Re: [ccp4bb] pdb format problem of an intermolecular disulfide bond from different symmetric units

Dear Prof. Eleanor Dodson,    Thanks for your good suggestion. It works for my pdb.   Best,zhongzhou> you add something like 2555 to define the required symmetry operator on the ssbond line. - the exact format is described in the pdb convention. But I think refmac does it i think if you as i

Re: [ccp4bb] pdb format problem of an intermolecular disulfide bond from different symmetric units

you add something like 2555 to define the required symmetry operator on the ssbond line. - the exact format is described in the pdb convention. But I think refmac does it i think if you as it to make disulphides. Eleanor On 28 June 2015 at 09:33, Zhongzhou Chen wrote: > Hello, everyone， > > >

[ccp4bb] pdb format problem of an intermolecular disulfide bond from different symmetric units

Hello, everyone， Recently, we found an intermolecular disulfide bond from different symmetric units. I want to define it to refine, such as by refmac5.  I know the regular format of a disulfide bond in the same symmetric unit and show it as below. SSBOND   1 CYS A  115    CYS A  191 My question

Re: [ccp4bb] pdb format

Hi Raja You can use a command-line script like this one: #!/bin/tcsh sed -e "/ATOM/ s/'/*/g" -e "/ATOM/ s/O5T/O3T/" -e "/ATOM/ s/ADE/ DA/g" -e "/ATOM/ s/CYT/ DC/g" -e "/ATOM/ s/GUA/ DG/g" -e "/ATOM/ s/THY/ DT/g" <$1>refmacok_$1 cat refmacok_$1|grep ATOM|more>/dev/tty Save the script in a ne

[ccp4bb] pdb format

Hi, The out pdb file from 'CNS' or from 'O' is not readable in 'CCP4'. I have dna and protein in my pdb file. Do you the best way to convert the pdb file I got from 'CNS" or from 'O' into 'CCP4' format? Especially CCP4 follows 1 letter code for dna whereas CNS and O follow 3 letter code.

Re: [ccp4bb] PDB format survey?

Ralf W. Grosse-Kunstleve wrote: I.e. the first 9 serial numbers are represented as usual. The following atoms use a base-36 system (10 digits + 26 letters) with upper-case letters. 43670016 (26*36**4) additional atoms can be numbered this way. If there are more than 43770015 (9+43670016)

Re: [ccp4bb] PDB format survey?

J. Bernstein > > Sent: Friday, August 10, 2007 8:53 AM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] PDB format survey? > > > > Actually, everything proposed with break some software. > > The real question is one of how much value the community >

Re: [ccp4bb] PDB format survey?

Dear George, > I like your hybrid_ 36 scheme and will implement it and the two character > hain IDs PDB file columns 21 and 22, right justified) when I next update > HELXL. Of course I will need to do some programming because of the SHELX > zero dependency' philosophy, but it seems to me to be str

Re: [ccp4bb] PDB format survey?

Of Herbert J. Bernstein > Sent: Friday, August 10, 2007 8:53 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] PDB format survey? > > Actually, everything proposed with break some software. > The real question is one of how much value the community > gains from how much of

Re: [ccp4bb] PDB format survey?

uded as well -- widespread > > > adoption of that simple convention would represent a major > > practical > > > advance for interoperability in structure-based drug discovery. > > > > > > Cheers, > > > Warren > > > > > > >

Re: [ccp4bb] PDB format survey?

> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > > > Behalf Of Santarsiero, Bernard D. > > > Sent: Friday, August 10, 2007 8:17 AM > > > To: CCP4BB@JISCMAIL.AC.UK > > > Subject: [ccp4bb] PDB format survey? > > > > > > Can I ask a dumb

Re: [ccp4bb] PDB format survey?

August 10, 2007 8:17 AM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: [ccp4bb] PDB format survey? > > > > Can I ask a dumb question? Just curious... > > > > Why are we now limited to 80 "columns"? In the old days, that > > was a limit with Fortran and punche

Re: [ccp4bb] PDB format survey?

Friday, August 10, 2007 8:17 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] PDB format survey? > > Can I ask a dumb question? Just curious... > > Why are we now limited to 80 "columns"? In the old days, that > was a limit with Fortran and punched cards. Can a &quo

[ccp4bb] PDB format survey?

2,-1,0,1,2,3,4] -- just an idea :)... >> >> With valences plus formal charges along with expansion of the >> cap on atom counts, I think we could support >> chemically-complete PDB files and push back the date of PDB >> demise for a few more years! >> >>

Re: [ccp4bb] PDB format survey?

Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Warren DeLano > Sent: Thursday, August 09, 2007 5:53 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] PDB format survey? > > Joe, > > I feel that atom serial numbers are pa

Re: [ccp4bb] PDB format survey?

I support CCP4 adopting the hybrid36 and 2 char chain id extensions too. If no-one else steps up to do it, I'll try and patch mmdb to support it when I get time. Kevin George M. Sheldrick wrote: I like your hybrid_ 36 scheme and will implement it and the two character chain IDs PDB file colum

Re: [ccp4bb] PDB format survey?

