Is this a copy-paste error in the e-mail text, or what is in actually the
input file?
{* separate chains by segid - a new segid starts a new chain *}
{+ choice: true false +}
{===>} n{============================= water files
=================================}
I do not see a value entered for the separate chains by segid line, which you
have for the protein entry.
Secondly, have you looked at the output for error messages and whether or not
the first RNA chain is being loaded at all? The input only lines are not
very useful without seeing the output messages. Also, it is much easier to
examine the script/output if they are attached as files, rather than pasted
into the e-mail text as that tends to disrupt formating, which is vital in
scripts running properly. I suggest repeating the generate run and making
sure to pass the output to a log file, ie;
cns < generate.inp > generate.log
and attaching both.
Stuart Endo-Streeter
On Friday 09 May 2008 10:49, you wrote:
> Hi Stuart,
>
> Thank you very much for your reply. Here are parts of the input files and
> input pdb files for protein and RNA.
>
> {============================ protein files
> ================================}
>
> {* Multiple coordinate files of the same type can be defined by duplicating
> all of the entries below and incrementing the file number *}
>
> {* protein coordinate file *}
> {===>} prot_coordinate_infile_1="pro1.pdb";
>
> {* protein coordinate file *}
> {===>} prot_coordinate_infile_1="";
>
> {* rename segid *}
> {+ choice: true false +}
> {===>} prot_rename_1=false;
>
> {* new segid *}
> {===>} prot_segid_1="";
>
> {* convert chainid to segid if chainid is non-blank *}
> {+ choice: true false +}
> {===>} prot_convert_1=false;
>
> {* separate chains by segid - a new segid starts a new chain *}
> {+ choice: true false +}
> {===>} prot_separate_1=true;
>
> {========================= nucleic acid files
> ==============================}
>
> {* Multiple coordinate files of the same type can be defined by duplicating
> all of the entries below and incrementing the file number *}
>
> {* nucleic acid coordinate file *}
> {===>} nucl_coordinate_infile_1="rna1_fix1.pdb";
>
> {* rename segid *}
> {+ choice: true false +}
> {===>} nucl_rename_1=false;
>
> {* new segid *}
> {===>} nucl_segid_1="";
>
> {* convert chainid to segid if chainid is non-blank *}
> {+ choice: true false +}
> {===>} nucl_convert_1=false;
>
> {* separate chains by segid - a new segid starts a new chain *}
> {+ choice: true false +}
> {===>} n{============================= water files
> =================================}
>
> {* Multiple coordinate files of the same type can be defined by duplicating
> all of the entries below and incrementing the file number *}
>
> {* water coordinate file *}
> {===>} water_coordinate_infile_1="wat1.pdb";
>
> {* rename segid *}
> {+ choice: true false +}
> {===>} water_rename_1=false;
>
> {* new segid *}
> {===>} water_segid_1="";
>
> {* convert chainid to segid if chainid is non-blank *}
> {+ choice: true false +}
> {===>} water_convert_1=false;
> ucl_separate_1=true;
>
> Protein file (in ccp4 format, chain id A and B, I tried TER in between two
> chains but I only got one chain without chain id in the output file):
>
> ATOM 3648 N MET A 441 -23.689 56.526 -2.956 1.00 44.50
> N ATOM 3649 CA MET A 441 -24.310 57.384 -1.938 1.00 44.45
> C ATOM 3650 CB MET A 441 -25.149 58.499 -2.579 1.00 44.50
> C ATOM 3651 CG MET A 441 -24.501 59.879 -2.532 1.00
> 44.46 C ATOM 3652 SD MET A 441 -22.874 59.965 -3.311
> 1.00 44.56 S ATOM 3653 CE MET A 441 -22.269 61.536
> -2.683 1.00 44.75 C ATOM 3654 C MET A 441 -25.123
> 56.631 -0.897 1.00 44.48 C ATOM 3655 O MET A 441
> -24.696 56.498 0.246 1.00 44.45 O ATOM 3656 N MET B 1
> -45.555 -9.417 -57.617 1.00113.93 N ATOM 3657 CA MET B
> 1 -45.130 -10.808 -57.279 1.00113.94 C ATOM 3658 CB MET
> B 1 -43.612 -10.967 -57.423 1.00113.96 C ATOM 3659 CG
> MET B 1 -43.090 -10.777 -58.844 1.00114.01 C ATOM 3660
> SD MET B 1 -41.347 -11.208 -59.036 1.00114.04 S ATOM
> 3661 CE MET B 1 -41.442 -12.983 -59.254 1.00113.94 C
> ATOM 3662 C MET B 1 -45.569 -11.200 -55.870 1.00113.87
> C ATOM 3663 O MET B 1 -45.526 -10.384 -54.946 1.00113.85
> O ATOM 8004 O3' CYT C 34 -52.544 55.320 4.307 1.00 19.69
> O TER
> ATOM 8005 P GUA D 1 -6.118 -6.004 -20.448 0.00 70.19
> P
>
> RNA file:
>
> ATOM 8003 C3' CYT C 24 -53.327 54.167 4.053 1.00 19.76
> C ATOM 8004 O3' CYT C 24 -52.544 55.320 4.307 1.00 19.69
> O TER
> ATOM 8005 P GUA D 1 -6.118 -6.004 -20.448 0.00 70.19
> P ATOM 8006 O1P GUA D 1 -4.884 -5.391 -20.997 0.00 70.16
> O
>
> The output file only has the second chain of RNA without the chain ID.
>
> Also where can I get the parameter and topology files for ATP, AMP and
> pyrophosphate?
>
> Please let me know if you need any further information.
>
> Thank you very much!
>
> Best,
>
> Sun
>
> Stuart Endo-Streeter <[EMAIL PROTECTED]> wrote: Does the log
> from generate show it reading in both RNA chains and do you have enough
> loading statements?
>
> Stuart Endo-Streeter
>
> On Thursday 08 May 2008 22:38, Sun Tang wrote:
> > Dear All,
> >
> > When I used CNS 1.2 to generate the pdb file for two molecules of
> > proteins and two chains of RNA (with different chain ids in format of
> > CCP4), only one RNA chain is generated. Can anyone tell me how to
> > correctly generate the files used for refinement with CNS 1.2?
> >
> > I downloaded the input files from the CNS website and I tried true and
> > false for the renaming segid but all did not work.
> >
> > Thank you very much!
> >
> > Best,
> >
> > Sun Tang
> >
> >
> > ---------------------------------
> > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try
> > it now.
--
______________________________________
Stuart T. Endo-Streeter
Structural Biology and Biophysics
Dept. Biochemistry
LSRC C266
Duke University
919-681-1668
[EMAIL PROTECTED]
