<br><br><div class="gmail_quote">On Thu, Dec 2, 2010 at 5:58 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Tsjerk<br>
<br>
some information exist in pdb file which are not peresent in pqr and vise versa.<br>
I want to convert them to eachother in a way to conclude one's information to the other file.<br>
as you know a typical pdb file has a definite colomns and each of them present a definite charachter(for example charge,X-coordinate,...)<br>
</blockquote>
<br></div>
Charges are not typically in .pdb files, and they certainly don't precede the x-coordinate.</blockquote><div>Ok.I agree with you <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
my pqr has more atoms than original pdb,but It dosen't have any coordinates.<br>
</blockquote>
<br></div>
Then it sounds like you have a useless .pqr file. The format of a proper .pqr file is identical to that of a .pdb file, except that in place of B-factor and occupancy fields, the charge and radius are given. Thus, what Tsjerk told you should work, but perhaps you have a mangled input file that makes this impossible.<br>
</blockquote><div><br>Ok.I will try to produce another .pqr file again.I think both are you are right ,it seems to me my file is useless.<br>Thanks <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
besides converting as you said dosen't solve the problem,because PYMOL can not read this converted <a href="http://file.it" target="_blank">file.it</a> <<a href="http://file.it" target="_blank">http://file.it</a>> needs a file who has included atoms coordinates<div class="im">
<br>
<br>
thanks in advance for your reply<br>
Mohsen<br>
<br></div><div class="im">
On Thu, Nov 25, 2010 at 9:44 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a> <mailto:<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>>> wrote:<br>
<br>
Hey,<br>
<br>
For this particular conversion you can also usually use 'mv':<br>
<br>
mv file.pqr file.pdb<br>
<br>
Btw, many of these file types are human readable. It usually helps<br>
quite a bit to look at the files and get acquainted with the file<br>
formats.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
On Nov 22, 2010 12:42 PM, "Mark Abraham" <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br></div><div class="im">
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
On 22/11/2010 10:16 PM, mohsen ramezanpour wrote: > > Dear All ><br>
> I had a pdb file who was incompl...<br>
<br>
Ask it for a pdb format. There should be no tool that builds atoms<br>
that cannot write a standard file format like PDB - particularly<br>
as PQR is a derivative of PDB.<br>
<br>
Oh, and this is a bit off-topic for this list :-)<br>
<br>
Mark<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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