Dear Ralf, I like your hybrid_ 36 scheme and will implement it and the two character chain IDs PDB file columns 21 and 22, right justified) when I next update SHELXL. Of course I will need to do some programming because of the SHELX 'zero dependency' philosophy, but it seems to me to be straigh

Re: [ccp4bb] PDB format survey?

superb idea -- of course, the goal should be to ultimately come up with a single well-defined standard set of hacks we all agree upon by supporting them in our code. Cheers, Warren -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Joe Krahn Sent: Thursday, Au

Re: [ccp4bb] PDB format survey?

Edward A. Berry wrote: Ethan A Merritt wrote: On Wednesday 08 August 2007 20:47, Ralf W. Grosse-Kunstleve wrote: Implementations to generate intuitive, maximally backward compatible numbers can be found here: http://cci.lbl.gov/hybrid_36/ From that URL: ATOM 8 SD MET L 48.

Re: [ccp4bb] PDB format survey?

Hi Ethan, > Is that "A" a hexidecimal number, or is it a decimal number > that just happens to have an "A" in front of it? > [A-Z][0-] gives a larger range of values than 5 bytes of hexadecimal, > so I'm guessing it's the former. But the example is not clear. > > (yes I could download and

Re: [ccp4bb] PDB format survey?

Ethan A Merritt wrote: On Wednesday 08 August 2007 20:47, Ralf W. Grosse-Kunstleve wrote: Implementations to generate intuitive, maximally backward compatible numbers can be found here: http://cci.lbl.gov/hybrid_36/ From that URL: ATOM 8 SD MET L 48.231 -64.383 -9.257 1.0

Re: [ccp4bb] PDB format survey?

On Wednesday 08 August 2007 20:47, Ralf W. Grosse-Kunstleve wrote: > > The solution to this problem is to simply treat the serial numbers and > residue numbers as strings. X-PLOR/CNS has been doing this forever, > maybe other programs, too. > Implementations to generate intuitive, maximally backwa

Re: [ccp4bb] PDB format survey?

Hi George, > It seems to me that column 21 of an ATOM or HETATM instruction > is always blank, and column 22 is the chain ID. So if we put a > two-character chain ID right justified in columns 21 and 22, for the > vast majority of structures there would be no change, and it would > be relatively e

Re: [ccp4bb] PDB format survey?

> > Single letter chain IDs cause me a bit of pain in buccaneer. > > Kevin > In general I think that the 'improvements' in the new PDB format are sensible, especially the tidying up of the DNA and RNA names. However the new way of naming hydrogen atoms will break many vintage programs such as m

Re: [ccp4bb] PDB format survey?

My frustration comes from what I deem to be an obvious action to disregard the opinion of the user community. From Bernhard's comments below, it sounds like a better plan of action is in the works. Bernhard Rupp wrote: ... > > Anyhow, if I understand correctly, your suggestion of polling the user

Re: [ccp4bb] PDB format survey?

Does it matter what the PDB use? They will export PDB and mmCIF for us to use, so what they use internally doesn't matter. (IIUC the EBI uses SQL). From my perspective as a developer I am not bothered in the slightest whether we use PDB or mmCIF, because I read everything through MMDB which ha

Re: [ccp4bb] PDB format survey?

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Joe Krahn Sent: Wednesday, August 01, 2007 5:17 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB format survey? Ethan Merritt wrote: > Examples include: > - very large structures, for which the current 80 column PDB forma

Re: [ccp4bb] PDB format survey?

Ethan Merritt wrote: > Examples include: > - very large structures, for which the current 80 column PDB format > runs out of space for atom numbers (4 columns -> max ) > or for chain ids (1 column -> single char A-Z 0-9) > [don't ask my why they don't want lower case] > - new classes of ex

Re: [ccp4bb] PDB format survey?

> ...One thing I don't like about it is that columns can be randomized (i.e. X, Y, and Z can be in any column) Rows too! Some anarchists even re-order the symmetry operations ;-) -Jon

Re: [ccp4bb] PDB format survey?

sbestos-free, all-natural organic firewall, -Tom -Original Message- From: CCP4 bulletin board on behalf of Ethan Merritt Sent: Wed 8/1/2007 3:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB format survey? On Wednesday 01 August 2007 14:10, Joe Krahn wrote: > In addition to ques

Re: [ccp4bb] PDB format survey?

On Wednesday 01 August 2007 14:10, Joe Krahn wrote: > In addition to questions about the PDB standard, it is probably > important to consider mmCIF. One thing I don't like about it is that > columns can be randomized (i.e. X, Y, and Z can be in any column), but > the mmCIF standards people have no

[ccp4bb] PDB format survey?

So, I am thinking about putting up a survey somewhere to get a measure of the user-communities interests, because RCSB and wwPDB seem uninterested in doing so. Maybe a group result would be more useful in influencing the standards. I am hoping that the wwPDB can become a better place for format sta