Sent: 10 January 2012 10:23 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] : Re: [ccp4bb] unusual bond lengths in PRODRG cif file "...available to anyone who has access to the Cambridge Structural Database System" How many academic labs will bother / can afford t

Re: [ccp4bb] : Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-10 Thread Stephen Graham
"...available to anyone who has access to the Cambridge Structural Database System" How many academic labs will bother / can afford to buy a CCSD license just to check the geometry of small molecule ligands, especially when they need to do so them only once every blue moon? The ability for the PD

[ccp4bb] : Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-10 Thread John Liebeschuetz
On 9 January 2012 06:13, Shveta Bisht wrote: > Dear all > > I have generated a refmac cif file for a molecule using PRODRG. I used > JME editor to draw the molecule and ran PRODRG online with the > options: Chirality-Yes, Charges-Reduced and EM-Yes. Please check the > attachments for the molecu

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-09 Thread Tom Peat
-Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Monday, 9 January 2012 11:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] unusual bond lengths in PRODRG cif file On 9 January 2012 06:13, Shveta Bisht wrote: > Dear all > &g

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-09 Thread Soisson, Stephen M
CP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Monday, January 09, 2012 7:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] unusual bond lengths in PRODRG cif file On 9 January 2012 06:13, Shveta Bisht wrote: > Dear all > > I have generated a refmac cif file for a molecule using PRODRG. I use

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-09 Thread Ian Tickle
On 9 January 2012 06:13, Shveta Bisht wrote: > Dear all > > I have generated a refmac cif file for a molecule using PRODRG. I used > JME editor to draw the molecule and ran PRODRG online with the > options: Chirality-Yes, Charges-Reduced and EM-Yes. Please check the > attachments for the molecule

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-09 Thread Eleanor Dodson
Thank you Shveta for NOTICING!!! Please - everyone - check your restraints - programs make mistakes - you (or the chemist who made the ligand) - are the experts Eleanor On 01/09/2012 10:05 AM, krish wrote: Dear Shveta, I have seen similar trends with PRODRG. I recommend you to use other

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-09 Thread Paul Emsley
On 09/01/12 06:13, Shveta Bisht wrote: I need advise on the way I have run prodrg and the explanations for the results. There is little room for manoeuvre when running prodrg. Prodrg is not the Font of All Ligand Wisdom. Prodrg makes mistakes. If you think that the bond lengths are wrong, ch

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-09 Thread krish
Dear Shveta, I have seen similar trends with PRODRG. I recommend you to use other molecular modeling programs like Hyperchem or Maestro to get more consistent geometric parameters for small molecules. Once you know the bondlengths and bond angles from aforesaid molecular modeling programs, you can