Hi Nick, indeed it works without the spaces. Thanks for the info. Cheers Christian Am Donnerstag 07 Juni 2012 18:53:21 schrieb Nicholas Sauter:

Christian,

The listed syntax might be slightly misleading, e.g., no spaces are permitted within the command line argument:

labelit.index /data/lysoz_#####.cbf 1 90 distl_minimum_number_spots_for_indexing=20

Try it like that and see if it works.

Cheers, Nick

On Thu, Jun 7, 2012 at 9:20 AM, Christian Roth <

[email protected]> wrote:

...

Dear Phenix-Team

I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command?

Best Regards

Christian _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Charles If you have a recent version, you can use the command-line program phenix.ligand_linking Usage: phenix.ligand_linking pdb_file_name Options: --version show program's version number and exit -h, --help show this help message and exit --show-defaults Display defaults to get the files needed for phenix.refine. Don't make a "super residue" as I believe that will make life difficult when you try to deposit to the PDB. Cheers Nigel PS. Happy to help you directly if you have issues. On Fri, Jun 8, 2012 at 9:40 AM, Charles Stewart Jr., PhD wrote:

Hello all,

I saw a couple of posts on this from a year ago but didn't find a conclusive answer to how to tell phenix to insert a covalent bond between a cysteine residue  and a bound inhibitor. I have the inhibitor (a small molecule) modeled in but haven't figured out how to insert the covalent bond. I used PRODRG to generate the inhibitor pdb and eLBOW to generate a cif file. The distance between the sulfur on the cysteine and the first carbon atom in the inhibitor is 1.8A.

Do I need to run eLBOW using the protein-inhibitor pdb to generate an appropriate cif file?

I see in phenix.refine under the PDB interpretation tab their is a box for "add link to CIF"....is this where I need to tell phenix to insert the covalent bond?

I guess I could just draw the inhibitor-cysteine complex as a modified amino acid and try inserting it that way.....

charles -- Charles Stewart Jr., PhD Research Associate Chemical Biology and Proteomics Laboratory-Noel Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037

Phone: (858) 453-4100 x1946 Fax: (858) 597-0855 Email: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709     Email : [email protected] Fax   : 510-486-5909       Web  : CCI.LBL.gov

Hi Pavel, What's the latest state of this default function to form an unusual covalent bond? I think it would be great useful. Tiantian On Sat, Jun 9, 2012 at 6:58 AM, Pavel Afonine wrote:

Hi Nigel,

can we do it as part of a default phenix.refine, as well as phenix.metal_coordination? I see a growing pressure to do this... I think there is more harm not doing this at all then doing this always but not very optimally.

Let's keep this in mind and discuss once we have a chance.

Pavel

On 6/8/12 12:50 PM, Nigel Moriarty wrote:

...

Charles

If you have a recent version, you can use the command-line program

phenix.ligand_linking Usage: phenix.ligand_linking pdb_file_name

Options: --version show program's version number and exit -h, --help show this help message and exit --show-defaults Display defaults

to get the files needed for phenix.refine. Don't make a "super residue" as I believe that will make life difficult when you try to deposit to the PDB.

Cheers

Nigel

PS. Happy to help you directly if you have issues.

On Fri, Jun 8, 2012 at 9:40 AM, Charles Stewart Jr., PhD wrote:

...

Hello all,

I saw a couple of posts on this from a year ago but didn't find a conclusive answer to how to tell phenix to insert a covalent bond between a cysteine residue and a bound inhibitor. I have the inhibitor (a small molecule) modeled in but haven't figured out how to insert the covalent bond. I used PRODRG to generate the inhibitor pdb and eLBOW to generate a cif file. The distance between the sulfur on the cysteine and the first carbon atom in the inhibitor is 1.8A.

Do I need to run eLBOW using the protein-inhibitor pdb to generate an appropriate cif file?

I see in phenix.refine under the PDB interpretation tab their is a box for "add link to CIF"....is this where I need to tell phenix to insert the covalent bond?

I guess I could just draw the inhibitor-cysteine complex as a modified amino acid and try inserting it that way.....

charles -- Charles Stewart Jr., PhD Research Associate Chemical Biology and Proteomics Laboratory-Noel Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037

Phone: (858) 453-4100 x1946 Fax: (858) 597-0855 Email: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Tiantian ****************************************************************** LIFE LIBERTY AND THE PURSUIT OF HAPPINESS ******************************************************************

Hi, in addition to Nigel's reply, here is what I typically do: you can define a bond between any pair of atoms (any number of such bonds), just like this: refinement.geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 1 and name N atom_selection_2 = chain A and resseq 2 and name O distance_ideal = 1.3 sigma = 0.02 } bond { atom_selection_1 = chain A and resseq 2 and name O atom_selection_2 = chain X and resseq 3 and name C distance_ideal = 1.4 sigma = 0.04 } } That is, save the lines above in a file and give this file to phenix.refine either in the command line or in the GUI. Let us know (through phenixbb) if you have any questions or problems related to this. All the best, Pavel On 6/8/12 9:40 AM, Charles Stewart Jr., PhD wrote:

Hello all,

I saw a couple of posts on this from a year ago but didn't find a conclusive answer to how to tell phenix to insert a covalent bond between a cysteine residue and a bound inhibitor. I have the inhibitor (a small molecule) modeled in but haven't figured out how to insert the covalent bond. I used PRODRG to generate the inhibitor pdb and eLBOW to generate a cif file. The distance between the sulfur on the cysteine and the first carbon atom in the inhibitor is 1.8A.

Do I need to run eLBOW using the protein-inhibitor pdb to generate an appropriate cif file?

I see in phenix.refine under the PDB interpretation tab their is a box for "add link to CIF"....is this where I need to tell phenix to insert the covalent bond?

I guess I could just draw the inhibitor-cysteine complex as a modified amino acid and try inserting it that way.....

charles